Biology Archives - Research Blog

Look at the nearest window. What did you see first—the glass itself or what was on the other side? For birds, that distinction is a matter of life and death.

A dead red-eyed vireo above the entrance to the Brodhead Center at Duke. Every year, millions of birds die after colliding with windows. Buildings with lots of glass are particularly dangerous.

Every year, up to one billion birds die from hitting windows. Windows kill more birds than almost any other cause of human-related bird mortality, second only to feral and domestic cats. Both the transparency and reflectiveness of glass can confuse flying birds. They either don’t see the glass at all and try to fly through it, or they’re fooled by reflections of safe habitat or open sky. And at night, birds may be disoriented by lit-up buildings and end up hitting windows by mistake. In all cases, the result is usually the same. The majority of window collision victims die on impact. Even the survivors may die soon after from internal bleeding, concussions, broken bones, or other injuries.

Madison Chudzik, a biology Ph.D. student in the Lipshutz Lab at Duke, studies bird-window collisions and migrating birds. “Purely the fact that we’ve built buildings is killing those birds,” she says.

Every spring and fall, billions of birds in the United States alone migrate to breeding and wintering grounds. Many travel hundreds or thousands of miles. During peak migration, tens of thousands of birds may fly across Durham County in a single night. Not all of them make it.

Chudzik’s research focuses on nocturnal flight calls, which migrating birds use to communicate while they fly. Many window collision victims are nocturnal migrants lured to their deaths by windows and lights. Chudzik wants to know “how we can use nocturnal flight calls as an indicator to examine collision risks in species.”

Chudzik (back) setting up one of her recording devices on the Museum of Science and Industry in Chicago. The devices record flight calls from birds migrating at night.
Image courtesy of Chudzik.

Previous research, Chudzik says, has identified a strong correlation between the number of flight calls recorded on a given night and the overall migration intensity that night. “If sparrows have a high number of detections, there is likely a high number migrating through the area,” Chudzik explains. But some species call more than others, and there is “taxonomic bias in collision risk,” with some species that call more colliding less and vice versa. Chudzik is exploring this relationship in her research.

Unlike bird songs, nocturnal flight calls are very short. The different calls are described with technical terms like “zeep” and “seep.” Chudzik is part of a small but passionate community of people with the impressive ability to identify species by the minute differences between their flight calls. “It’s a whole other world of… language, basically,” Chudzik says.

Chudzik can identify a species not only by hearing its flight call but also by seeing its spectrogram, a visual representation of sound. This spectrogram, from a recording on Adler Planetarium, has flight calls from four species. The x-axis represents time, while the y-axis shows frequency. The brightness or intensity indicates amplitude.
Image from Chudzik.

She began studying nocturnal flight calls for research she did as an undergraduate, but her current project no longer needs to rely on talented humans to identify every individual call. A deep learning model called Nighthawk, trained on a wealth of meticulous flight call data, can identify calls from their spectrograms with 95% accuracy. It is free and accessible to anyone, and much of the data it’s been trained on comes from non-scientists, such as submissions from a Facebook community devoted to nocturnal flight calls. Chudzik estimates that perhaps a quarter of the people on that Facebook page are researchers. “The rest,” she says, “are people who somehow stumbled upon it and… fell in love with nocturnal flight calling.”

In addition to studying nocturnal flight calls, Chudzik’s research will investigate how topography, like Lake Michigan by Chicago, affects migration routes and behavior and how weather affects flight calls. Birds seem to communicate more during inclement weather, and bad weather sometimes triggers major collision events. Last fall in Chicago, collisions with a single building killed hundreds of migratory birds in one night.

Chudzik had a recorder on that building. It had turned off before the peak of the collision event, but the flight call recordings from that night are still staggering. In one 40-second clip, there were 300 flight calls identified. Normally, Chudzik says, she might expect a maximum of about seven in that time period.

Nights like these, with enormous numbers of migrants navigating the skies, can be especially deadly. Fortunately, solutions exist. The problem often lies in convincing people to use them. There are misconceptions that extreme changes are required to protect birds from window collisions, but simple solutions can make a huge difference. “We’re not telling you to tear down that building,” Chudzik says. “There are so many tools to stop this from happening that… the argument of ‘well, it’s too expensive, I don’t want to do it…’ is just thrown out the window.”

A yellow-bellied sapsucker collision casualty in front of the French Family Science Center last year.

What can individuals and institutions do to prevent bird-window collisions?

Turn off lights at night.

For reasons not completely understood, birds flying at night are attracted to lit-up urban areas, and lights left on at night can become a death trap. Though window collisions are a year-round problem, migration nights can lead to high numbers of victims, and turning off non-essential lights can help significantly. One study on the same Chicago building where last year’s mass collision event occurred found that halving lighted windows during migration could reduce bird-window collisions by more than 50%.

Chudzik is struck by “the fact that this is such a big conservation issue, but it literally just takes a flip of a switch.” BirdCast and Audubon suggest taking actions like minimizing indoor and outdoor lights at night during spring and fall migration, keeping essential outdoor lights pointed down and adding motion sensors to reduce their use, and drawing blinds to help keep light from leaking out.

Use window decals and other bird-friendly glass treatments.

There are many products and DIY solutions intended to make windows safer for birds, like window decals, external screens, patterns of dots or lines, and strings hanging in front of a window at regular intervals. For window treatments to be most effective, they should be applied to the exterior of the glass, and any patterning should be no more than two inches apart vertically and horizontally. This helps protect even the smallest birds, like kinglets and hummingbirds.

It can be hard to see from a distance, but these windows on Duke’s Fitzpatrick Center have been retrofitted with tiny white dots, an effective strategy to reduce bird-window collisions.

A 2016 window collision study at Duke conducted by several scientists, including Duke Professor Nicolette Cagle, Ph.D., identified the Fitzpatrick Center as a window collision hotspot. As a result, Duke retrofitted some of the building’s most dangerous windows with bird-friendly dot patterning. Ongoing collision monitoring has revealed about a 70% reduction in collisions for that building since the dots were added.

One obstacle to widespread use of bird-friendly design practices and window treatments is concerns about aesthetics. But bird-friendly windows can be aesthetically pleasing, too, and “Dead birds hurt your aesthetic anyway.”

If nothing else, don’t clean your windows.

Bird-window collisions don’t just happen in cities and on university campuses. In fact, most fatal collisions involve houses and other buildings less than four stories tall. Window treatments like the dots on the Fitzpatrick building can be costly for homeowners, but anything you can put on the outside of a window will help.

“Don’t clean your windows,” Chudzik suggests—smudges may also help birds recognize the glass as a barrier.

Window collisions at Duke

The best thing Duke could do, Chudzik says, is to be open to treating more windows. Every spring, students in Cagle’s Wildlife Surveys class, which I am taking now, collect data on window collision victims found around several buildings on campus. Meanwhile, a citizen science iNaturalist project collects records of dead birds seen by anyone at campus. If you find a dead bird near a window at Duke, you can help by submitting it to the Bird-window collisions project on iNaturalist. Part of the goal is to identify window collision hotspots in order to advocate for more window treatments like the dots on the Fitzpatrick Center.

Spring migration is happening now. BirdCast’s modeling tools estimate that 260,000 birds crossed Durham County last night. They are all protected under the Migratory Bird Treaty Act. However, Chudzik says, “We haven’t thought to protect them while they’re actually migrating.” The law is intended to protect species that migrate, but “it’s not saying ‘while you are migrating you have more protections,’” Chudzik explains. Some have argued that it should, however, suggesting that the Migratory Bird Treaty Act should mandate safer windows to help protect migrants while they’re actually migrating.

“This whole world comes alive while we’re asleep, and… most people have no idea,” Chudzik says about nocturnal flight calls. She is shown here on Northwestern University, one of the Chicago buildings where she has placed recorders for her research.
Photo courtesy of Chudzik.

We can’t protect every bird that passes overhead at night, but by making our buildings safer, we can all help more birds get one step closer to where they need to go.

Post by Sophie Cox, Class of 2025

To get a fuller picture of a forest, sometimes research requires a team effort

By Robin Smith

On April 1, 2024

In Animals, Biology, Climate/Global Change, Environment/Sustainability, Field Research, Lemurs

Film by Riccardo Morrelas, Zahava Production

For some people, the word “rainforest” conjures up vague notions of teeming jungles. But Camille DeSisto sees something more specific: a complex interdependent web.

For the past few years, the Duke graduate student has been part of a community-driven study exploring the relationships between people, plants and lemurs in a rainforest in northern Madagascar, where the health of one species depends on the health of others.

Many lemurs, for example, eat the fruits of forest trees and deposit their seeds far and wide in their droppings, thus helping the plants spread. People, in turn, depend on the plants for things like food, shelter and medicines.

But increasingly, deforestation and other disturbances are throwing these interactions out of whack.

DeSisto and her colleagues have been working in a 750,000-acre forest corridor in northeast Madagascar known as the COMATSA that connects two national parks.

The area supports over 200 tree species and nine species of lemurs, and is home to numerous communities of people.

A red-bellied lemur (*Eulemur rubriventer*) in a rainforest in northeast Madagascar. Photo by Martin Braun.

“People live together with nature in this landscape,” said DeSisto, who is working toward her Ph.D. in ecology at the Nicholas School of the Environment.

But logging, hunting and other stressors such as poverty and food insecurity have taken their toll.

Over the last quarter century, the area has lost 14% of its forests, mostly to make way for vanilla and rice.

This loss of wild habitats risks setting off a series of changes. Fewer trees also means fewer fruit-eating lemurs, which could create a feedback loop in which the trees that remain have fewer opportunities to replace themselves and sprout up elsewhere — a critical ability if trees are going to track climate change.

DeSisto and her colleagues are trying to better understand this web of connections as part of a larger effort to maximize forest resilience into an uncertain future.

To do this work, she relies on a network of a different sort.

The research requires dozens of students and researchers from universities in Madagascar and the U.S., not to mention local botanists and lemur experts, the local forest management association, and consultants and guides from nearby national parks, all working together across time zones, cultures and languages.

Forest field team members at camp (not everyone present). Photo credit: Jane Slentz-Kesler.

Together, they’ve found that scientific approaches such as fecal sampling or transect surveys can only identify so much of nature’s interconnected web.

Many lemurs are small, and only active at night or during certain times of year, which can make them hard to spot — especially for researchers who may only be on the ground for a limited time.

To fill the gaps, they’re also conducting interviews with local community members who have accumulated knowledge from a lifetime of living on the land, such as which lemurs like to munch on certain plants, what parts they prefer, and whether people rely on them for food or other uses.

By integrating different kinds of skills and expertise, the team has been able to map hidden connections between species that more traditional scientific methods miss.

For example, learning from the expertise of local community members helped them understand that forest patches that are regenerating after clear-cutting attract nocturnal lemurs that may — depending on which fruits they like to eat — promote the forest’s regrowth.

Camille DeSisto after a successful morning collecting lemur fecal samples.

Research collaborations aren’t unusual in science. But DeSisto says that building collaborations with colleagues more than 9,000 miles away from where she lives poses unique challenges.

Just getting to her field site involves four flights, several bumpy car rides, climbing steep trails and crossing slippery logs.

“Language barriers are definitely a challenge too,” DeSisto said.

She’s been studying Malagasy for seven years, but the language’s 18 dialects can make it hard to follow every joke her colleagues tell around the campfire.

To keep her language skills sharp she goes to weekly tutoring sessions when she’s back in the U.S., and she even helped start the first formal class on the language for Duke students.

“I like to think of it as language opportunities, not just language barriers,” DeSisto said.”

“Certain topics I can talk about with much more ease than others,” she added. “But I think making efforts to learn the language is really important.”

When they can’t have face-to-face meetings the team checks in remotely, using videoconferencing and instant messaging to agree on each step of the research pipeline, from coming up with goals and questions and collecting data to publishing their findings.

“That’s hard to navigate when we’re so far away,” DeSisto said. But, she adds, the teamwork and knowledge sharing make it worth it. “It’s the best part of research.”

This research was supported by Duke Bass Connections (“Biocultural Sustainability in Madagascar,” co-led by James Herrera), Duke Global, The Explorers Club, Primate Conservation, Inc., Phipps Conservatory and Botanical Gardens, and the Garden Club of America.

Glowing Waterdogs and Farting Rivers: A Duke Forest Research Tour

By Sophie Cox

On January 25, 2024

In Animals, Biology, Climate/Global Change, Environment/Sustainability, Field Research, Science Communication & Education

Jonny Behrens looks for aquatic macroinvertebrates with Duke Forest Research Tour participants.

“Who would be surprised if I told you that rivers fart?”

Nick Marzolf, Ph.D., went on to explain that streams release greenhouse gases from decaying matter and gas-producing bacteria. This revelation was one of several new facts I learned at the annual Duke Forest Research Tour in December.

“First and foremost,” says Duke Forest Senior Program Coordinator Maggie Heraty, “the Duke Forest is a teaching and research laboratory.” The Office of the Duke Forest hosts an annual Research Tour to showcase research activities and connect to the wider community. “Connecting people to science and nature, and demystifying scientific research, is a key part of our goals here,” Heraty says.

Duke Forest, which consists of over 7,000 acres in Durham, Orange, and Alamance Counties, lies within the Cape Fear and Neuse river basins, two of seventeen river basins in North Carolina. What exactly is a river basin? Heraty quoted a poetic definition from North Carolina Environmental Education:

“A river basin encompasses all the land surface drained by many finger-like streams and creeks flowing downhill into one another and eventually into one river, which forms its artery and backbone. As a bathtub catches all the water that falls within its sides and directs the water out its drain, a river basin sends all the water falling within its surrounding ridges into its system of creeks and streams to gurgle and splash downhill into its river and out to an estuary or the ocean.”

Located within the Cape Fear River Basin, the headwaters of New Hope Creek, which passes through the Korstian Division of Duke Forest, are fed by roughly 33,000 acres of land, over 5,000 of which are in the Duke Forest. Land outside of the Forest is of vital importance, too. Duke Forest is working in partnership with other local conservation organizations through the Triangle Connectivity Collaboration, an initiative to connect natural areas, create wildlife corridors, reduce habitat fragmentation, and protect biodiversity in the Triangle region.

New Hope Creek in the Korstian Division of the Duke Forest.

Dwarf waterdogs

We walked down a short trail by the creek, and the tour split into two groups. Our group walked farther along the stream to meet two herpetologists studying the elusive dwarf waterdog.

Bryan Stuart, Ph.D., Research Curator of Herpetology at the North Carolina Museum of Natural Sciences, and Ron Grunwald, Ph.D., Duke University Senior Lecturer Emeritus, are involved in a study looking for dwarf waterdog salamanders (Necturus punctatus) in New Hope Creek. Dwarf waterdogs are paedomorphic, Stuart said, meaning they retain larval characteristics like external gills and a flat tail throughout their lives. In fact, the genus name Necturus means “tail swimmer” in reference to the species’s flat tail.

According to Stuart, on October 3, 1954, Duke professor and herpetologist Joe Bailey collected a dwarf waterdog in New Hope Creek. It was the first record of the species in Orange County.

The Duke Forest is in the westernmost part of the species’ Piedmont range, though it extends farther west in parts of the sandhills. “To have a dwarf waterdog record in Orange County—that’s almost as interesting as it gets,” Stuart said.

Ron Grunwald and Bryan Stuart discuss dwarf waterdog research at New Hope Creek.
Photo provided by The Office of the Duke Forest.

In the late 1960s, Michael A. Fedak, Bailey’s graduate student, did a thesis on dwarf waterdogs in the area. His specimens are still stored in the collections of the North Carolina Museum of Natural Sciences.

No one had studied this population since—until now.

Dwarf waterdogs are very sensitive to pollution and habitat disturbance, Stuart said, on top of the fact that New Hope Creek is already at the edge of the species’s habitat. When Fedak studied them several decades ago, the salamanders were abundant. Are they still?

Stuart, Grunwald, and other researchers want to find out. “The challenge of salamander biology,” Grunwald said, “is that it always happens when it’s freezing.” Surveying salamander populations, he explains, isn’t like watching birds or counting trees. It requires you to go where the salamanders are, and for dwarf waterdog research, that means dark, cold streams on nights when the water temperature is below 55 degrees Fahrenheit.

Researchers bait funnel traps with chicken liver or cat food and set them underwater overnight. Sometimes they catch crayfish. Sometimes they catch nothing. And sometimes they catch exactly what they’re hoping to find: the elusive dwarf waterdog. After all this time, these slippery, nocturnal, chicken-liver-loving salamanders are still here.

Two dwarf waterdogs in a funnel trap before being released back into New Hope Creek.

Though the traps have been successful at capturing some individuals, they will never catch them all, so researchers calculate the recapture rate to estimate the total population. Imagine a bag of rice, Grunwald said. You could count each individual grain, but that would be challenging and time-consuming. Alternatively, you could pull out one grain of rice, color it, and put it back in the bag, then estimate the total number by calculating the probability of pulling out the same colored grain of rice again. In a very small bag, you might draw the same rice grain several times. But the more rice you have, the less likely you are to draw the same grain twice.

To figure out if any of the dwarf waterdogs they catch are recaptures, the researchers mark each individual with a visual implant elastomer, which is “just a fancy way of saying rubber that we can see,” Grunwald said. The material is injected under a salamander’s “armpit” with a small syringe, creating a pattern visible under ultraviolet light. With two colors (fluorescent yellow and red) and four possible injection locations (one behind each leg), there are plenty of distinct combinations. Grunwald showed us a waterdog that had already been marked. Under a UV flashlight, a spot just below its right foreleg glowed yellow.

Captured dwarf waterdogs are injected with a special rubber material that glows under a UV light. Each salamander is marked with a distinct pattern so researchers can recognize it if it’s ever recaptured.

Establishing a recapture rate is essential to predicting the total population in the area. The current recapture rate? Zero. The sample size so far is small—about a dozen individuals—and none of them have been caught twice. That’s an obstacle to statistical analysis of the population, but it’s good news for the salamanders. Every new individual is one more dwarf waterdog survivor in New Hope Creek.

Ron Grunwald with Research Tour participants looking at dwarf waterdogs in bags.
Photo provided by The Office of the Duke Forest.

Stream health

Next, at a different spot along the stream, we met Nick Marzolf, Ph.D., a postdoctoral scholar, and Jonny Behrens, a Ph.D. student, to learn more about New Hope Creek itself. Marzolf and Behrens have both been involved with aquaterrestrial biogeochemistry research in the lab of Emily Bernhardt, Ph.D., at Duke University.

Protecting New Hope Creek requires understanding individual organisms—like dwarf waterdogs—but also temperature, precipitation, oxygen levels, pesticide runoff, and biodiversity overall. When humans get stressed, Behrens said, different organs have different physiological reactions. Similarly, different organisms in a stream play different roles and respond to stress in different ways.

Jonny Behrens and Research Tour participants look at aquatic macroinvertebrate samples.
Photo provided by The Office of the Duke Forest.

Behrens passed around vials containing aquatic macroinvertebrates—specimens big enough to see with the naked eye—such as the larvae of mayflies, crane flies, stoneflies, and dragonflies. They are known for being good indicators of stream health because there are many species of macroinvertebrates, and they have different tolerances to stressors like pollution or changes in water temperature.

Aquatic macroinvertebrates can indicate the health of a stream through their species diversity and abundance.
Photo provided by The Office of the Duke Forest.

The water downstream of a nearby wastewater treatment plant is much warmer in winter than other waterways in the area, so researchers see more emergent adult midges and caddisflies there than they do here. Aside from temperature, organisms need to adapt to other changing conditions like oxygen levels and storms.

“Rain is really fun to watch in streams,” Behrens said. The water level rises, pulling up organic matter, and sand bars change. You can tell how high the water got in the last storm by looking for accumulated debris on trees along river banks.

Farting rivers and the peanut butter cracker hypothesis

Marzolf studies hydrology, or “how water moves through not only the landscape but also the river itself.”

Nick Marzolf demonstrates a technique to measure gasses in streams using a syringe.

Part of his research involves measuring gases in water. Streams, like cars and cows and people, release greenhouse gases, including carbon dioxide and methane. In fact, Marzolf and colleagues hypothesize that New Hope Creek contributes more CO₂ to the atmosphere per unit area than anywhere else in the Duke Forest.

Decaying matter produces CO₂, but that isn’t the only source of greenhouse gasses in the creek. Microscopic organisms, like methane-producing bacteria, produce gases as well.

The “peanut butter cracker hypothesis,” Marzolf said, compares organic matter such as leaves to a cracker, while the “peanut butter,” which makes the cracker more palatable, is the microbes. Scrumptious.

Disturbing the sediment at the bottom of New Hope Creek causes bubbles to rise to the surface due to the metabolic activities of gas-producing bacteria.

Marzolf turned to Behrens. “Do you want to walk around and see if you can stir up some methane bubbles?” Behrens waded into the stream, freeing bubbles from the pressure of the overlying water keeping them in leaf mats. We watched the bubbles rise to the surface, evidence of the activities of organisms too small to see.

Behrens walks around in New Hope Creek to stir up gas bubbles from aquatic bacteria.

Restoring a stream to protect its pigtoe

Finally, Sara Childs, Executive Director of the Duke Forest, discussed stream restoration projects. Though structures in the Duke Forest like remnants of old mills and dams can alter and damage ecosystems, they can also have historical and cultural significance. Duke Forest prioritizes restoration projects that have meaningful ecological, teaching, and research benefits while honoring the history of the land.

For instance, the Patterson Mill Dam was built in the late 1700s and probably remained in use for about 100 years. The stream has already adapted to the structure’s presence, and there isn’t necessarily ongoing degradation because of it. Duke Forest restoration projects, Childs said, don’t revolve around very old structures like the Patterson Mill Dam. Instead, they are planning to remove two more recent structures that are actively eroding banks, threatening wildlife habitat, and creating impounded, oxygen-poor areas in the stream.

One of the structures they are hoping to remove is a concrete bridge that’s endangering a threatened freshwater mussel species called the Atlantic pigtoe (Fusconaia masoni). Freshwater mussels, according to Childs, require a fish species to host the developing mussel larvae on their gills, and the Atlantic pigtoe favors the creek chub (Semotilus atromaculatus). The concrete bridge forms a barrier between the pigtoe and the chub, but removing it could reunite them.

Before starting construction, they will relocate as many mussels as possible to keep them out of harm’s way.

New Hope Creek, home to waterdogs and pigtoe and farting microbes, is precious to humans as well. Heraty describes it as “a really spectacular and beautiful waterway that we are lucky to have right in our backyards here in Durham.”

Post by Sophie Cox, Class of 2025

Scientific Passion and the Aspirations of a Young Scientist

By Guest Post

On January 4, 2024

In Biology, Global Health, Medicine

Note: Each year, we partner with Dr. Amy Sheck’s students at the North Carolina School of Science and Math to profile some unsung heroes of the Duke research community. This is the fifth of eight posts.

Meet Dr. Oyindamola Adefisayo – Oyinda to her friends – a Postdoctoral Research Fellow at Duke. She’s exploring bacterial factors in host-pathogen interactions using mice.

During our interview, parallels in our journeys became clear. Even as a high school senior, I could strongly identify with Dr. Adefisayo’s work and share similar passions. I envisioned myself evolving into an inspiring scientist just like her and felt a strong connection with my aspirations as a high school senior.

Originally from Lagos, Nigeria, Dr. Adefisayo came to the U.S. via the African Leadership Academy in Johannesburg. Like me, she left home at 16 for a two-year residential program for teenagers. It was filled with passionate and driven students like I’m with at NCSSM. Oyinda earned her B.A. in Biology at Clark University, specializing in the genetic basis of wing and eye development in the fruitfly Drosophila melanogaster.

Her Ph.D. at Memorial Sloan Kettering in New York City focused on Immunology and Microbial Pathogenesis. She studied mycobacteria, examining DNA damage response pathways, antibiotic resistance, and mutagenesis. The work connected with her knowledge of Nigeria’s high tuberculosis burden as she sought practical applications. She found that a delay in the machinery of DNA copying itself triggered a damage repair pathway called PafBC.

Beyond the lab, Oyinda’s passion for ballroom dancing reflects her belief that science is an art, since there’s so much creativity and artistic sense that goes into being a scientist. This resonated with me too. I use painting as an outlet during my research on environmental stressors and antibiotics at NCSSM.

I was inspired by Dr. Adefisayo’s beliefs and passions. She continues her scientific career by delving deeper into protocol development, data analysis, and global knowledge-sharing. Her goal is to learn from bacterial and host genetics and contribute to simplifying and expediting life science research for professionals worldwide.

Guest post by Emily Alam, North Carolina School of Math and Science, Class of 2024.

How Do Animals – Alone or in Groups – Get Where They’re Going?

By Guest Post

On January 2, 2024

In Animals, Biology, Computers/Technology, Guest Post

Note: Each year, we partner with Dr. Amy Sheck’s students at the North Carolina School of Science and Math to profile some unsung heroes of the Duke research community. This is the of fourth eight posts.

In the intricate world of biology, where the mysteries of animal behavior unfold, Dr. Jesse Granger emerges as a passionate and curious scientist with a Ph.D. in biology and a penchant for unraveling the secrets of how animals navigate their surroundings.

Her journey began in high school when she posed a question to her biology teacher about the effect of eye color on night vision. Unable to find an answer, they embarked together on a series of experiments, igniting a passion that would shape Granger’s future in science.

Granger’s educational journey was marked by an honors thesis at the College of William & Mary that delved into the potential of diatoms, single-cell algae known for their efficiency in capturing light, to enhance solar panel efficiency. This early exploration of light structures paved the way for a deeper curiosity about electricity and magnetism, leading to her current research on how animals perceive and use the electromagnetic spectrum.

Currently, Granger is involved in projects that explore the dynamics of animal group navigation. She is investigating how animals travel in groups to find food, with collective movement and decision-making.

Among her countless research endeavors, one project holds a special place in Granger’s heart. Her study involved creating a computational model to explore the dynamics of group travel among animals. She found that agents, a computational entity mimicking the behavior of an animal, are way better at getting where they are going as part of a group than agents who are traveling alone.

Granger’s daily routine in the Sönke Johnson Lab revolves around computational work. While it may not seem like a riveting adventure to an outsider, to her, the glow of computer screens harbors the key to unlocking the secrets of animal behavior. Coding becomes her toolkit, enabling her to analyze data, develop models, and embark on simulations that mimic the complexities of the natural world.

Granger’s expertise in coding extends to using R for data wrangling and NetLogo, an agent-based modeling program, for simulations. She describes the simulation process as akin to creating a miniature world where coded animals follow specific rules, giving rise to emergent properties and valuable insights into their behavior. This skill set seamlessly intertwined with her favorite project, where the exploration of group dynamics and navigation unfolded within the intricate landscapes of her simulated miniature world.

In the tapestry of scientific exploration, Jesse Granger emerges as a weaver of knowledge, blending biology, physics, and computation to unravel the mysteries of animal navigation. Her journey, marked by curiosity and innovation, not only enriches our understanding of the natural world but also inspires the next generation of scientists to embark on their unique scientific odysseys.

Guest Post by Mansi Malhotra, North Carolina School of Science and Math, Class of 2025.

Inventors, Assemble: The Newest Gadgets Coming Out of Duke

By Michelle Li

On December 15, 2023

In Biology, Biomedical Engineering, Engineering, Entrepreneurship, Faculty, Medicine, Science Communication & Education

What do a smart toilet, an analog film app, and metamaterial computer chips have in common? They were all invented at Duke!

The Office for Translation & Commercialization—which supports Duke innovators bringing new technologies to market—recently hosted its fifth annual Invented at Duke celebration. With nine featured inventors and 300 attendees, it was an energetic atmosphere to network and learn.

*Attendees mingle in Penn Pavilion. Credit: Brian Mullins Photography.*

When event organizer Fedor Kossakovski was selecting booths, the name of the game was diversity—from medicine to art, from graduate students to faculty. “Hopefully people feel like they see themselves in these [inventors] and it’s representative of Duke overall,” he said. Indeed, as I munched through my second Oreo bar from the snack table and made the rounds, this diversity became apparent. Here are just two of the inventions on display:

Guided Medical Solutions

The first thing you’ll notice at Jacob Peloquin’s booth is a massive rubber torso.

As he replaces a punctured layer of rubber skin with a shiny new one, Peloquin beckons us over to watch. Using his OptiSETT device, he demonstrates easy insertion and placement of a chest tube.

“Currently, the method that’s used is you make an incision, and then place your fingers through, and then take the tube and place that between your fingers,” Peloquin explained. This results in a dangerously large incision that cuts through fascia and muscle; in fact, one-third of these procedures currently end in complications.

Peloquin’s device is a trocar—a thin plastic cylinder with a pointed tip at one end and tubing coming out of the other. It includes a pressure-based feedback system that tells you exactly how deep to cut, avoiding damage to the lungs or liver, and a camera to aid placement. Once the device is inserted, the outer piece can be removed so only the tubing remains.

*Peloquin demonstrates his OptiSETT device. Credit: Brian Mullins Photography.*

Peloquin—a mechanical engineering graduate student—was originally approached by the surgeons behind OptiSETT to assist with 3D printing. “They needed help, so I kind of helped those initial prototypes, then we realized there might be a market for this,” he said. Now, as he finishes his doctorate, he has a plethora of opportunities to continue working on OptiSETT full-time—starting a company, partnering with the Department of Defense, and integrating machine learning to interpret the camera feed.

It’s amazing how much can change in a couple years, and how much good a rubber torso can do.

GRIP Display

This invention is for my fellow molecular biology enthusiasts—for the lovers of cells, genes, and proteins!

The theme of Victoria Goldenshtein’s booth is things that stick together. It features an adorable claw machine that grabs onto its stuffed animal targets, and a lime green plastic molecule that can grab DNA. Although the molecule looks complex, Goldenshtein says its function is straightforward. “This just serves as a glue between protein and the DNA [that encodes it].”

*Goldenshtein—a postdoctoral associate in biomedical engineering—uses her lime green molecular model to demonstrate GRIP’s function. Credit: Brian Mullins Photography.*

Goldenshtein applies this technology to an especially relevant class of proteins—antibodies. Antibodies are produced by the immune system to bind and neutralize foreign substances like disease. They can be leveraged to create drug therapies, but first we need to know which gene corresponds to which antibody and which disease. That’s where GRIP steps in.

“You would display an antibody and you would vary the antibody—a billion different variations—and attach each one to the system. This grabs the DNA,” Goldenshtein said.

Then, you mix these billions of antibody-DNA pairs with disease cells to see which one attaches. Once you’ve found the right one, the DNA is readily available to be amplified, making an army of the same disease-battling antibody. Goldenshtein says this method of high-throughput screening can be used to find a cancer cure.

Although GRIP be but small, its applications are mighty.

Explore Other Booths

Coprata: a smart toilet that tracks your digestive health
inSoma Bio: a polymer that aids soft-tissue reconstruction
Spoolyard: a platform for exploring digital footage with analog film techniques
FaunaLabs: smart watches for our furry friends
G1 Optics: a tonometer to automatically detect eye pressure
TheraSplice: precision RNA splicing to treat cancer
Neurophos: metamaterial photonics for powering ultra-fast AI computation

As I finished my last Oreo bar and prepared for the trek back to East Campus, I was presented with a parting gift—a leather notebook with “Inventor” embossed on the cover. “No pressure,” said the employee who was handing them out with a wink.

I thought about the unique and diverse people I’d met that night—an undergraduate working in the Co-Lab, an ECE graduate student, and even a librarian from UNC—and smiled. As long as we each keep imagining and scribbling in our notebooks, there’s no doubt we can invent something that changes the world.

Post by Michelle Li, Class of 2027

Most Highly Cited: 30 for ’23

By Karl Bates

On November 15, 2023

In Behavior/Psychology, Biology, Cardiology, Medicine, Neuroscience, Physics

It’s that most wonderful time of the year: The official list of Clarivate’s Most Highly Cited Scientists came out this morning. Scientists all over the world came racing down the stairs in their PJs to see if Clarivate had left a treat under the tree for them.

L-R: Odgers, Scolnic, Dong, Hernandez, Harrington, Smith, Ostrom and Lopes.

Good news – there are 30 Duke names on the list!

Being highly cited is a point of pride for researchers. To make the cut, a paper has to be ranked in the top 1 percent for its field for the last decade. Clarivate’s “Institute for Scientific Information” crunches all the numbers.

Mostly, the names on this year’s list of Duke authors are the usual titans. Oddly, some returning names have changed categories since last year — but that’s okay, they’re still important.

And there are three fresh faces: Cardiologist Renato Delascio Lopes, MD Ph.D., who studies atrial fibrillation; David R. Smith Ph.D. of physics and electrical engineering, who’s a leading light in the field of metamaterials; and Dan Scolnic Ph.D. of physics, who’s measuring the expansion of the universe and trying to figure out the dark energy that apparently drives it.

Five of the Duke names on the list this year are co-authors in the Terrie Moffit and Avshalom Caspi lab, a hugely influential group of psychologists and social scientists. Honnalee Harrington, Renate Houts, Caspi, Moffitt, and UC Irvine professor and Duke adjunct Candice Odgers are studying human development from cradle to grave using two cohorts of life-long study participants in New Zealand and England.

Two other longitudinal scientists, Jane Costello and William Copeland of the Great Smoky Mountains Study, are also on the list.

There are 6,938 highly cited scientists this year, from 69 countries and regions. Several appear in more than one division. The United States still dominates with 38 percent of the honorees, but Chinese scientists are on the rise at 16 percent.

The most highly cited Duke authors are:

Biology and Biochemistry

Charles A. Gersbach

Clinical Medicine

Christopher Bull Granger

Adrian F. Hernandez

Renato D. Lopes

Cross-Field

Stefano Curtarolo

Xinnian Dong

HonaLee Harrington

Renate Houts

Tony Jun Huang

Ru-Rong Ji

Robert Lefkowitz

Jason Locasale

David B. Mitzi

Christopher B. Newgard

Michael J. Pencina

Bryce B. Reeve

Pratiksha I. Thakore

Mark R. Wiesner

Microbiology

Barton F. Haynes

Neuroscience and Behavior

Quinn T. Ostrom

Pharmacology and Toxicology

Evan D. Kharasch

Physics

David R. Smith

Plant and Animal Science

Sheng Yang He

Psychiatry and Psychology

Avshalom Caspi

E. Jane Costello

Terrie E. Moffitt

Space Science

Dan Scolnic

Duke Affiliated:

Cross Field

Po-Chun Hsu – University of Chicago, Adjunct Assistant Professor in Mechanical Engineering and Materials Science at Pratt School of Engineering

Candice Odgers, UC Irvine, Adjunct at Duke

Environment and Ecology

Robert B. Jackson, Stanford University, Adjunct Professor of Earth and Ocean Science at Nicholas School of the Environment

William E. Copeland, University of Vermont, adjunct in psychiatry and behavioral sciences, School of Medicine.

The Controversial Birth of American Gynecology

By Jakaiyah Franklin

On October 27, 2023

In Biology, Global Health, History

As a woman, I am familiar with the gynecologist. In fact, thinking about it right now, I may need to create an appointment for one soon. However, I am not just a woman; I am a black woman, and in addition to being familiar with what the gynecologist is, I am also familiar with the dangers of the gynecologist. I know that if I were to become pregnant, I would be three times more likely to die by pregnancy-related causes compared with my white counterparts. This phenomenon is not new; in fact, it is a symptom of the racism within American Gynecology. The founding of this system is not pretty, or pure; it is ugly and distasteful, and during her lecture, historian Deirdre Cooper Owens explains it perfectly.

Dr. Deirdre Cooper Owens and I after her wonderful lecture

Cooper Owens is an associate professor of History and African studies at the University of Connecticut, and earlier this semester, she gave an insightful talk on how slavery and modern American gynecology are interconnected.

The controversial “father of gynecology” was J. Marion Sims, who experimented on enslaved women in Alabama. When talking about the racism in gynecology today and in the past, Sims mainly gets the blunt end of the stick. However, it was not just Sims; it was much bigger than him, Cooper Owens said.

Dr. Samual Cartwright was the first doctor for the Confederacy. Through his experiences with enslaved people, he believed that black people did not feel pain. Furthermore, he created a theory that if an enslaved person ran away or thought about running away, then they had a mental illness. Through the use of a spirometer (a medical tool still used today), he noted that black people have smaller lung capacity than white people. His findings were used to prove that there was a biological difference between races, which is not true.

This idea separated people and placed them in a hierarchy where white people were perceived as superior and black people inferior. The thought of this is damaging in itself, but back then, and sometimes now, they used this ideology as an excuse for the pain they caused African Americans.

Ephriam McDowell, for instance, removed a tumor from the ovaries of a white woman. From this, he then decided to “perfect” this surgery on five black women; four were enslaved, and one was freed. From this group, one person died, and other than that, there is no record of the women’s personal lives.

Dr. Francis M Prevost performed C-sections on enslaved people. These experiments did not take the pain of these women into account; due to the fact that he believed black people did not feel pain, but they did and still do. Now one would hope that a black woman’s relationship with C-sections has improved, but, from 1832 until two years ago, Louisiana was the state where a black woman’s body was used the most for a C-section. Today, that state is Mississippi.

John Peter Mettauer performed experiments on a white woman and a black woman. After the experiment, he claimed that the white woman was cured, but the black woman was not. As a result, he operated on the black woman eight times and claimed that if she did not have intercourse, she would have been cured. However, he failed to take into account that the woman was enslaved and had no control of her body autonomy. So how could she say no to both unwanted sexual encounters and to him?

Lastly, there is James Marion Sims, who is notorious for his contributions to American gynecology. However, such contributions were based on the bodies of enslaved women who had no choice. He used these experiments to advance his techniques and deepen his understanding of gynecology. In fact, it even went to the point where he built a hospital for the sole purpose of experimenting on enslaved women.

J. Marion Sims with his assistants and the victims of his experiments

While the acts and experiments that these men conducted were atrocious, they raised a question for me, why black women? At that time, black people were viewed as an inferior race; they were not equal in physical components and intelligence compared to white people. Therefore, if they are genetically different, why experiment with black women to find cures for white women? When asking that question, the answer is obvious; they knew there was no difference, so they chose to ignore it. They chose to continuously bring harm to these women, and until recently, they were rewarded for it.

Image provided by Harvard T.H. Chan School of Public Health

I learned a lot from this lecture, but if I had to choose only one thing that stuck with me, it would be that the victims of these heinous acts were only referred to as enslaved persons with no name and no story. The only story that was told was the point of view of those committing the acts.

I hope one day, the mortality rate of black women giving birth will decrease to the point that it is simply unheard of. Still, for society and our health system to reach that point, we must understand American gynecology’s true history.

New Blogger Michelle Li: Shrek, Minecraft, and Discovering New Things

By Michelle Li

On October 13, 2023

In Biology, Entrepreneurship, Science Communication & Education, Students

My mom likes to introduce me by telling a childhood story. She’s told the same one for years, but it never fails to crack her up. (Watch out—she will genuinely cry from laughter!) It goes like this:

I was in second grade, and I was taking the ESL test. It’s straightforward—they show you flashcards, and you name them in English. I breezed through tree and house; but when I saw a bird, I fell silent.

“Don’t you know what a bird is?” my mom asked.

Cheeks red, I responded, “I knew it was a bird, I just wasn’t sure what species.”

At this point we’re both chortling, and she tells me that aiyah, Michelle, you were always so serious as a child.

*That’s me on the left looking resolute at preschool graduation.*

Which is a fair analysis—I was shy. I overthought. And I was a perfectionist. If I didn’t have the best answer or the most interesting remark, I was often too scared to speak at all.

But I love formulating answers, and I love talking to people. So going into high school, I told myself this mindset would change. I would shoot every shot and carpe every diem, fear be darned.

Like all new things, it was difficult. The learning curve was so steep it may as well have had a vertical asymptote. (If you liked that math joke, ask me about my calculus-themed promposal!)

Fortunately, life has a way of placing us in situations that help us grow. Sophomore year, I volunteered to teach STEM classes to middle schoolers. The chaos of pre-teens with pent-up quarantine energy is unparalleled—needless to say, I was terrified. But I found solace in the familiarity of science—as I rambled about CRISPR-Cas9 and coral ecology, I became more comfortable speaking to others.

I learned that Shrek is an icon, Minecraft is a competitive sport, and I should never click links in the Zoom chat—lest I be lured into a Rickroll. I also discovered that it didn’t matter whether my presentation was perfect or even if I acted a little weird.

*Zooming with my middle school STEM buddies—note the Elmo background.*

What mattered was watching students who’d never heard of engineering before prototyping egg parachutes and Rube Goldberg machines. What mattered was seeing Vicky return for a second year, evolving from student to TA. What mattered was watching a kid’s face light up with the joy of learning something new.

That’s what I hope to accomplish with the Duke Research Blog. As a freshman, I know the endless possibilities on campus—while a blessing—can be intimidating. STEM and academia have seemingly high barriers to entry. But I’ve also seen that discovering something new can be the best feeling in the world. I hope to play a small part in helping you, the reader, get there.

And as a baby Dukie, I hope to connect with the inspiring community here. Whether through a Research Blog interview or a quick conversation on the crowded C1, I am so excited to meet y’all.

So, if you see me around campus, come say hello! And if you’re a people-person-but-introverted like me and could use a conversation starter, here are a couple:

Tell me what songs you’re jamming to! I’m currently looping Gracie Abrams and Wallows. Debussy and Tchaikovsky are also regulars—String Quartet No. 1 goes so hard.
Talk about football! As a lifelong Cincinnatian, Joe Burrow is our king.
Share whatever you’re working on! Whether it be uber-complicated math (shoutout to Nikhil) or the perfect matcha latte (shoutout to Krishna), I’d love to know what you’re experimenting with.

Until then, remember to stay hydrated and keep discovering new things. ☺️

Post by Michelle Li, Class of 2027

“Wonders and Realities of the Universe”: Rachel Carson’s Legacy

By Sophie Cox

On October 12, 2023

In Biology, Climate/Global Change, Environment/Sustainability, Lecture, Science Communication & Education

Rachel Carson was a twentieth-century marine scientist, conservationist, and writer. She is the author of Silent Spring, a groundbreaking book about the dangers of DDT and other pesticides.
Photo courtesy of the Rachel Carson Council.

Robert K. Musil, Ph.D., M.P.H., recently visited Duke to talk about Rachel Carson’s environmental legacy and its implications for North Carolina today. Musil is the president and CEO of the Rachel Carson Council, an environmental organization founded in 1965 by friends and colleagues of Rachel Carson — a twentieth-century marine scientist, conservationist, and writer — after her death.

Robert K. Musil, Ph.D., M.P.H., president and CEO of the Rachel Carson Council.
Photo courtesy of Musil.

Musil began his presentation with a stirring quote by Carson: “The more clearly we can focus our attention on the wonders and realities of the universe about us the less taste we shall have for the destruction of our race. Wonder and humility are wholesome emotions, and they do not exist side by side with a lust for destruction.”

Rachel Carson is famous for writing Silent Spring, a groundbreaking book warning of the dangers of DDT and other pesticides. Carson published Silent Spring in 1962. She died in 1964. In 1972, the United States banned DDT.

More than half a century later, in our world of climate crisis and biodiversity loss, Carson’s devotion to the natural world is still incredibly timely.

Rachel Carson’s Silent Spring documented how the insecticide DDT was harming not just insects but also animals farther up the food chain, human health, and the environment as a whole. The book spent thirty-one weeks on the New York Times bestseller list.
Image courtesy of the Rachel Carson Council.

Carson, Musil says, “believed that you had to develop real empathy for other creatures, other beings, other people, other nations… that unless you loved it, you would destroy it.” In Carson’s first book, Under the Sea-Wind, she takes the perspective of animals like the black skimmer, the mackerel, and the eel. Carson was writing about the perils facing marine ecosystems, but she was doing it “from the point of view of the ‘other,’” as Musil puts it, focusing our attention on creatures other than ourselves.

A black skimmer, a bird Rachel Carson wrote about in Under the Sea-Wind.
“Black skimmer (Rynchops niger) in flight” by Charles J. Sharp is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

“With the dusk a strange bird came to the island from its nesting grounds on the outer banks. Its wings were pure black, and from tip to tip their spread was more than the length of a man’s arm. It flew steadily and without haste across the sound, its progress as measured and as meaningful as that of the shadows which little by little were dulling the bright water path. The bird was called Rynchops, the black skimmer.”

-A passage from Under the Sea-Wind by Rachel Carson. Rynchops, Carson’s name for the black skimmer, comes from the bird’s genus name.

Musil describes how Carson would lie on the beach and hear crabs scratching the sand and listen to birds and imagine “how this life came to be, how these creatures, incredibly unique, came to this place in evolution.”

Carson was a marine scientist well before she published Silent Spring. She attended graduate school in marine biology with a full fellowship to Johns Hopkins University. At the same time, Musil says, she was working as a research assistant, teaching part-time at the University of Maryland and Johns Hopkins, and caring for extended family. Afterward, she worked for the Department of Fish and Wildlife and eventually became an author. Under the Sea-Wind was her first book; she wrote Silent Spring two decades later.

Carson is credited with spurring the modern environmental movement. Silent Spring and the concerns Carson raised about DDT prompted the President’s Science Advisory Committee, under the orders of John F. Kennedy, to investigate its dangers. Ultimately, DDT was banned in the United States, though Carson didn’t live to see it.

Rachel Carson and Hawk Mountain - Rachel Carson Council — An “iconic photo” by Shirley Briggs of Rachel Carson on Hawk Mountain.
Photo courtesy of the Rachel Carson Council.

But Musil emphasizes that throughout all Carson’s accomplishments, she did not act alone. He shows an “iconic photo,” as he describes it, of Rachel Carson sitting on Hawk Mountain and looking off into the distance through binoculars. The same photo is on the cover of Musil’s book Rachel Carson and Her Sisters: Extraordinary Women Who Have Shaped America’s Environment. He looks at the audience and asks a question: “Is Rachel alone on top of the mountain?” In the photo, Carson seems to be alone in a great expanse of wilderness, but the obvious answer to Musil’s question is no. Someone, after all, had to be there to take the picture.

That someone was Shirley Briggs, a friend of Carson’s and a scientist in her own right. “Rachel Carson,” Musil emphasizes, “was not alone.” Friends, colleagues, and mentors worked alongside her. And many of those people continued her work after she was gone. Before Carson died, Musil says, she asked Shirley Briggs and others to form an organization to carry on her work. The Rachel Carson Council was founded the following year. Nearly six decades later, the Council is still committed to “Carson’s ecological ethic that combines scientific concern for the environment and human health with a sense of wonder and reverence for all forms of life in order to build a more sustainable, just, and peaceful future,” according to a statement on their website.

According to Musil, North Carolina was one of Carson’s favorite places. After she had a breast cancer operation, he says, “she took refuge at Nags Head and walked its beaches.” The Rachel Carson Reserve commemorates Carson and preserves coastal habitats and wildlife. Musil believes that Carson’s legacy has broader environmental implications as well. One pressing issue in North Carolina today is Concentrated Animal Feeding Operations, or CAFOs, where many animals are raised in confinement. North Carolina produces ten billion gallons of hog waste from CAFOs each year—enough to fill 1500 Olympic swimming pools, according to Musil.

This is an ecological and animal welfare issue but also an environmental justice case. CAFOs are more often built near lower income and minority communities, and the waste from CAFOs can negatively affect human health, pollute waterways, and lead to fish kills and other ecological problems. Living near CAFOs is associated with higher rates of asthma and other health conditions, according to Musil. He acknowledged Francesca Cetta in the audience, who along with Lucy Goldman, both Duke Stanback Fellows at the Rachel Carson Council, did the research and writing on the Rachel Carson Council report, Swine and Suffering: An Introduction to the Hidden Harms of Factory Farms.

Environmental justice was not a term Carson used, but she had similar concerns about who was most affected by environmental issues. In Silent Spring, Musil says, Carson wrote about farmers who dealt directly with DDT and how unjust that was. Today, environmental justice is gaining momentum as organizations and governments wrestle with fairness and equality in the environmental sphere.

In spite of ongoing environmental degradation, Musil remains hopeful. “I have incredible hope for the future,” he says, because of his organization and its mentoring of future generations of environmentalists. “It’s not like every single person has to go out and go birdwatching — though I would recommend it,” he says, but he does believe it is important to learn about and appreciate the natural world and to recognize how it intersects with, for instance, capitalism and social justice. “Designing a much more equitable, greener society is critical,” he says, and when it comes to working toward that future, he is “never going to stop.”

He references the photo he showed earlier of Carson on the mountain: “I like to think instead of looking at hawks, she’s looking across those ridges and seeing… ranks and ranks of young people from Duke and across the country carrying on her vision.”

Post by Sophie Cox, Class of 2025

Following the people and events that make up the research community at Duke

Category: Biology Page 1 of 31

We Are Killing Birds. Solutions Exist. Research Can Help.

To get a fuller picture of a forest, sometimes research requires a team effort

Glowing Waterdogs and Farting Rivers: A Duke Forest Research Tour

Scientific Passion and the Aspirations of a Young Scientist

How Do Animals – Alone or in Groups – Get Where They’re Going?

Inventors, Assemble: The Newest Gadgets Coming Out of Duke

Most Highly Cited: 30 for ’23

The Controversial Birth of American Gynecology

New Blogger Michelle Li: Shrek, Minecraft, and Discovering New Things

“Wonders and Realities of the Universe”: Rachel Carson’s Legacy