Madagascar’s Conservation Superhero to Visit Campus

Guest Post By Sheena Faherty, Ph.D. Candidate in Biology

Dame Alison Richard is the epitome of someone who puts her money where her mouth is. And her dedication is directed precisely where it’s needed most.

Richard, a protector of lemurs, artisanal salt entrepreneur and endless optimist, is not just doing something about Madagascar’s conservation crisis. She’s doing everything about it.

Alison Richard (Photo: HHMI)

Alison Richard (Photo: HHMI)

She’ll visit Duke March 3-5 to give three-part lecture series discussing her role in over forty years of community-based conservation efforts in Madagascar.

Members of the Duke community know all too well that our beloved lemurs— many of which can only be found at the Duke Lemur Center or in Madagascar—are in dire straights.

Their plight has been a life’s work for Richard, who is best known for her research on sifakas in the spiny forests of Madagascar.  But she also lays claim to having been the first female vice-chancellor at Cambridge. She has now returned to Yale, where she spent most of her career, as a senior research scientist and professor emerita.

“Sometimes I think that because I’m covering so many bases, I end up doing nothing very well,” Richard said. “But it’s what I do and I can’t imagine not doing any of them—so it’s too bad,” she said laughing.

Richard is a conservationist who understands that without considering the local people’s well-being, all attempts to save wildlife habitats will fail.

“There are a variety of ways in which we are trying to facilitate socio-economic enhancements to people’s lives,” Richard said. “[On a recent trip to Madagascar] I met with the association of women salt producers, who are producing artisanal salt by techniques that have been in place for hundreds of years.”

In collaboration with a start-up company that is highly focused on sustainability, she recently shipped the first 500 kilos of the Madagascan salt to the U.S.

Verreaux's Sifaka, a favorite of Richard's in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Verreaux’s Sifaka, a favorite of Richard’s in Southwestern Madagascar. (Credit: Flickr user nomis-simon, CC)

Taking time away from protecting the lemurs and enhancing the lives of the Malagasy people, Richard said her Duke lectures will have broad appeal for anyone interested in conservation, or for those who just enjoy seeing adorable pictures of lemurs.

She hopes to focus on writing a book, the topic of which will draw from her public lecture on March 5 at 6:00 pm at the Great Hall of the Mary Duke Biddle Trent Semans Center for Health Education. This lecture is set to explore how an array of different sciences has changed our understanding of Madagascar’s history.

And the conservationist who said she does everything has some advice for conserving her own mental sanity.

“One thing I need to do going forward is to find things to stop doing,” she admits. “And I’m not good at that because they are all too interesting and seemingly too important,” she said.

So, what’s next for Alison Richard?

“More of doing everything!” she said.

Richard's installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from  her Majesty Queen Elizabeth II, who's husband, Prince Philip, is the chancellor.

Richard’s installation as vice chancellor of Cambridge in November 2009 was occasioned by a visit from her majesty Queen Elizabeth II, who’s husband, Prince Philip, is the chancellor.

Joining the Team: Anika Ayyar

By Anika Ayyar

Hi! My name is Anika Ayyar and I am currently a Duke freshman. I grew up in warm, lovely Saratoga, California, where I picked up my love for long distance running, organic farming, and the ocean. When I was 14, I moved to across the country to Exeter, New Hampshire to attend a boarding high school, and here I developed a deep interest in biology and medicine. Exeter’s frost and snow were far from the Cali weather I was used to, but my fascinating classes, caring teachers, and wonderful friends more than made up for the cold.

My sophomore semester abroad program at The Island School, on an island called Eleuthera in the Bahamas, certainly provided a welcome change to East coast weather as well. At the Island School I studied marine biology and environmental conservation, earned my SCUBA certification, and spent time with the local middle schoolers refurbishing a library and stocking it with books. I was also part of a research team that studied species richness and diversity on patch reefs off the coast of the island.

Dissecting fruit fly larvae under the microscope at the Seung Kim Lab at Stanford.

Dissecting fruit fly larvae under the microscope at the Seung Kim Lab at Stanford.

My marine research stint in the Bahamas drove me to join a molecular biology lab the summer after I returned; a decision that transformed my passion for science. At the Seung Kim Lab for Pancreas Development at Stanford University, I worked on a project that used binary systems to study the expression of specific genes related to insulin production and diabetes in fruit flies. I soon grew so immersed in my work that I wanted to share the project with others in the scientific community at Exeter, and my research mentors, biology professors, and I worked to create a novel course where other students could take part in the project as well. This unique research collaboration, called the “StanEx” project, proved to be a huge success, allowing other students to experience the trials and joys of real-world research while also generating Drosophila fly strains that were useful to the larger scientific community. If you are interested in reading more, check out my website about the StanEx project!

While my current interests lie more at the intersection of technology and medicine, I hope to be involved in equally compelling and fulfilling research here at Duke. Hearing about the various projects my professors are working on, and reading about the discoveries made in labs on campus, I have no doubt that this will be the case.

Outside of classes and research, I enjoy being part of the Duke Debate team, and Lady Blue, one of Duke’s all-female a cappella groups. You can often find me on the trails on a long run, or trying out a new dessert recipe I found on Pinterest. I am beyond excited to be a part of the research blogging team, and can’t wait to start attending talks and interviewing research personalities whose stories I can share with our readers!

Grave Effects of the Great Migration

Sometimes a great move can have grave consequences — particularly when that move is a massive migration. In the 20th Century, millions of African-Americans relocated from the Deep South to search for greater quality of life in an exodus known as the Great Migration. However, the gains many made were clouded by higher mortality rates in old age. Despite having access to greater opportunities for work and education, Duke economist Seth Sanders found that men and women who relocated to the North and West were more likely to die before reaching their 70s than their counterparts who remained in the rural South. Here’s a glimpse at how city living took a late-life toll on migrants:

grave-effects-great-migration_infographic
You can read the full story on Duke Today.

Origami-Inspired Chemistry Textbook Brings Molecules To Life

by Anika Radiya-Dixit

Your college textbook pages probably look something like the picture below – traffic jams of black boats on a prosaic white sea.

blackAndWhiteText

Textbook without illustrations.

But instead of reading purely from static texts, what if your chemistry class had 3D touch-screens that allowed you to manipulate the colors and positions of atoms to give you visual sense of how crystal and organic structures align with respect to each other? Or what if you could fold pieces of paper into different shapes to represent various combinations of protein structures? This is the future of science: visualization.

Duke students and staff gathered in the Levine Science Research Center last week to learn more about visualizing chemical compounds while munching on their chili and salad. Robert Hanson, Professor in the Department of Chemistry at St. Olaf College, was enthusiastic to present his research on new ways to visualize and understand experimental data.

Exhibition poster of “Body Worlds”

 

Hanson opened his talk with various applications of visualization in research. He expressed a huge respect for medical visualization and the people who are able to illustrate medical procedures, because “these artists are drawing what no one can see.” Take “Body Worlds,” for example, he said. One of the most renowned exhibitions displaying the artistic beauty of the human body, it elicited a myriad of reactions from the audience members, from mildly nauseated to animatedly pumped.

Hanson also spoke about the significance of having an effective visualization design. Very simple changes in visualization, such as a table of numbers versus a labeled graph, can make a “big difference in terms of ease of the audience catching on to what the data means.” For example, consider the excerpt of a textbook by J. Willard Gibbs below. One of the earliest chemists to study the relationship between pressure and temperature, Gibbs wrote “incredibly legible, detailed, verbatim notes,” Hanson said. Then he asked the audience: Honestly, would one read the text fervently, and if so, how easy would it be to understand these relationships?

Gibbs'Text

Excerpt of J. Gibbs’ text.

Not very, according to James C. Maxwell, a distinguished mathematician and physicist, who attempted to design a simpler mechanism with his inverted 3D plaster model.

Maxwell'sPlaster

Maxwell’s plaster model of Gibbs’ surface

Subsequent scientists created the graph shown below to represent the relationships. Compared to the text, the diagram gives several different pieces of information about entropy and temperature and pressure that allow the reader to “simply observe and trace the graph to find various points of equilibrium that they couldn’t immediately understand” from a block of black and white text.

Graph

Graphical view of Gibbs’ theory on the relation between temperature and pressure.

Hanson went further in his passion to bring chemistry to the physical realm in his book titled “Molecular Origami.” The reader photocopies or tears out a page from the book, and then folds up the piece of paper according to dotted guidelines in order to form origami molecular “ornaments.” The structures are marked with important pieces of information that allow students to observe and appreciate the symmetry and shapes of the various parts of the molecule.

origami

3D origami model of marcasite (scale: 200 million : 1)

 

One of his best moments with his work, Hanson recounted, was when he received a telephone call from some students in a high school asking him for directions on how to put together a 3D model of bone. After two hours of guiding the students, he asked the students what the model finally looked like – since he had knowledge of only the chemical components – and was amused to hear a cheeky “He doesn’t know.” Later that year, Hanson was rewarded to see the beautiful physical model displayed in a museum, and was overjoyed when he learned that his book was the inspiration for the students’ project.

More recently, Hanson has worked on developing virtual software to view compounds in 3D complete with perspective scrolling. One of his computer visualizations is located in the “Take a Nanooze Break” exhibition in Disneyland, and allows the user to manipulate the color and location of atoms to explore various possible compounds.

TouchAMolecule

“Touch-A-Molecule” is located in the Epcot Center in Disneyland.

By creating images and interactive software for chemical compounds, Hanson believes that good visualization can empower educators to gain new insights and make new discoveries at the atomic level. By experimenting with new techniques for dynamic imagery, Hanson pushes not only the “boundaries of visualization,” but more importantly, the “boundaries of science” itself.

Hanson

Professor Hanson explains how to visualize points of interaction on a molecule.

 

Contact Professor Hanson at hansonr@stolaf.edu

Read more about the event details here.

View Hanson’s book on “Molecular Origami” or buy a copy from Amazon.

Research, New Policies Protect “The Lungs of India”

Guest Post By Sheena Faherty, Ph.D. Candidate in Biology

You can’t see into the lungs of the people of Agra, India, home of the Taj Mahal. But just a glance at what should be pristine white marble domes of the local landmark shows that air quality is a major concern. The iconic domes are tarnished and need frequent cleaning to keep them white.

taj mahal

A cleaning in progress shows how much discoloration grimy air  deposits on the Taj Mahal. (Courtesy of Mike Bergin)

A study by Duke researchers published in Environmental Science and Technology has determined the exact air particles that are the cause of the Taj’s discoloration and threat to the health of the local people.

“The Taj Mahal can be thought of as the lungs of India,” says Mike Bergin, the lead author of the study and a new faculty member in Duke’s Civil and Environmental Engineering department, who credits his wife Michelle with coming up with the analogy.

What he means is that the same particles discoloring the Taj Mahal are depositing in the lungs of people in Agra and are having a negative impact on their health.

Within weeks of the publication of the study, the Indian government started putting air pollution control strategies in place. In the city of Agra, diesel-guzzling vehicles have been banned from the streets, new policies are being enacted to stop the burning of trash and refuse, and local governments are replacing the traditional heating and cooking method of dung-burning with free compressed natural gas.

Air sampling devices were set up to determine the exact particles causing the discoloration. (Courtesy of Mike Bergin)

Air sampling devices were set up to determine the exact particles causing the discoloration. (Courtesy of Mike Bergin)

This might be one of the fastest “science into policy” actions ever and Bergin couldn’t be more pleased.

His research looks at how small particles in the atmosphere have impacts on human health and climate. A few years back, while attending a scientific meeting in India, he visited the Taj Mahal and noticed something strange.

“Part of it was covered in scaffolding and under the scaffold, part of the dome was brown, and there was a thick line that was white. I took a photo right away and thought, ‘That’s the weirdest thing I have ever seen.’”

He started asking people about it and kept getting the same story: The Taj Mahal gets really dirty. It has something to do with the quality of the air. We don’t know what it is, but we clean it off.

And for Bergin—a scientist whose expertise lies in air quality—the wheels began to turn.

While serving as faculty at Georgia Tech, he assembled a multi-disciplinary team from international in both the US (University of Wisconsin at Madison) and India (IIT Kanpur and the Archaeological Survey of India) to tackle the challenge of sampling both particulates in the air, as well as those that collect on the surface of the Taj Mahal, to determine which particles were the cause of the unblemished white domes turning brown.

The team found that collected samples contained high concentrations of carbon-based particles and dust. Both sources are known to absorb light, which gives the appearance of a brown hue.

Findings from this study and the impact it has had on policy-makers in India demonstrate how deeply celebrated our cultural icons, such as the Taj Mahal, are.

“People knew the air there was bad, but nobody was really doing that much about it. The interesting thing is that they moved very quickly because they didn’t want to see the Taj Mahal getting discolored,” Bergin says.

Mapping Science: The Power of Visualization

By Lyndsey Garcia

Mobile Landscapes: Using Location Data from Cell Phones for Urban Analysis

Mobile Landscapes: Using Location Data from Cell Phones for Urban Analysis

We are constantly surrounded by visuals: television, advertisements and posters. Humans have been using visuals such as cartographic maps of the physical world to help guide our exploration and serve as a reminder of what we have already learned.

But as research has moved into more abstract environments that are becoming more difficult to interact with or visualize, the art of science mapping has emerged to serve as a looking glass to allow us to effectively interpret the data and discern apparent outliers, clusters and trends.

Now on display from from January 12 to April 10, 2015, the exhibit Places & Spaces: Mapping Science serves as a fascinating and intriguing example of the features and importance of science mapping.

The end result of a ten-year effort with ten new maps added each year, all one hundred maps are present at Duke at three different locations: the Edge in Bostock Library, the third floor of Gross Hall, and the second floor of Bay 11 in Smith Warehouse.

Visualizing Bible Cross-References

Visualizing Bible Cross-References

Science maps take abstract concepts of science and make them more visible, concrete, and tangible. The scope of the exhibit is broad, including science maps of the internet, emerging pandemics in the developing world, even the mood of the U.S. based on an analysis of millions of public tweets. Science mapping is not limited to the natural or technological sciences. Several maps visualize social science data such as Visualizing Bible Cross Connections and Similarities Throughout the Bible, where the axis represents the books of the Bible and the arches portray connections or similar phraseology between the books.

Angela Zoss, the exhibit ambassador who brought the project to Duke, comments, “The visualization helps at multiple phases of the research process. It helps the researcher communicate the data and understand his or her data better. When we try to summarize things with equations or summary statistics, such as the average, the mean, or the median, we could be glossing over very important patterns or trends in the data. With visualization, we can often visualize every single point in space for small data sets. One might be able to detect a pattern that you would never have been lost in simple summary statistics.”

The physical exhibit holds importance to the Places & Spaces project due to the physical printing of the maps. Some of the details on the maps are so intricate that they require an in-person viewing of the map in order to appreciate and understand the information portrayed. Such as, A Chart Illustrating Some of the Relations Between the Branches of Natural Science and Technology, is a hand-drawn map from 1948 showing the relationships between the branches of natural sciences and technology by using a distance-similarity metaphor, in which objects more similar to each other are more proximate in space.

A Chart Illustrating Some of the Relations between the Branches of Natural Science and Technology. Used by permission of the Royal Society

The maps look more like works of art in a museum than a collection of maps to interpret data. Angela Zoss explains her love of visualization as, “Visual graphics can inspire an emotion and excitement in people. It can encourage people to feel for information that would otherwise seem dry or intangible. The exhibit heightens those emotions even more because you see so many wonderful examples from so many different viewpoints. Every visualizing person is going to make a different choice in the details they want represented. Being able to see that variety gives people a better idea of how much more is possible.”

Ben Wang: Food lover and undergraduate researcher

Ben Wang in rural Appalachia Credit: Ben Wang

Ben Wang in rural Appalachia Credit: Ben Wang

By Nonie Arora

Ben Wang, a senior Evolutionary Anthropology major from New Jersey, strongly believes we are what we eat. A foodie, scientist, and future health care practitioner, he thinks that changing food habits can improve our nation’s health.

“When we came to Duke, our summer reading book was Eating Animals,” he said.  “I felt so many emotions while I was reading the book. It really impacted the way I think about food. In fact, I became a pescetarian (a fish-eating vegetarian).”

Freshman year, Wang knew he had this interest in food, but he didn’t know how to incorporate it into his academic world.

During his second year, Wang started to find his way. “I remembered the topic when I was hunting for a research lab, and started working in Dr. Tso-Pang Yao’s metabolism lab so that I could learn more about how nutrition directly impacts health,” he said.

Wang spent time investigating proteins that increase or decrease the amount of “mitochondrial fusion” that happens in cells. Wang explained that metabolism is how our bodies process food and distribute nutrients, and these compounds help in that process.

“I really enjoyed this lab because the topic was directly related to patient care and our research had direct pharmacologic applications,” Wang said.

Farm Fresh tomatoes! Credit: Ben Wang

Farm Fresh tomatoes! Credit: Ben Wang

In the summer of 2014, he pursued a Bass Connections fellowship in rural Appalachia, in one of the most impoverished counties in the US.

He participated in a Farm-to-Table partnership between local Appalachian farms and a middle school. This partnership was part of a broader program for Appalachian girls. He coordinated the logistics and ended up doing much of the culinary work for the partnership, cooking up delicacies with ingredients like swiss chard, beets, and kale.

“I really wanted to go all the way in introducing a fresh perspective to these women,” Wang said, “I had to convince the girls that these veggies would taste good.”

Farm to Table initiative in action. Credit: Ben Wang

Farm to Table initiative in action. Credit: Ben Wang

They did not always like his creations.
He says one student told him, “I’m not going to eat this hippie food.”

But he persevered, and ultimately most of the girls were excited about what they had learned and reevaluated the way they ate.

Maintaining lasting gains will be difficult because much of the food would have been unaffordable to the girls on their own. In the town that they live in, the closest supermarket is a Walmart a half hour away. Other than that, there is a Dollar General and Hillbilly Market, neither of which stock fresh produce, according to Wang.

However, Wang thinks that showing these girls there are food options beyond those that they have experienced was valuable, and that they can choose to strive for them if they want to.

Changing eating habits, one delicious meal at a time. Credit: Ben Wang

Changing eating habits, one delicious meal at a time. Credit: Ben Wang

As for Wang, he is headed to dental school in the fall and hopes to include nutritional awareness in his future practice to help his patients achieve better systemic health.

 

 

Behind the Scenes at Duke’s Student-Run Science Journal

By Nonie Arora

What do tuberculosis vaccines, water quality, and protein trafficking share in common? All may be featured in articles for the upcoming issue of Duke Science Review. I spoke with Matthew Draelos, co-editor-in-chief, and other publication team members.

Duke Science Review Publication. Credit: Nonie Arora

Duke Science Review Publication. Credit: Nonie Arora

Draelos explained that the Duke Science Review deals with broad topics with an emphasis on review articles and draws from the undergraduate, graduate, and professional school communities.

Draelos’s motivations for leading the Duke Science Review stem from his previous research experiences. Draelos worked in an undergraduate lab for four years at NC State University. There, he felt integrated into the publication process in the laboratory of Dr. Gavin Williams. At Duke, he is excited to have the opportunity to get involved in a student-run science journal and take on a leadership role.

His interest in science is focused on pharmaceutical development, particularly antibiotics. He has worked previously with enzymes called polyketide synthases, which are nature’s machinery for making antibiotics. He hopes to someday develop novel chemical solutions to unsolved medical problems.

Students learn about the publication process. Credit: Nonie Arora.

Students learn about the publication process. Credit: Nonie Arora.

“I think it’s important for students to publish their research primarily because in the current funding environment it’s publish or perish. This is increasingly true for young scientists. We must be able to write well, and the Duke Science Review establishes a risk-free forum for students to practice scientific writing,” Draelos commented.

A second reason he mentioned for enabling students to publish their work is that people spend considerable time and energy writing papers for courses, and a lot of that effort is wasted if only the professor is able to read their work. This journal is a way for people to spread their work to a larger audience and perhaps gain some additional recognition.

Lefko Charalambous, an editor for the journal, added that it is important to improve scientific communication and literacy in budding scientists. “It’s a way for us to appreciate what goes into producing a journal article and the reward from having it published at our age,” he said.

“We hope to enrich the scientific discourse, especially for freshmen and sophomores who are looking into scientific research and don’t know where to start,” Draelos said.

To submit an abstract for a potential report or article, check out their website.

Is the “Wizarding Gene” Dominant or Recessive?

By Nonie Arora

Dr. Spana explains the wizarding gene to eager students. Credit: Arnab Chatterjee

Dr. Spana explains the wizarding gene to eager students. Credit: Arnab Chatterjee

How do recessive alleles and the world of Harry Potter connect? Some students found out last week from Dr. Eric Spana, a faculty member in the Biology department.

He started off by explaining how a mutation in the MC1R (melanocortin 1 receptor) gene causes red hair in humans because of the way it affects a pigment called eumelanin. He added that MC1R is a recessive gene, and showed a pedigree of the Weasley family tree. Professor Spana pointed out that J. K. Rowling had gotten the genetics right. The Weasley clan has red hair and so does Harry’s daughter Lily. This makes sense because Harry must have a recessive allele for red hair since his mother, also Lily, had red hair. Whether this is intentional or just fortuitous casting, who can really say?

He then explained some potential retroactive genetic “crosses” that could be done to determine whether the “wizarding gene” was dominant or recessive. As a quick refresher, recessive alleles require both the mom and dad to pass on the same genetic sequence to the child for the condition to occur, while dominant alleles require only one copy.

According to Professor Spana, Step 1 was to check whether a witch and a muggle who mated ould produce a wizard. Indeed, this is possible, and the evidence is Seamus Finnigan, a half-blood wizard. Due to these results, the gene could still be dominant or recessive.

In Step 2, he explained, you mate a wizard to someone who could not have the wizarding gene. Fridwulfa, the giantess, married Mr. Hagrid, a wizard, to produce our beloved Rubeus Hagrid, who was a wizard. Since giants cannot have the wizarding gene, but Hagrid is still a wizard, the wizarding gene must be dominant!

Crowd of students ask provocative questions about squibs and recessive vs. dominant inheritance. Credit: Arnab Chatterjee

Crowd of students ask provocative questions about squibs and recessive vs. dominant inheritance. Credit: Arnab Chatterjee

You’ll have to stop by Dr. Spana’s office to ask him more about where muggle-borns and squibs come from. There’s a few different genetic explanations, and I encourage you to do some thinking and exploration.

Outside of his work on the genetics of Harry Potter, Dr. Spana also researches and teaches Genetics & Developmental Biology at Duke.