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Richard Sever, Assistant Director of Cold Spring Harbor Laboratory Press in New York and Executive Editor for the Cold Spring Harbor Perspectives journals. Sever spoke at Duke about the benefits of sharing preprints of scientific papers.
Photo courtesy of Sever.

Quality is of utmost importance in the world of scientific publishing, but speed can be crucial, too. Early in the COVID-19 pandemic, for instance, researchers needed to share updates quickly with other scientists. One solution is disseminating preprints of studies that have not yet been peer reviewed or published in a traditional academic journal. Richard Sever, Assistant Director of Cold Spring Harbor Laboratory Press in New York and Executive Editor for the Cold Spring Harbor Perspectives journals, recently visited Duke to discuss his work as the co-founder of bioRxiv and medRxiv, two of a number of servers that post preprints of scientific papers.

In traditional publishing, Sever says, “When you submit a paper to a good journal… most of the time it’s immediately rejected.” Of the papers that are considered by the journal, about half will ultimately be rejected by editors. Even for successful papers, the entire process can take months or years and often ends with the paper being placed behind a paywall.

Posting preprints on servers like bioRxiv, according to Sever, doesn’t preclude the studies from eventually being published in journals. It just “means the information is public much more quickly.”

In 2013, Cold Spring Harbor Laboratory released bioRxiv. In the time since, there has been a “proliferation of discipline-specific servers” like chemRxiv, socarXiv, NutriXiv, and SportRxiv.

How do these preprint servers work? Scientists submit a study to an Rxiv server, and then after a brief screening process the paper is made visible to everyone within hours to days. A frequent concern about these servers is that they could be used to disseminate poor-quality science or false information. Since the priority is to share information rapidly, the staff and volunteers in charge of screening cannot perform extensive peer review of every submission. Instead, the screening process focuses on a few key criteria. Is the information plagiarized? Is it actual research? Is it science or non-science? And most importantly, could it be dangerous?

In 2019, Sever and his colleagues at Cold Spring Harbor collaborated with Yale and the BMJ Group to launch medRxiv, a server that focuses on health research. Since the consequences of posting misleading clinical information could be more severe, it uses enhanced screening for the papers that are submitted.

Papers can also be revised after being uploaded to a server like bioRxiv. A scientific journal, on the other hand, may occasionally publish a correction for a published article but not a completely new version.

What are the benefits of preprint servers? Releasing preprints allows scientists to transmit study results more quickly. It can also increase visibility, especially for scientists early in their careers who don’t have extensive publishing records. Grant or hiring committees can look at preprints months before a paper would be published in a journal. This emphasis on speed also accelerates communication and discovery, and the lack of paywalls could make science more accessible. Additionally, preprint servers can give researchers an opportunity to get broader feedback on their work before they submit to journals.

So why submit to scientific journals at all? Traditional publishing is slower, but it aims to assess scientific rigor and quality and, critically, the importance of the work. “The currency of academic career progression,” Sever says, “is journal articles.” Another attendee of Sever’s lecture brought up the value of curation, using the example of movie reviews on Rotten Tomatoes. Sever believes that the sort of curation performed by journals is different. Movie reviewers give their opinions later in the process; they don’t stop production of a movie halfway through, saying “I want a happy ending.” Sever believes preprint servers allow science to be shared more widely without putting the final decision in the hands of editors.

What are the concerns regarding preprint servers? One concern scientists may have is being “scooped,” or sharing information only for another researcher to claim it as their own. Sever does not find the scooping argument to be very persuasive. “How can you be scooped if you’re using an anti-scooping device?” He believes that Rxiv servers, since they allow rapid dissemination of results, actually provide a safeguard against people passing ideas off as their own because the preprint author is in control of the timing. Another concern occasionally expressed is that having a paper on an Rxiv server may make it harder to get it accepted by a journal. Sever is unconvinced, pointing out that most papers are rejected by journals anyway.

A more pressing concern may be the potential for preprint servers to disseminate bad science, though Sever notes that there are “a lot of not-very-good papers in traditional publishing” as well. Besides, academics’ careers depend on producing high-quality work, which should be an incentive not to share bad work, whether on preprint servers or in scientific journals.

Nonetheless, people do sometimes submit pseudoscience to preprint servers. “We have been sent HIV denialism, we have been sent anti-vaxx things,” Sever says. Some people, unfortunately, are motivated to share false information disguised as legitimate science. That is why bioRxiv screens submissions—less for accuracy and more for outright misinformation.

A more recent concern is the potential for AI-generated “papers.” But like journal articles, all papers posted on bioRxiv are kept there permanently, so even a fake paper that makes it through the screening process could be caught later. Anyone doing this risks future exposure. A more insidious form of this problem, Sever says, is “citation spam,” where someone generates papers under another person’s name but cites themselves in the references to improve their own citation record.

“Like anything,” Sever says, “we’ll have to accept that there’s some garbage in there, there’s some noise.” The vessel, he says, is no guarantee of accuracy, and “at some point you have to trust people.”

Sever believes preprint servers play an important role by “decoupling dissemination from certification.” He hopes they can open the door to “stimulating evolution of publishing.”

Post by Sophie Cox, Class of 2025

Working Toward “Interspecies Flourishing”: Food Sovereignty in the Catawba Community

By Sophie Cox

On October 1, 2024

In Biology, Environment/Sustainability, Responsible Conduct

From left: Courtney Lewis, Roo George-Warren, and Aaron Baumgardner at a Duke Gardens panel about food sovereignty.

“Larger mainstream society is so removed from their food,” says Courtney Lewis, a Duke professor and Cherokee Nation citizen. She recently moderated a discussion at the Duke Gardens about food sovereignty with two Catawba Nation citizens.

Roo George-Warren is an artist, educator, and eco-cultural restorationist, and Aaron Baumgardner is a basket maker, seed steward, and plant ecologist. Their conversation was moderated by Lewis, who is the Crandall Family Associate Professor of Cultural Anthropology and Inaugural Director of the Native American Studies Initiative at Duke University.

What is food sovereignty?

“Most people… are more familiar with the term food security,” says George-Warren, but he considers that term insufficient “because technically that can be solved through Walmart gift cards.” Food sovereignty, in George-Warren’s view, encompasses bigger questions about cultural value, rights to seeds, and who performs labor involving food.

“How are we going to take control of our food systems on a systematic level?” he asks.

Baumgardner thinks about food sovereignty as a “community’s ability to take control of the entire food system and not have to rely on any outside factors.” That means asking questions like “Where’s the food coming from, and how’s the food getting to people’s tables?” as well as what food is on people’s tables.

Food sovereignty, Baumgardner says, is about the ability to take care of ourselves, even in a crisis, by controlling food production and distribution. “If we aren’t a food-sovereign nation, are we really a sovereign nation?”

Gourds in the Southeastern Indigenous Peoples’ Garden seasonal display area at the Duke Gardens. Some of the seeds in this garden were shared by Lewis, who got them from the Eastern Band of Cherokee, Cherokee Nation seed banks, community members, and her own garden. Photo by Duke Gardens volunteer photographer Sue Lannon.

How does seed stewardship relate to food sovereignty?

“The seeds are our relatives, and those seeds need to grow,” Baumgardner says. Certain plants hold great importance to the Catawba people, and efforts to “rematriate” their seeds helps ensure the plants’ survival now and in the future.

Seed stewardship, Baumgardner says, is about more than preserving seeds. It also involves actively using the plants that have been important to Catawba culture for generations, restoring a “relationship… of seed-saving.”

Corn, George-Warren says, has been grown by the Catawba for millennia. “We’re standing at one end of the last 500 years,” he says, “looking back at everything that has been lost and taken from us.” That requires mourning but also efforts to move forward.

Baumgardner sees value in blending traditional knowledge and western science. He mentions a partnership with Davidson College in which Catawba citizens and researchers at the college are collaborating on experiments with corn. There are records of Catawba people bending corn stalks back at a certain point in their development, and the work at Davidson is exploring whether that practice could help protect corn from fungus.

George-Warren discusses another program that distributes local produce to tribal families, serving 250-300 families per month. Such programs aim to increase access to local food and restore relationships between people and plants.

Job’s tears, another plant in the Southeastern Indigenous Peoples’ Garden seasonal display area. Photo by Sue Lannon.

How does natural resource management relate to your work?

“I don’t think that that accurately reflects how our people see the world or our relationship to it,” Baumgardner says about the term “natural resources.” He explains that the Catawba language does not have a word that directly translates to “natural” or “resources.” The term resources, he says, “implies that something is to be used… that it has a finite purpose,” which is not how the Catawba have historically viewed the environment. And in a world not divided into “natural” and “unnatural,” that linguistic distinction wasn’t needed, either.

Baumgardner believes that natural and cultural resources should be intertwined and that relationships to food should “create space for ceremony, create space for thanksgiving.”

Land can be nurtured without viewing it as an expendable, finite “resource.” European settlers, Lewis says, viewed the Appalachian region as a garden of Eden. “The reason it was that beautiful,” she says, “is you had entire nations actually managing that forest.”

George-Warren references a false narrative that native peoples just have an intuitive or magical knowledge of the earth. That is “ludicrous,” he says—knowledge comes from experimentation, observation, and having lived in a place for a long time.

George-Warren describes himself and Baumgardner as “ecocultural restorationists,” working to preserve both culture and ecology. The idea that humans and nature are inherently divided, he says, plays into dangerous narratives: that humans are a “virus” whose “only role is a damaging one” and that we should “put nature in a glass box” to protect it.

“I hate both of those views,” George-Warren says, “because the reality is we are a part of nature… we can help it flourish.”

“We have to create the culture of caring about those things,” George-Warren says. “We want people to work toward that interspecies flourishing.”

Post by Sophie Cox, Class of 2025

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

By Sophie Cox

On April 11, 2024

In Animals, Biology, Environment/Sustainability, Science Communication & Education

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.

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

Category: Biology Page 1 of 31

“Communicating at the Speed of Science”: Can preprints make science more accessible?

Working Toward “Interspecies Flourishing”: Food Sovereignty in the Catawba Community

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