Students Share Research Journeys at Bass Connections Showcase

From the highlands of north central Peru to high schools in North Carolina, student researchers in Duke’s Bass Connections program are gathering data in all sorts of unique places.

As the school year winds down, they packed into Duke’s Scharf Hall last week to hear one another’s stories.

Students and faculty gathered in Scharf Hall to learn about each other’s research at this year’s Bass Connections showcase. Photo by Jared Lazarus/Duke Photography.

The Bass Connections program brings together interdisciplinary teams of undergraduates, graduate students and professors to tackle big questions in research. This year’s showcase, which featured poster presentations and five “lightning talks,” was the first to include teams spanning all five of the program’s diverse themes: Brain and Society; Information, Society and Culture; Global Health; Education and Human Development; and Energy.

“The students wanted an opportunity to learn from one another about what they had been working on across all the different themes over the course of the year,” said Lori Bennear, associate professor of environmental economics and policy at the Nicholas School, during the opening remarks.

Students seized the chance, eagerly perusing peers’ posters and gathering for standing-room-only viewings of other team’s talks.

The different investigations took students from rural areas of Peru, where teams interviewed local residents to better understand the transmission of deadly diseases like malaria and leishmaniasis, to the North Carolina Museum of Art, where mathematicians and engineers worked side-by-side with artists to restore paintings.

Machine learning algorithms created by the Energy Data Analytics Lab can pick out buildings from a satellite image and estimate their energy consumption. Image courtesy Hoël Wiesner.

Students in the Energy Data Analytics Lab didn’t have to look much farther than their smart phones for the data they needed to better understand energy use.

“Here you can see a satellite image, very similar to one you can find on Google maps,” said Eric Peshkin, a junior mathematics major, as he showed an aerial photo of an urban area featuring buildings and a highway. “The question is how can this be useful to us as researchers?”

With the help of new machine-learning algorithms, images like these could soon give researchers oodles of valuable information about energy consumption, Peshkin said.

“For example, what if we could pick out buildings and estimate their energy usage on a per-building level?” said Hoël Wiesner, a second year master’s student at the Nicholas School. “There is not really a good data set for this out there because utilities that do have this information tend to keep it private for commercial reasons.”

The lab has had success developing algorithms that can estimate the size and location of solar panels from aerial photos. Peshkin and Wiesner described how they are now creating new algorithms that can first identify the size and locations of buildings in satellite imagery, and then estimate their energy usage. These tools could provide a quick and easy way to evaluate the total energy needs in any neighborhood, town or city in the U.S. or around the world.

“It’s not just that we can take one city, say Norfolk, Virginia, and estimate the buildings there. If you give us Reno, Tuscaloosa, Las Vegas, Pheonix — my hometown — you can absolutely get the per-building energy estimations,” Peshkin said. “And what that means is that policy makers will be more informed, NGOs will have the ability to best service their community, and more efficient, more accurate energy policy can be implemented.”

Some students’ research took them to the sidelines of local sports fields. Joost Op’t Eynde, a master’s student in biomedical engineering, described how he and his colleagues on a Brain and Society team are working with high school and youth football leagues to sort out what exactly happens to the brain during a high-impact sports game.

While a particularly nasty hit to the head might cause clear symptoms that can be diagnosed as a concussion, the accumulation of lesser impacts over the course of a game or season may also affect the brain. Eynde and his team are developing a set of tools to monitor both these impacts and their effects.

A standing-room only crowd listened to a team present on their work “Tackling Concussions.” Photo by Jared Lazarus/Duke Photography.

“We talk about inputs and outputs — what happens, and what are the results,” Eynde said. “For the inputs, we want to actually see when somebody gets hit, how they get hit, what kinds of things they experience, and what is going on in the head. And the output is we want to look at a way to assess objectively.”

The tools include surveys to estimate how often a player is impacted, an in-ear accelerometer called the DASHR that measures the intensity of jostles to the head, and tests of players’ performance on eye-tracking tasks.

“Right now we are looking on the scale of a season, maybe two seasons,” Eynde said. “What we would like to do in the future is actually follow some of these students throughout their career and get the full data for four years or however long they are involved in the program, and find out more of the long-term effects of what they experience.”

Kara J. Manke, PhD

Post by Kara Manke

Visualizing the Fourth Dimension

Living in a 3-dimensional world, we can easily visualize objects in 2 and 3 dimensions. But as a mathematician, playing with only 3 dimensions is limiting, Dr. Henry Segerman laments.  An Assistant Professor in Mathematics at Oklahoma State University, Segerman spoke to Duke students and faculty on visualizing 4-dimensional space as part of the PLUM lecture series on April 18.

What exactly is the 4th dimension?

Let’s break down spatial dimensions into what we know. We can describe a point in 2-dimensional space with two numbers x and y, visualizing an object in the xy plane, and a point in 3D space with 3 numbers in the xyz coordinate system.

Plotting three dimensions in the xyz coordinate system.

While the green right-angle markers are not actually 90 degrees, we are able to infer the 3-dimensional geometry as shown on a 2-dimensional screen.

Likewise, we can describe a point in 4-dimensional space with four numbers – x, y, z, and w – where the purple w-axis is at a right angle to the other regions; in other words, we can visualize 4 dimensions by squishing it down to three.

Plotting four dimensions in the xyzw coordinate system.

One commonly explored 4D object we can attempt to visualize is known as a hypercube. A hypercube is analogous to a cube in 3 dimensions, just as a cube is to a square.

How do we make a hypercube?

To create a 1D line, we take a point, make a copy, move the copied point parallely to some distance away, and then connect the two points with a line.

Similarly, a square can be formed by making a copy of a line and connecting them to add the second dimension.

So, to create a hypercube, we move identical 3D cubes parallel to each other, and then connect them with four lines, as depicted in the image below.

To create an n–dimensional cube, we take 2 copies of the (n−1)–dimensional cube and connecting corresponding corners.

Even with a 3D-printed model, trying to visualize the hypercube can get confusing. 

How can we make a better picture of a hypercube? “You sort of cheat,” Dr. Segerman explained. One way to cheat is by casting shadows.

Parallel projection shadows, depicted in the figure below, are caused by rays of light falling at a  right angle to the plane of the table. We can see that some of the edges of the shadow are parallel, which is also true of the physical object. However, some of the edges that collide in the 2D cast don’t actually collide in the 3D object, making the projection more complicated to map back to the 3D object.

Parallel projection of a cube on a transparent sheet of plastic above the table.

One way to cast shadows with no collisions is through stereographic projection as depicted below.

The stereographic projection is a mapping (function) that projects a sphere onto a plane. The projection is defined on the entire sphere, except the point at the top of the sphere.

For the object below, the curves on the sphere cast shadows, mapping them to a straight line grid on the plane. With stereographic projection, each side of the 3D object maps to a different point on the plane so that we can view all sides of the original object.

Stereographic projection of a grid pattern onto the plane. 3D print the model at Duke’s Co-Lab!

Just as shadows of 3D objects are images formed on a 2D surface, our retina has only a 2D surface area to detect light entering the eye, so we actually see a 2D projection of our 3D world. Our minds are computationally able to reconstruct the 3D world around us by using previous experience and information from the 2D images such as light, shade, and parallax.

Projection of a 3D object on a 2D surface.

Projection of a 4D object on a 3D world

How can we visualize the 4-dimensional hypercube?

To use stereographic projection, we radially project the edges of a 3D cube (left of the image below) to the surface of a sphere to form a “beach ball cube” (right).

The faces of the cube radially projected onto the sphere.

Placing a point light source at the north pole of the bloated cube, we can obtain the projection onto a 2D plane as shown below.

Stereographic projection of the “beach ball cube” pattern to the plane. View the 3D model here.

Applied to one dimension higher, we can theoretically blow a 4-dimensional shape up into a ball, and then place a light at the top of the object, and project the image down into 3 dimensions.

Left: 3D print of the stereographic projection of a “beach ball hypercube” to 3-dimensional space. Right: computer render of the same, including the 2-dimensional square faces.

Forming n–dimensional cubes from (n−1)–dimensional renderings.

Thus, the constructed 3D model of the “beach ball cube” shadow is the projection of the hypercube into 3-dimensional space. Here the 4-dimensional edges of the hypercube become distorted cubes instead of strips.

Just as the edges of the top object in the figure can be connected together by folding the squares through the 3rd dimension to form a cube, the edges of the bottom object can be connected through the 4th dimension

Why are we trying to understand things in 4 dimensions?

As far as we know, the space around us consists of only 3 dimensions. Mathematically, however, there is no reason to limit our understanding of higher-dimensional geometry and space to only 3, since there is nothing special about the number 3 that makes it the only possible number of dimensions space can have.

From a physics perspective, Einstein’s theory of Special Relativity suggests a connection between space and time, so the space-time continuum consists of 3 spatial dimensions and 1 temporal dimension. For example, consider a blooming flower. The flower’s position it not changing: it is not moving up or sideways. Yet, we can observe the transformation, which is proof that an additional dimension exists. Equating time with the 4th dimension is one example, but the 4th dimension can also be positional like the first 3. While it is possible to visualize space-time by examining snapshots of the flower with time as a constant, it is also useful to understand how space and time interrelate geometrically.

Explore more in the 4th dimension with Hypernom or Dr. Segerman’s book “Visualizing Mathematics with 3D Printing“!

Post by Anika Radiya-Dixit.

 

 

Where Some Ski, Others Do Science

For most people, Lost Trail is a ski spot located at 7,000 feet in the Rocky Mountains on the border of Idaho and Montana. Skiers and snowboarders descend down steep slopes, past forests and alpine meadows that get more than 25 feet of snow each year. But for a team of researchers led by Duke biology professor Thomas Mitchell-Olds, buried beneath the snow is a hidden population of native plants on the cusp of dividing into two new species.

Molly Rivera-Olds shovels snow at Lost Trail Pass.

Studying a spindly North American wildflower called Boechera stricta, Mitchell-Olds and colleagues suspected that a process called chromosomal inversion — in which part of a chromosome breaks off and reattaches itself upside down — plays a central role in speciation. To test the idea, they planted Boechera stricta seedlings in a mountaintop meadow near the Lost Trail resort.

To reach the meadow, the researchers carried thousands of seedlings up the mountain in specially constructed backpacks. They also lugged up nine empty garbage cans and filled them with snow to water the plants throughout the summer.

Once the seedlings matured, the researchers measured flowering time, seed production, and survival. They found that plants with the chromosomal inversion had a leg up on the steep slopes of the Rocky Mountains. Eventually, the researchers say, this can lead to plants with the inverted DNA splitting off and forming a new species.

The findings were published April 3, 2017 in the journal Nature Ecology & Evolution.

# # #

CITATION:  “Young Inversion with Multiple Linked QTLs Under Selection in a Hybrid Zone,” Cheng-Ruei Lee, Baosheng Wang et al. Nature Ecology & Evolution, April 3, 2017. DOI:10.1038/s41559-017-0119.

Guest post by Molly Rivera-Olds

 

 

 

 

 

Durham Students Give Themselves a Hand Up

Picture this: a group of young middle schoolers are gathered trying to get a “hand” they’ve built out of drinking straws, thread and clay to grasp a small container. What could such a scene possibly have to do with encouraging kids to stay in school and pursue science? It turns out, quite a lot!

brothers keeper

Angelo Moreno (right), a graduate student in molecular genetics and microbiology, helps students with their soda straw hand.

This scene was part of an event designed just for boys from Durham schools that took place one March evening at the Durham Marriot and Convention Center. It was hosted by Made in Durham, a local non-profit focused on helping Durham’s young people graduate from high school, go to college, and ultimately be prepared for their careers, and My Brother’s Keeper Durham, the local branch of former President Obama’s mentoring initiative for young men of color.

The first evening of a convention centered on building equity in education and was geared toward career exploration. Each of the boys got to choose from a series of workshops that highlighted careers in science, technology, engineering, art, and mathematics — also known as STEAM. The workshops ranged from architectural design to building body parts, which was where they learned to build the artificial hands.

Sharlini Sankaran, the executive director of Duke’s Regeneration Next Initiative, who heard about my outreach activities from earlier this year, contacted me, and together we drummed up a group of scientists for the event.

With the help of Victor Ruthig in Cell Biology, Angelo Moreno in Molecular Genetics and Microbiology, Ashley Williams in Biomedical Engineering, and Devon Lewis, an undergraduate in the Biology program, we dove into the world of prosthetics and tissue engineering with the young men who came to our workshop.

Biology undergrad Devon Lewis (top) worked with several of the students.

After some discussion on what it takes to build an artificial body part, we let the boys try their hand at building their own. We asked them what the different parts of the hand were that allowed us to bend them and move them in certain ways, and from there, they developed ideas for how to turn our household materials into fully functioning hands. We used string as tendons and straws as finger bones, cutting notches where we wanted to create joints.

There was a lot of laughter in the room, but also a lot of collaboration between the different groups of kids. When one team figured out how to make a multi-jointed finger, they would share that knowledge with other groups. Similar knowledge sharing happened when one group figured out how to use the clay to assemble all their fingers into a hand. Seeing these young men work together, problem solve, and be creative was amazing to watch and be a part of!

According to feedback from event organizers, “ours was the most popular session!” Sharlini said. When we reached the end of our session, the kids didn’t want to leave, and instead wanted to keep tinkering with their hands to see what they could accomplish.

The boys had a lot of fun, asked a lot of good questions, and got to pick our brains for advice on staying in school and using it to propel them towards career success. I have distilled some of the best pieces of advice from that night, since they’re good for everyone to hear:

  • Don’t be afraid to ask a lot of questions.
  • Don’t be discouraged when someone tells you no. Go for it anyways.
  • Don’t be afraid of failure.
  • And don’t think you have to fit a particular mold to succeed at something.

“I left feeling really inspired about our future generation of scientists and engineers,” Sharlini said. ”It’s good to know there are so many Duke students with the genuine and selfless desire to help others.”

It was a joy to participate in this event. We all had fun, and left having learned a lot — even the parents who came with their sons!

Outreach like this is incredibly important. Being mentors for young people with a budding interest in science can make the difference between them pursuing it further or dropping it altogether. Engaging with them to show them the passion we have for our work and that we were kids just like they are allows them to see that they can do it too.

Guest Post by Ariana Eily

Data Geeks Go Head to Head

For North Carolina college students, “big data” is becoming a big deal. The proof: signups for DataFest, a 48-hour number-crunching competition held at Duke last weekend, set a record for the third time in a row this year.

DataFest 2017

More than 350 data geeks swarmed Bostock Library this weekend for a 48-hour number-crunching competition called DataFest. Photo by Loreanne Oh, Duke University.

Expected turnout was so high that event organizer and Duke statistics professor Mine Cetinkaya-Rundel was even required by state fire code to sign up for “crowd manager” safety training — her certificate of completion is still proudly displayed on her Twitter feed.

Nearly 350 students from 10 schools across North Carolina, California and elsewhere flocked to Duke’s West Campus from Friday, March 31 to Sunday, April 2 to compete in the annual event.

Teams of two to five students worked around the clock over the weekend to make sense of a single real-world data set. “It’s an incredible opportunity to apply the modeling and computing skills we learn in class to actual business problems,” said Duke junior Angie Shen, who participated in DataFest for the second time this year.

The surprise dataset was revealed Friday night. Just taming it into a form that could be analyzed was a challenge. Containing millions of data points from an online booking site, it was too large to open in Excel. “It was bigger than anything I’ve worked with before,” said NC State statistics major Michael Burton.

DataFest 2017

The mystery data set was revealed Friday night in Gross Hall. Photo by Loreanne Oh.

Because of its size, even simple procedures took a long time to run. “The dataset was so large that we actually spent the first half of the competition fixing our crushed software and did not arrive at any concrete finding until late afternoon on Saturday,” said Duke junior Tianlin Duan.

The organizers of DataFest don’t specify research questions in advance. Participants are given free rein to analyze the data however they choose.

“We were overwhelmed with the possibilities. There was so much data and so little time,” said NCSU psychology major Chandani Kumar.

“While for the most part data analysis was decided by our teachers before now, this time we had to make all of the decisions ourselves,” said Kumar’s teammate Aleksey Fayuk, a statistics major at NCSU.

As a result, these budding data scientists don’t just write code. They form theories, find patterns, test hunches. Before the weekend is over they also visualize their findings, make recommendations and communicate them to stakeholders.

This year’s participants came from more than 10 schools, including Duke, UNC, NC State and North Carolina A&T. Students from UC Davis and UC Berkeley also made the trek. Photo by Loreanne Oh.

“The most memorable moment was when we finally got our model to start generating predictions,” said Duke neuroscience and computer science double major Luke Farrell. “It was really exciting to see all of our work come together a few hours before the presentations were due.”

Consultants are available throughout the weekend to help with any questions participants might have. Recruiters from both start-ups and well-established companies were also on site for participants looking to network or share their resumes.

“Even as late as 11 p.m. on Saturday we were still able to find a professor from the Duke statistics department at the Edge to help us,” said Duke junior Yuqi Yun, whose team presented their results in a winning interactive visualization. “The organizers treat the event not merely as a contest but more of a learning experience for everyone.”

Caffeine was critical. “By 3 a.m. on Sunday morning, we ended initial analysis with what we had, hoped for the best, and went for a five-hour sleep in the library,” said NCSU’s Fayuk, whose team DataWolves went on to win best use of outside data.

By Sunday afternoon, every surface of The Edge in Bostock Library was littered with coffee cups, laptops, nacho crumbs, pizza boxes and candy wrappers. White boards were covered in scribbles from late-night brainstorming sessions.

“My team encouraged everyone to contribute ideas. I loved how everyone was treated as a valuable team member,” said Duke computer science and political science major Pim Chuaylua. She decided to sign up when a friend asked if she wanted to join their team. “I was hesitant at first because I’m the only non-stats major in the team, but I encouraged myself to get out of my comfort zone,” Chuaylua said.

“I learned so much from everyone since we all have different expertise and skills that we contributed to the discussion,” said Shen, whose teammates were majors in statistics, computer science and engineering. Students majoring in math, economics and biology were also well represented.

At the end, each team was allowed four minutes and at most three slides to present their findings to a panel of judges. Prizes were awarded in several categories, including “best insight,” “best visualization” and “best use of outside data.”

Duke is among more than 30 schools hosting similar events this year, coordinated by the American Statistical Association (ASA). The winning presentations and mystery data source will be posted on the DataFest website in May after all events are over.

The registration deadline for the next Duke DataFest will be March 2018.

DataFest 2017

Bleary-eyed contestants pose for a group photo at Duke DataFest 2017. Photo by Loreanne Oh.

s200_robin.smith

Post by Robin Smith

From Sunfish-Seeker to Planet-Saver: Dr. Tierney Thys

Marine biologist Tierney Thys believes that science make us superheroes. In her words, the tools of science are the superpowers that “allow us to explore worlds that are invisible to the naked eye.”

As a National Geographic Explorer, Research Associate at the California Academy of Sciences, and, in my humble opinion, one of the most effective, passionate science communicators out there, she may as well be a superhero already.

Dr. Tierney Thys snorkels with some aquatic research subjects. Photo credit: Tierney Thys.

Thys, an alumna of Duke’s Biology Department, presented at the Marine Science and Conservation Leaders’ (MSCL) inaugural Marine Science Symposium on Saturday, March 25. She was one of four featured speakers — all women in STEM— whose research interests range from marine biology to physical oceanography.

Though she discussed her own research and life story in depth, the main point Thys drove home was the importance of (and science behind) powerful science communication.

Like most marine biologists, Thys’ love for the ocean began when she was a child. She received her Ph.D. from Duke in 1998, an endeavor which, she said, “looked interminable while [she] was in the midst of grad school but, in retrospect, was just a blink of an eye.”

Among the many fun tidbits she has gleaned studying ocean science are the following:

  • As adults, humans retain a lot of characteristics from our fish-like time in the womb; e.g. “we can thank fish for washboard abs.”
  • Humans, for all our obsession with large brains, have nothing on the African elephantfish, which has a “higher brain weight to body weight ratio than any other vertebrate.”
  • Fish had the gender continuum “totally nailed” before it became trendy among humans, with fish of many species having the ability to change sex at will.

Thys, right, and her dissertation advisor, Dr. Stephen Wainwright, left. Photo credit: Tierney Thys.

Her most impactful lesson out of Duke, however, came from her dissertation advisor Stephen Wainwright, James B. Duke Professor emeritus of zoology. Wainwright is the founder of Duke’s Bio-Design Studio, an art studio within a scientific research laboratory employing a full-time sculptor “to create three-dimensional working models of biological systems for research,” as reported by Duke Magazine. Exposure to this unique melding of disciplines in the final stages of Thys’ education set her on what she said was “an eclectic career path” that would also seek to fuse the artistic and the scientific.

Thys’ research specialty out of graduate school is the Mola mola, more commonly known as the Ocean sunfish—the heaviest bony fish on the planet. According to Thys, sunfish can grow to “60 million times their starting weight,” the equivalent of a human child growing to the weight of six Titanic ships. The heaviest Mola ever caught weighed over 5000 lbs., though, surprisingly, jellies (what most folks would call jellyfish) comprise most of the adult sunfish’s diet.

Thys hailed pop-off satellite tags as the “superpower” of science that allows her to track sunfish through the world ocean, generating data that can improve environmental protection of the species.

A fun graphic Thys used in her presentation to explain the technology of pop-off tags for tracking Mola mola, pictured right. Photo credit: Mike Johnson.

“Studying the sunfish has eclipsed studying any other fish for me. [They’re ] a massive part of the bycatch in driftnet fisheries all over the world—[but] we need to keep our jelly-eaters intact. With data, we can figure out the [sunfish] hotspots, and work to protect those areas,” Thys said.

Thys has tackled this problem herself by adapting the discipline-blending approach of her advisor, Wainwright. She has primarily used filmmaking to bridge the gap between the arts and sciences, playing key roles in high-profile documentary projects meant to improve public understanding of marine science, technology, and conservation. These include the Strange Days on Planet Earth series with National Geographic, The Shape of Life series with PBS, and several short documentary films. She has also collaborated with dance companies to create conservation-oriented dance productions, K-6 schools for educational art projects, and prisons to improve inmates’ scientific literacy with nature imagery—all to widen the scope of her science-education efforts. Thys supports her creative ideas with science itself:

“One very large filter exists between our conscious mind and subconscious mind, she said. “Our conscious mind can only process a tiny amount of the information gathered by our subconscious mind.”

“A good story can cut through these filters and light up our brains in new ways,” Thys said “By using different forms of art to tell stories infused with scientific information, we can message in profound ways. We can reach people who might not otherwise be interested or receptive to science. The arts are not a luxury, but rather a powerful vehicle for helping message, teach and share our vital scientific findings,” Thys said.

A mural Thys made with students out of bottle caps at a California elementary school, one of Thys’ many efforts to spread public awareness of scientific issues. Photo credit: Tierney Thys.

As though she hadn’t already empowered everyone in the audience to save the world, Thys concluded with a compelling piece of advice: “Be a part of something much bigger than yourself.”

Post by Maya Iskandarani

Mental Shortcuts, Not Emotion, May Guide Irrational Decisions

If you participate in a study in my lab, the Huettel Lab at Duke, you may be asked to play an economic game. For example, we may give you $20 in house money and offer you the following choice:

  1. Keep half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In such a scenario, most participants choose 1, preferring a sure win over the gamble.

Now imagine this choice, again starting with $20 in house money:

  1. Lose half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In this scenario, most participants prefer the gamble over a sure loss.

If you were paying close attention, you’ll note that both examples are actually numerically identical – keeping half of $20 is the same as losing half of $20 – but changing whether the sure option is framed as a gain or a loss results in different decisions to play it safe or take a risk. This phenomenon is known as the Framing Effect. The behavior that it elicits is weird, or as psychologists and economists would say, “irrational”, so we think it’s worth investigating!

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

In a study published March 29 in the Journal of Neuroscience, my lab used brain imaging data to test two competing theories for what causes the Framing Effect.

One theory is that framing is caused by emotion, perhaps because the prospect of accepting a guaranteed win feels good while accepting a guaranteed loss feels scary or bad. Another theory is that the Framing Effect results from a decision-making shortcut. It may be that a strategy of accepting sure gains and avoiding sure losses tends to work well, and adopting this blanket strategy saves us from having to spend time and mental effort fully reasoning through every single decision and all of its possibilities.

Using functional magnetic resonance imaging (fMRI), we measured brain activity in 143 participants as they each made over a hundred choices between various gambles and sure gains or sure losses. Then we compared our participants’ choice-related brain activity to brain activity maps drawn from Neurosynth, an analysis tool that combines data from over 8,000 published fMRI studies to generate neural maps representing brain activity associated with different terms, just as “emotions,” “resting,” or “working.”

As a group, when our participants made choices consistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental disengagement (i.e. “resting” or “default”). When they made choices inconsistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental engagement (i.e. “working” or task”). These results supported the theory that the Framing Effect results from a lack of mental effort, or using a decision-making shortcut, and that spending more mental effort can counteract the Framing Effect.

Then we tested whether we could use individual participants’ brain activity to predict participants’ choices on each trial. We found that the degree to which each trial’s brain activity resembled the brain maps associated with mental disengagement predicted whether that trial’s choice would be consistent with the Framing Effect. The degree to which each trial’s brain activity resembled brain maps associated with emotion, however, was not predictive of choices.

Our findings support the theory that the biased decision-making seen in the Framing Effect is due to a lack of mental effort rather than due to emotions.

This suggests potential strategies for prompting people to make better decisions. Instead of trying to appeal to people’s emotions – likely a difficult task requiring tailoring to different individuals – we would be better off taking the easier and more generalizable approach of making good decisions quick and easy for everyone to make.

Guest post by Rosa Li

Hidden No More: Women in STEM reflect on their Journeys

Back when she was a newly-minted Ph.D., Ayana Arce struggled to picture her future life as an experimental physicist. An African American woman in a field where the number of black women U.S. doctorates is still staggeringly small, Arce could not identify many role models who looked like her.

“I didn’t know what my life would look like as a black postdoc or faculty member,” Arce said.

But in the end, Arce – an associate professor of physics at Duke who went on to join the international team of physicists who discovered the Higgs Boson in 2012 — drew inspiration from her family.

“I looked to the women such as my mother who had had academic careers, and tried to think about how I could shape my life to look something like that, and I realized that it could be something I could make work,” Arce said.

Adrienne Stiff-Roberts, Fay Cobb Payton, Kyla McMullen, Robin Coger and Valerie Ashby on stage at the Hidden Figures No More panel discussion.

Adrienne Stiff-Roberts, Fay Cobb Payton, Kyla McMullen, Robin Coger and Valerie Ashby on stage at the Hidden Figures No More panel discussion. Credit: Chris Hildreth, Duke Photography.

Arce joined five other African American women faculty on the stage of Duke’s Griffith Film Theater March 23 for a warm and candid discussion on the joys and continuing challenges of their careers in science, technology, engineering and math (STEM) fields.

The panel, titled “Hidden Figures No More: Highlighting Phenomenal Women in STEM,” was inspired by Hidden Figures, a film which celebrates three pioneering African American women mathematicians who overcame racial segregation and prejudice to play pivotal roles in NASA’s first manned space flight.

The panel discussion was spearheaded by Johnna Frierson, Director of the Office of Diversity and Inclusion at the Pratt School of Engineering, and co-sponsored by the Duke Women’s Center. It was followed by a free screening of the film.

Though our society has made great strides since the days depicted in the film, women and minorities still remain under-represented in most STEM fields. Those who do pursue careers in STEM must overcome numerous hurdles, including unconscious bias and a lack of colleagues and role models who share their gender and race.

“In my field, at some of the smaller meetings, I am often the only black woman present at the conference, many times I’m the only black person at all,” said Adrienne Stiff-Roberts, an Associate Professor of Electrical and Computer Engineering at Duke. “In that atmosphere often it can be very challenging to engage with others in the way that you are supposed to, and you can feel like an outsider.”

Valerie Ashby and Ayana Arce onstage at the Hidden Figures No More panel discussion

Valerie Ashby and Ayana Arce shared their experiences. Credit: Chris Hildreth, Duke Photography

Stiff-Roberts and the other panelists have all excelled in the face of these challenges, making their marks in fields that include physics, chemistry, computer science, mechanical engineering and electrical engineering. On Thursday they shared their thoughts and experiences with a diverse audience of students, faculty, community members and more than a few kids.

Many of the panelists credited teams of mentors and sponsors for bolstering them when times got tough, and encouraged young scientists to form their own support squads.

Valerie Ashby, Dean at Duke’s Trinity College of Arts and Sciences, advised students to look for supporters who have a vision for what they can become, and are eager to help them get there. “Don’t assume that your help might come from people who you might expect your help to come from,” Ashby said.

The importance of cheerleading from friends, and particularly parents, can never be overestimated, the panelists said.

“Having someone who will celebrate every single positive with you is a beautiful thing,” said Ashby, in response to a mother seeking advice for how to support a daughter majoring in biomedical engineering. “If your daughter is like many of us, we’ll do 99 great things but if we do one wrong thing we will focus on the one wrong thing and think we can’t do anything.”

Women in STEM can also be important and powerful allies to each other, noted Kyla McMullen, an Assistant Professor of Computer and Information Science at the University of Florida.

“I have seen situations where a woman suggests something and then the male next her says the same thing and gets the credit,” McMullen said. “That still happens, but one thing that I see help is when women make an effort to reiterate the points made by other women so people can see who credit should be attributed to.”

With all the advice out there for young people who are striving to succeed in STEM – particularly women and underrepresented minorities – the panelists advocated that everyone to stay true to themselves, above all.

“I want to encourage everyone in the room – whether you are a budding scientist or woman scholar – you can be yourself,” Ashby said. “You should make up in your mind that you are going to be yourself, no matter what.”

Kara J. Manke, PhD

Post by Kara Manke

Closing the Funding Gap for Minority Scientists

DURHAM, N.C. — The barriers to minority students in science, technology, engineering and math (STEM) don’t go away once they’ve finished school and landed a job, studies show. But one nationwide initiative aims to level the playing field once they get there.

With support from a 3-year, $500,0000 grant from the National Science Foundation, assistant professors and postdoctoral fellows who come from underrepresented minorities are encouraged to apply by May 5 for a free grant writing workshop to be held June 22-24 in Washington, D.C..

It’s no secret that STEM has a diversity problem. In 2015, African-Americans and Latinos made up 29 percent of the U.S. workforce, but only 11 percent of scientists and engineers.

A study published in the journal Science in 2011 revealed that minority scientists also were less likely to win grants from the National Institutes of Health, the largest source of research funding to universities.

Based on an analysis of 83,000 grant applications from 2000 to 2006, the study authors found that applications from black researchers were 13 percent less likely to succeed than applications from their white peers. Applications from Asian and Hispanic scientists were 5 and 3 percent less likely to be awarded, respectively.

Even when the study authors made sure they were comparing applicants with similar educational backgrounds, training, employers and publication records, the funding gap persisted — particularly for African-Americans.

Competition for federal research dollars is already tough. But white scientists won 29 percent of the time, and black scientists succeeded only 16 percent of the time.

Pennsylvania State University chemistry professor Squire Booker is co-principal investigator of a $500,000 initiative funded by the National Science Foundation to help underrepresented minority scientists write winning research grants.

“That report sent a shock wave through the scientific community,” said Squire Booker, a Howard Hughes Medical Institute investigator and chemistry professor at Pennsylvania State University. Speaking last week in the Nanaline H. Duke building on Duke’s Research Drive, Booker outlined a mentoring initiative that aims to close the gap.

In 2013, Booker and colleagues on the Minority Affairs Committee of the American Society for Biochemistry and Molecular Biology decided to host a workshop to demystify the grant application process and help minority scientists write winning grants.

Grant success is key to making it in academia. Even at universities that don’t make funding a formal requirement for tenure and promotion, research is expensive. Outside funding is often required to keep a lab going, and research productivity — generating data and publishing results — is critical.

To insure underrepresented minorities have every chance to compete for increasingly tight federal research dollars, Booker and colleagues developed the Interactive Mentoring Activities for Grantsmanship Enhancement program, known as IMAGE. Program officers from NIH and NSF offer tips on navigating the funding process, crafting a successful proposal, decoding reviews and revising and resubmitting. The organizers also stage a mock review panel, and participants receive real-time, constructive feedback on potential research proposals.

Participants include researchers in biology, biophysics, biochemistry and molecular biology. More than half of the program’s 130 alumni have been awarded NSF or NIH grants since the workshop series started in 2013.

Booker anticipates this year’s program will include more postdoctoral fellows. “Now we’re trying to expand the program to intervene at an earlier stage,” Booker said.

To apply for the 2017 workshop visit http://www.asbmb.org/grantwriting/.  The application deadline is May 5.

s200_robin.smith

Post by Robin Smith

What is Money Really Worth?

“Yesterday, I was at an event and I sat next to an economist,” Brian Hare told my class. “I asked him: how old is money? He was completely lost.”

I was in Hare’s class on a Monday at noon, laughing at his description of the interaction. We had so far been exploring the origins of humans’ particular ways of making sense of the world through his course in Human Cognitive Evolution and we were faced with a slide that established the industrial period as less than 200 years old. As compared to a hunting and gathering lifestyle, this stretch of time is minuscule on an evolutionary scale.

Slide from Dr. Hare’s class. Reproduced with permission.

Why then do so many studies employ money as a proxy for the measurement of human behaviors that have been shaped by hundreds of thousands of years? This kind of research is trying to get at “prosociality,” (the ability to be altruistic and cooperative towards others) or empathy and guilt aversion, just to name a few.

I had started to wonder about this months before as a summer intern at the University of Tokyo. As I listened to a graduate student describe an experiment employing money to understand how humans behaved cooperatively, I grew puzzled. I eventually asked: Why was money used in this experiment? The argument was made that money was enough of a motivator for this sample population of college students to generalize that if they chose to share it, it must mean something.

During a panel discussion about prosociality at the American Association for the Advancement of Science meeting in Boston last month, my chance came to ask the question again. Alan Sanfey, professor at the Donders Institute for Brain, Cognition and Behavior, used experimental paradigms that rewarded participants with money to tease out the particular effects of guilt on generous behavior.

“Is money a good proxy for understanding evolutionarily ancient behavior?” I asked. Robin Dunbar, professor of evolutionary psychology at Oxford University took a dig at my question and mentioned that the barter system would have likely been the best ancient representative of money. However, the barter system likely came to life during the agricultural period, which itself is less than 10,000 years old.

Dollar bills. Public domain.

Stephen Pluháček, an attendee at the event and a senior scholar at the University of New Hampshire, said in a followup email to me that he “was interested in [my] question to the panel and disappointed by their response — which I found indicative of the ways we can become so habituated to a way of looking at things that we find it difficult to even hear questions that challenge our foundational assumptions.”

“As I said in our brief conversation, I am not convinced that money can stand as a proxy for prosocial behavior (trust, generosity) in humans prior to the advent of agriculture,” Pluháček wrote. “And even barter or gift exchange may be limited in their applicability to early humans (as well as to modern humans prior to the cognitive revolution).” 

So, I’m not alone in my skepticism. However, in my discussion with Leonard White, my advisor and associate director for education in the Duke Institute for Brain Sciences, he pointed out:

“The brain is remarkably facile. We have this amazing capacity for proxy substitution.”

In essence, this would mean that our brain would be able to consider money as a reward just like any reward that might have mediated the evolution of our behavior over time. We would thus be able to test subjects with “modern” stimuli, it appears.

It is clear that an evolutionary narrative is important to creating a more complete picture of contemporary human behavior. But sometimes the proxies we choose to make these measures don’t fit very well with our long history.

By Shanen Ganapathee

 

The Road to a Tastier Tomato

This week, I discovered that I’ve lived life deprived of a good tomato.

As a tomato-lover, I was surprised to learn from Professor Harry Klee of the University of Florida that the supermarket tomatoes I’ve enjoyed throughout my 18-year existence are all flavorless compared to the tomatoes of the past. He spoke at Duke as a guest of the University Program in Genetics and Genomics on Feb. 28.

It turns out that commercial tomato growers, by breeding more profitable (i.e. higher-yield, redder-color, larger-fruit) tomato varieties over the past 50 years, inadvertently excluded what Klee believes is the most important tomato trait of all:

Commercial tomato growers have bred larger, redder tomatoes that are less flavorful than heirloom and older varieties. Image courtesy of Harry Klee.

Flavor.

Apparently, I was one of very few people unaware of this issue. The public outcry in response to the increasing flavorlessness of commercial tomatoes began over a decade ago, when Klee first began to study tomato genetics.

From his research, Klee has drawn several important, unexpected conclusions, chief among them:

1: Flavor has more to do with smell than taste;

2: Lesser-known biochemical compounds called “volatiles” influence the flavor of tomatoes more than sugars, acids, and other well-known, larger compounds;

3: These “volatiles” are less present in modern tomato varieties than in tastier, older, and heirloom varieties;

But fear not—

4: Tomatoes can be back-bred to regain the genes that code for volatile compounds.

In other words, Klee has mapped the way back to the flavorful tomatoes of the past. His work culminated in a cover story of the Jan. 27 issue of Science. The corresponding paper describing the analysis of over 300 tomato strains to identify the chemicals associated with “good” and “bad” tomatoes.

Dr. Harry Klee and collaborators in his lab at the University of Florida. Image courtesy of Harry Klee.

To prove that modern tomatoes have less of the compounds that make them tasty, Klee and his team recruited a panel of 100 taste-testers to rank 160 representative tomato varieties. According to Klee, the team “developed statistical models to explain the chemistry of ‘liking’ [tomatoes],” then narrowed down the list of compounds that correlated with “liking” from 400 to 26. After tracing these 26 compounds to genetic loci, they used whole-genome sequencing to show that these loci are less expressed in modern tomatoes than in “cerasiforme” (i.e. old) and heirloom tomato varieties.

Further studies showed that tomato weight is inversely correlated with sugar content—in other words, “a gigantic fruit doesn’t taste as good,” Klee said.

If Klee can convince tomato growers that consumers value flavor over size, color, and quantity, then he might just single-handedly put flavorful tomatoes back on the shelves. Nevertheless—and despite the publicity surrounding his work—Klee understands it make take a while before commercial tomato growers see the light.

Klee and his team of scientists have genetically mapped the way back to the tasty tomatoes of the past. Image courtesy of Harry Klee.

“Growers get no more money if the tomato tastes good or bad; they’re paid for how many pounds of red objects they put in a box…[but] we can’t just blame the modern breeders. We’ve been selecting bigger and bigger fruit for millennia, and that has come at the cost of reducing flavor,” Klee said.

Post by Maya Iskandarani

Venturing Out of the Lab to Defend Science

It’s 6 p.m. on a Wednesday and the grad students aren’t at their lab benches. IM softball doesn’t start till next week, what gives?

We’ve snuck out of our labs a bit early to take in a dose of U.S. policy for the evening.

Politics fall far outside our normal areas of expertise. I’m a biology Ph.D. student studying plants — even with my liberal arts education, politics isn’t my bread and butter.

Buz Waitzkin of Science & Society (blue shirt) gave grad students a highly accelerated intro to matters of science policy.

But the current political climate in the U.S. has many scientists taking a more careful look into politics. Being scholars who have a sense of the world around us has become more important than ever.

“Agency regulation, funding, it’s all decided by our branches of government,” says Ceri Weber, a 3rd year Ph.D. candidate in Cell Biology.

Weber, a budding “sci-pol” enthusiast and the general programming chair for the student group INSPIRE, feels passionately about getting scientists informed about policy.

So she organized this event for graduate scientists to talk with the deputy director of Duke Science & Society, Buz Waitzkin, who previously served as special counsel to President Bill Clinton, and now teaches science policy classes cross-listed between Duke’s Biomedical Science programs and the Law School.

Seated with food and drinks—the way to any grad student’s heart—we found ourselves settling in for an open discussion about the current administration and the impact its policies could have on science.

We covered a lot of ground in our 2-hour discussion, though there was plenty more we would love to continue learning.

We discussed: lobbying, executive orders, the balances of power, historical context, tradition, and civil actions, to name a few.

There were a lot of questions, and a lot of things we didn’t know.

Even things as simple as “what exactly is a regulation?” needed to be cleared up. We’ve got our own definition in a biological context, but regulation takes on a whole new meaning in a political one. It was neat having the chance to approach this topic from the place of a beginner.

We were floored by some of the things we learned, and puzzled by others. Importantly, we found some interesting places of kinship between science and policy.

When we discussed the Congressional Review Act, which impacts regulations—the main way science policy is implemented—we learned there is ambiguity in law just like there is in science.

One area on all of our minds was how we fit into the picture. Where can our efforts and knowledge as scientists and students can make a difference?

I was shocked to learn of the lack of scientists in government: only five ever in Congress, and three in the Cabinet.

But luckily, there is space for us as science advisors in different affiliations with the government. There are even Duke graduate students working on a grant to develop science policy fellowships in the NC state legislature.

At the end of the night, we were all eager to learn more and encouraged to participate in politics in the ways that we can. We want to be well-versed in policy and take on an active role to bring about change in our communities and beyond.

Hopefully, as the years go on, we’ll have more opportunities to deepen our knowledge outside of science in the world around us. Hopefully, we’ll have more scientists who dare to step out of the lab.

Guest Post by Graduate Student Ariana Eily