Sophie Cox, Author at Research Blog

A few blocks from Duke’s East Campus, there is a small building whose past lives include a dentist office, a real estate office, and a daycare. Now it is a museum.

With over 35,000 specimens, the Duke Lemur Center Museum of Natural History holds the largest and most diverse collection of primate fossils in North America.

A mural on the back wall of the museum, showing animals like the elephant bird at full size.
Photo courtesy of Matt Borths, Ph.D.

Glass cases in the front room are lined with ancient fossils and more recent specimens less than 10,000 years old. Take Lagonomico, a creature that lived some 12-15 million years ago and whose name means “pancake,” in reference to the smashed shape of its remains. Or the tiny skull of a modern-day cotton-top tamarin. Even the enormous egg of an elephant bird, a ten-foot-tall bird that lived in Madagascar until it went extinct sometime in the last 1000 years.

A back room holds fossil discoveries still encased in rock. Special tools and scanning technology will reveal the creatures inside, relics of a very different world that can still yield revelations millions of years after their deaths.

These fossils are still partly encased in rock. Special technology like CT scans can reveal which part of a rock contains a fossil. The marks on the paper indicate where a fossil is located.

Matt Borths, Ph.D., curator of the Duke Lemur Center’s fossils, explained that while many fossil collections focus on a particular location, this one has a different theme: the story of primate evolution.

Lemurs, Borths said, are our most distant primate relatives. About 60 million years ago, soon after the extinction of the dinosaurs, the “lemur line and monkey-ape-human line split.” Studying both modern lemurs and their ancestors can give us a “glimpse of a distant past.”

An ancient lemur ancestor from Wyoming. Primates went extinct in North America over 30 million years ago.

Primates are a group of mammals that include humans and other apes, monkeys, lemurs, lorises, bushbabies, and tarsiers. Many primates today live in Africa and South America, but they did not originate on either continent. Primates are believed to have evolved further north and migrated into Africa about 50 million years ago. As the global climate grew cooler and dryer, equatorial Africa remained warm and wet enough for primates. Over time, apes, monkeys, and lemurs diverged from their shared primate ancestors, but not all of them stayed in Africa.

Africa is currently home to bushbabies and lorises, which are both lemur relatives, but most of lemur evolution and diversification took place in Madagascar, the island nation where all of the world’s 100 species of lemurs live today. “New World monkeys,” meanwhile, are found in South America. How did lemurs and monkeys get from Africa—which was at the time completely surrounded by water—to where they live today? Both groups are believed to have crossed open ocean on rafts of plant material.

Scientists have direct evidence of modern animals rafting across bodies of water, and they believe that ancient lemur and monkey ancestors reached new land masses that way, too. Mangrove systems, adapted to ever-changing coastal conditions, are particularly prone to forming rafts that break away during storms. Animals that are on the plants when that happens can end up far from home. Not all of them survive, but those that do can shape the history of life on earth.

“Given enough time and enough unfortunate primates,” Borths said, “eventually you get one of these rafts that goes across the Mozambique Channel” and reaches Madagascar. Madagascar has been isolated since the time of the dinosaurs, and most of its species are endemic, meaning they are found nowhere else on earth. When lemur ancestors reached the island, they diversified into dozens of species filling different ecological niches. A similar process led to the evolution of New World monkeys in South America.

Some of the species in this case went extinct within the past few centuries.

The history of primate evolution is still a work in progress. The Duke Lemur Center Museum of Natural History seeks to fill in some of the gaps in our knowledge through research on both living lemurs and primate fossils. This museum, Borths said, “brings basically all of primate evolution together in one building.” Meanwhile, living lemurs at the Lemur Center can help researchers understand how primate diets relate to teeth morphology, for example.

Paleontology is the study of fossils, but what exactly is a fossil? The word “fossil,” Borths said, originally referred to anything found in the ground. Over time, it came to mean something organic that turns to stone. Some ancient organisms are not fully fossilized. They can still preserve bone tissue and even proteins, evidence that they have not yet transformed completely into stone. The current definition of a fossil, according to Borths, is “anything from a living organism that is older than 10,000 years old.” Specimens younger than that are called subfossils.

Fossil Preparator Karie Whitman in the Duke Lemur Center Museum of Natural History. The grooves in the stones are made by air scribe tools, which are used to separate fossils from surrounding rock.

The Lemur Center does important research on fossils, but that is not the only component of its mission. Education Programs Manager Megan McGrath said that the Lemur Center weaves together research, conservation, and education in an “incredibly unique cocktail” that “all forms a feedback loop.” McGrath and Borths also co-host a Duke Lemur Center podcast.

Conservation is a crucial component of the study of lemurs. Lemurs are the most endangered mammals on the planet, and some are already gone.

Human and wildlife survival are interlinked in complex ways, and conservation solutions must account for the wellbeing of both. Subsistence agriculture and other direct human activities can decimate ecosystems, but extinctions are also caused by broader issues like climate change, which threatens species on a global scale. Humanity’s impact on Madagascar’s wildlife over the last several thousand years is a “really complicated puzzle to tease apart,” McGrath said.

A display case in the museum, including an egg from the extinct elephant bird and a seed from a mousetrap tree. The mousetrap tree relies on large animals to disperse its seeds. That role was once filled by now-extinct species like the elephant bird. Now humans and cattle disperse the seeds instead.

Some of the museum’s specimens are truly ancient, but others are from modern animals or species that went extinct only recently. Giant elephant birds roamed Madagascar as recently as a thousand years ago. The sloth lemur may have survived until 400 years ago. Borths puts the timescale of recent extinctions into perspective. At a time when modern species like the white-tailed deer were already roaming North America, Madagascar was still home to creatures like sloth lemurs and ten-foot elephant birds.

A model of a sloth lemur skeleton (center, hanging from branch). Sloth lemurs lived in Madagascar until they went extinct about 400 years ago.

A model of a sloth lemur hangs in the museum, but no one alive has ever seen one breathing. No one will ever see or hear one again. But a ghost of it may exist in Malagasy stories about the tretretre, a monster that was said to have long fingers and a short tail. The word tretretre is thought to be an onomatopoeia of the call of a sloth lemur, an animal whose own voice is gone forever.

Learn about these and other stories of our evolutionary cousins at the museum’s next open house on Saturday, November 23, from 1-4 PM.

Post by Sophie Cox, Class of 2025

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

By Sophie Cox

On October 23, 2024

In Artificial Intelligence, Biology, Medicine, Responsible Conduct, Science Communication & Education

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

Meet Maggie Heraty, Duke Forest Senior Program Coordinator

By Sophie Cox

On August 8, 2024

In Environment/Sustainability, Science Communication & Education

Maggie Heraty, Senior Program Coordinator for the Duke Forest, shows students how to identify little heartleaf (Hexastylis minor) during a Duke Spring Breakthrough program in 2024.
Photo credit Bill Snead, Duke University Communications.

For a few lucky people at Duke, a typical work day might include a walk in the woods. Take Maggie Heraty of the Duke Forest, for instance.

What is your job position?

As senior program coordinator for the Duke Forest, Heraty is involved in many projects. She manages two volunteer programs: the Herpetofauna Community Science Program, which collects data on reptile and amphibian populations, and the Forest Stewards Program, which divides volunteers into small teams to “monitor for the effects of recreation in the Duke Forest.”

Heraty is also involved with community engagement and leading tours, such as the annual tour of the Shepherd Nature Trail — which she describes as “one of our ‘core’ tour offerings” — along with a few other themed tours focused on flora and fauna, for instance, or a research tour about ongoing studies occurring in the Duke Forest. “Essentially,” Heraty says, “every season of the year we try to lead one tour… that’s just a free and open to the public tour.”

She also leads field trips or tours by request, such as for middle school programs, specific college classes, or Duke orientation groups.

What is your job like?

“Two weeks never look the same,” Heraty says. This week, she spent Monday and Tuesday wrapping up a Data+ project she’d been involved with this summer. Data+ is an interdisciplinary summer research program for undergraduate and graduate students. On Wednesday Heraty had a staff meeting and a meeting with the Nasher Museum of Art. The Duke Forest and the Nasher are planning a collaborative event focused on the Anthropocene to coincide with an upcoming exhibit at the Nasher called Second Nature: Photography in the Age of the Anthropocene. Later in the week Heraty would be reviewing reports from Forest Steward volunteers, and if time allowed, she would spend rest the of the week either quality controlling data from the herpetology project, helping update the strategic plan for the Duke Forest, or completing tasks for coordinating the Forest’s deer herd reduction program.

What is the deer herd reduction program?

Every year, from September to December, the Duke Forest partners with a select group of skilled hunters to reduce its overabundant white-tailed deer population. Historically, predators like mountain lions, black bears, and wolves kept the deer population in check, but “Humans have killed off all of the top predators in our ecosystem.”

“We now have coyotes who are making their way into this area and are kind of filling that niche a little bit,” Heraty says, but not enough to control an exploding deer population. The hunting program is a way to reduce it to healthier levels in the absence of natural predators.

Disease spreads more rapidly when the density of an animal population is too high, and the resources in an environment can only sustain a certain number of deer. Maintaining a more balanced deer population also supports plant diversity in the forest since having too many deer can decimate plants and slow forest regeneration.

What is the Duke Forest for?

The Duke Forest consists of 7100 acres in Durham, Orange, and Alamance Counties. It is managed by a staff of nine people, often along with a student intern or assistant. “We have a small, very dedicated team,” Heraty says.

The Forest was founded in 1931 and “has always been intricately linked with the university itself.” The primary mission of the Duke Forest is as a teaching and research laboratory in a “natural environment that is conserved and managed sustainably and that people can study.” Recreation and conservation are an “ancillary benefit,” but the Duke Forest is “not like your average state park or land conservancy.” Teaching and research are at the forefront of what the Duke Forest is for.

Researchers conduct many studies in the Duke Forest. Studies can be scientific, such as evaluating impacts of climate change or humans on the forest, but there are also studies on history, art, and engineering.

Heraty with the 2024 Duke Forest Herpetofauna Data+ team, showing off their project work. (Data+ teammates from left to right: postdoctoral research associate Sarah Roberts, PhD student Caroline Rowley, undergraduate student Harssh Golechha, Professor Nicki Cagle, and graduate student Qianyu Zhu).
Photo credit Duke Forest staff; caption provided by Heraty.

How can people use the Duke Forest responsibly?

Balancing recreational use with the other missions can present challenges. The Forest Stewards volunteer program that Heraty oversees was created to help understand and address those issues. “The impetus for [the Forest Stewards program] was in the pandemic,” Heraty says, when people tended to “flock to outdoor spaces to get… a respite from quarantine.” That created a “huge uptick” in recreational use of the Duke Forest, which can have detrimental effects on land and ecosystems. The Forest Stewards act as “ambassadors” for the Forest and serve as “more eyes on the ground,” helping to notice and report issues like fallen signs or unauthorized trails.

Heraty says some of those unauthorized trails are established when people unknowingly follow incorrect directions on a hiking app. More people have started using apps like AllTrails and Strava, which can help people find and navigate new trails but can also lead to problems if someone follows an unauthorized trail while using the apps. Other users of the same app can then follow the same route.

To use the forest responsibly and avoid unauthorized trails or sensitive research sites, Heraty encourages visitors to refer to official websites and maps, which can both help you avoid getting lost and offer resources that “allow you to build more of a connection to the place that you’re visiting.” She suggests a free app called Avenza that lets you upload official Duke Forest maps ahead of time.

How does the Duke Forest balance the impacts of recreation with its other missions?

The Duke Forest encourages sustainable recreation while prioritizing research and conservation. “There’s always something intense happening in the world, and so going outside can be a respite for people, but also—sometimes there is a consumer mindset that happens there, where it’s just like, ‘I need to get in and get out… and never think about it again,’” Heraty says. “A culture that we’re interested in… instilling… is one where we all feel an actual connection to the land we’re living on.”

“Especially in our urbanizing and developing world… it’s really special that this place is preserved,” Heraty adds, and “engaging people in that stewardship mission is important.”

This image has an empty alt attribute; its file name is Heraty2Image-1024x771.jpg — Heraty leads orientation training for Herpetofauna of the Duke Forest community scientist volunteers.
Photo credit Duke Forest staff.

What is your favorite thing about the forest, or something that might surprise us?

“The things I’m constantly amazed by in my job are really when I get to interact with teachers or researchers,” Heraty says. There are “so many brilliant people who are learning and thinking about the land or the forest.” One study that’s happened since Heraty joined the Duke Forest staff in 2021 was a UNC archaeological dig along New Hope Creek studying indigenous life. You can learn more about this research project in this article or this video.

Heraty also enjoys education and outreach, especially outside in the forest itself. Part of her background is in on-the-ground conservation stewardship, so “whenever I do get to actually be in the woods in Duke Forest, that is one of my favorite parts.” She enjoys helping to “interpret what people are seeing,” like explaining that a piece of flagging tape represents a research study or showing someone how to identify a tree.

What do you do for fun outside of work?

“I love reading sci-fi and fantasy,” Heraty says. Right now she’s reading a book called “Black Sun” by Rebecca Roanhorse, which a friend recommended. She is also involved with grassroots organizing for social justice groups and enjoys indoor rock-climbing.

Post by Sophie Cox, Class of 2025

AI Time Travel: Reimagining Ancient Landscapes

By Sophie Cox

On May 9, 2024

In Anthropology, Art, Artificial Intelligence, History, Visualization

You are looking at a field of fluffy, golden grass dotted with yellow flowers. There are trees in the background and mountains beyond that. Where are you?

Now you’re facing a terracotta sarcophagus. Where are you? When are you?

A new exhibit in the Rubenstein Arts Center uses AI to bring viewers into ancient Roman and Etruscan landscapes spanning 1300 years, from about 1000 BCE to 300 CE. (The field is Roman, the sarcophagus Etruscan.)

An AI-generated image of a summer meadow near Vulci (Viterbo, Italy). Preserved pollen evidence has revealed which plant species dominated these landscapes, and the prompts used to generate images like this one include lists of plant species.

Along one wall, screens show springtime landscapes representing ancient Rome. The written prompts AI used to create each image include detailed information on plant species found in each landscape. One titled “Sedges in shallow water of an ephemeral pond” mentions “sparse trees of alder (Alnus glutinosa), white willow (Salix alba), and white poplar (Populus alba), and few herbaceous plants.” You can view examples of the written prompts on the exhibit’s website, AI Landscapes – Rethinking the Past.

Models of pollen grains from different plant species. Real pollen grains are microscopic, but these magnified representations help show how different their shapes can be.

Historians know what plants were likely to be in these landscapes because of evidence from preserved pollen grains. Different species have distinct pollen shapes, which makes it possible to identify plants even centuries or millennia later.

Part of the exhibit uses AI and a camera to turn interactive prompts into ancient Roman scenes.

An interactive display near the front of the room has a camera pointed at props like building models, pillars, toy horses, and pieces of styrofoam. An AI model reinterprets the camera’s images to create hypothetical scenes from ancient Rome. “See how the columns get reinterpreted as statues?” says Felipe Infante de Castro, who helped program the AI. The AI attempts to add detail and backgrounds to simple props to create realistic scenes. “The only thing that we’re forcing,” he says, “are essentially shapes—which it may or may not respect.” It may reinterpret a hand as a horse’s head, for instance, or a strangely shaped building.

The model is more precise with plants than buildings, says Augustus Wendell, Assistant Professor of the Practice in Art, Art History and Visual Studies and one of the exhibit designers. Latin names for plants are widely used in modern taxonomy, and the AI is likely to have encountered more plants in its training than ancient Roman architecture styles. The AI is a “generic model” asked to “draw on its presuppositions” about Roman buildings, says Felipe. It “wasn’t trained on specifically Roman landscapes…. It just tries its best to interpret it as such.” The results aren’t always completely authentic. “In the background,” Wendell says, “the city is often quite modern Tuscan, not at all ancient Roman.”

It’s interesting to see how the AI responds when you place unfamiliar objects in front of the camera, like your hand. Here, it tried to turn my hand into some sort of building.

“We can use an AI,” Felipe says, “to give us a representation of the past that is compatible with what we believe the past should look like.”

In another part of the exhibit, you can use an AI chatbot to talk to Pliny the Elder, a Roman scholar. Caitlin Childers, who helped design the exhibit, explains that the chatbot was trained on Pliny the Elder’s 37 books on natural history. When I asked Pliny what the chatbot was designed for, he told me, “I do not have the ability to access external articles or specific information beyond the knowledge I possess as Pliny the Elder up to the year 79 AD.”

He can give you information on plants and their uses in ancient Rome, but when I asked Pliny what his favorite plant was, he couldn’t decide. “I find it challenging to select a favorite plant among the vast array of flora that the Earth provides. Each plant contributes uniquely to the balance and beauty of nature.” According to Professor Maurizio Forte, “This AI chatbot can speak in English, French, Italian and also in Latin! So it is possible to formulate questions in Latin and requiring a response in Latin or ask a question in English and expect a reply in Latin as well.”

A virtual reality headset lets you see a three-dimensional model of an Etruscan sarcophagus. The real sarcophagus is encased in glass in the Villa Giulia Museum in Rome, but the virtual reality experience puts it right in front of you. The experimental VR-AI installation also allows viewers to ask questions to the sarcophagus out loud. The sarcophagus has a statue of a man and woman, but historians don’t know whose ashes are buried inside. “It’s not important how they look,” says Forte. “It’s important how they want to be.”

The sarcophagus would have been a “symbolic, aristocratic way to show power,” Forte explains. The design of the sarcophagus represents an intentional choice about how its owners wanted the world to see them after their death. “This is eternity,” Forte says. “This is forever.”

A display of quotes at the “Rethinking the Past” exhibit.

The exhibit, called “Rethinking the Past,” is on display at the Rubenstein Arts Center until May 24.

Blueberrying and More: Expanding the History of Bennett Place

By Sophie Cox

On May 1, 2024

In Anthropology, Field Research, History, Science Communication & Education

Two of the buildings at Bennett Place, a preserved family farm in Durham known largely for its role in a Civil War surrender. Kalei Porter, a Duke Liberal Studies graduate student, recently led an event focusing on the natural history and land use of Bennett Place over time.

Bennett Place, a North Carolina State Historic Site in Durham, is known for its role in a Civil War surrender, but a recent event focusing on the site’s natural history sought to broaden that story. Kalei Porter, a Graduate Liberal Studies student at Duke, led the event, which focused on changing land use at Bennett Place over time.

Jim Barrett, a volunteer tour guide, led a tour of Bennett Place focused on the more well known parts of its history. “The Civil War was a series of five military surrenders,” he explains. The first occurred in Appomattox Court House in Virginia, but while that marked a symbolic end to the war, technically only the Confederate Army of Northern Virginia surrendered there. Another surrender meeting occurred on the land now known as Bennett Place, where Union General Sherman and Confederate General Johnston met at the Bennett family’s small farm to discuss their terms of surrender.

That meeting ultimately led to the preservation of the farm as a historic site, but the history of Bennett Place “should not be an exclusive Civil War story,” Porter says. She has a degree in environmental biology, and her work at Bennett Place combines her interests in ecology and history.

For the past two academic years, Porter has been involved with the North Carolina Lives and Legacies Project, which uses research to tell more nuanced, inclusive stories about land use at sites like Bennett Place. The project, which is based in Duke’s Information Science + Studies, has also received support from Bass Connections in the Vice Provost’s Office for Interdisciplinary Studies and Duke University Libraries. This summer, Kalei will continue her research as a Graduate Project Manager in a History+ team.

James Bennett and his family were small-scale, yeoman farmers. They had about 200 acres, Porter says, “sustaining four to ten people.” They grew most of their own food and sold handmade clothing and crops like watermelons and vegetables at a local market, Barrett says. The site was preserved by civil leaders, including one of Washington Duke’s sons, according to Barrett. The original house was destroyed in a fire in 1921 but was rebuilt in 1962 with material from a similar house, Porter explains. On Barrett’s tour, he mentioned that Sherman brought an illustrator to the surrender meeting, and the pictures from that day still exist, so we know what the house originally looked like. The new house was rebuilt to resemble the old one.

Porter’s event included a display of plants from Duke’s herbarium. The dried plants she chose were collected in North Carolina in different decades, preserving important information about flowering time and native flora in specific sites. “You have a little slice of spring from as far back as the 30’s,” Porter says about the plants she chose.

Two large sheets of blotter paper with dried plants carefully arranged and taped in place upon them. Each herbarium specimen sheet also includes a small envelope for seeds and a one paragraph label and description. — Plants from Duke’s herbarium were on display at the event. Specimens like these can preserve important information like what time of year plants were flowering in different decades.

The exhibit at the event includes other items, too, like a list of who has used this land at different points in history. Before 1782, according to a sign at the event, several Native American tribes inhabited the area, including the Seponi, Cheraw, Catawba, Lumbee, Occaneechi, and Shakori. In 1782, Jacob Baldwin purchased the land, and it changed hands at least twice again before James Bennett bought it in 1846.

There is also a detailed soil map from 1920 on display. Such surveys can make farming more profitable since different crops do best in different soil conditions. Porter says the first geological survey in North Carolina was conducted in the 1850s, making North Carolina only the third state—and the first state in the South—to do soil surveys.

Porter has been working on transcribing Bennett’s ledger papers, which she describes as “a cross between a diary, a planner, and a credit card log.” They provide a record of daily life for a small farmer in North Carolina. Porter says Bennett made a lot of notes about fixing his tools.

Later in the day, Porter led a tour of the site with a focus on natural history. We start on a path lined with fences. Historically, it was a road that went from Raleigh to Hillsborough, and it also “roughly lines up with some of the Native American trading routes that predated the property,” Porter says.

The Unity Monument at Bennett Place. The monument was built in the 1920s, and its original meaning isn’t entirely clear.

We stop at the Unity monument, built in the 1920s soon after the Bennett house burned down. Robert Buerglener, Research Associate, Duke Information Science + Studies, explained to me earlier that the Unity monument may have survived because its meaning is more ambiguous than many Confederate monuments. Porter says the monument incorporated stone from the North, West, and South to represent the theme of unity.

We tour the house and separate kitchen. Both give glimpses into the lives of the Bennett Family. A ladle made from a dried gourd. Jars of persimmon seeds and other items that, according to Barrett, were used as wartime replacements for more typical ingredients. Wood siding on the house that Porter says dates from the 1850s.

It’s not just the buildings that reveal the story of this land. Porter points out trees, shrubs, and fences as well.

Before the Civil War, she says, livestock here roamed free. Buildings and gardens would have been fenced to keep the livestock out. After the war, however, fencing became more expensive, and people started creating fences around the livestock instead and building cheaper, less sturdy fences.

As we walk toward a nature trail at the back of the property, Porter draws our attention to the pine trees. Both loblolly and shortleaf pines grow here. Historically, shortleaf would have been more common in this area, but places that have been recently managed for timber tend to have loblolly. Most of these pines are still relatively young; they were not here when the Bennetts lived on this land.

In the forest, many of the low-growing plants we pass are species of blueberry. Porter has searched through digitized North Carolina newspapers for records of the word “blueberry.” It was first mentioned in the 1880s as a verb, blueberrying (women going out to pick wild blueberries) but wasn’t grown commercially in this area until the 1930s.

Porter ends her tour by asking us to look at the sky. Even the sky could have changed in the centuries since the Bennetts farmed this land. Today it’s clear and blue, but modern pollution could make it less blue than it used to be, Porter says, and some days we might see airplane contrails, which the Bennetts would never have seen back then. “Sometimes the sky is even asynchronous with time,” Porter says.

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

“Biodiversity Is Essential, and It’s Not a Nice-to-Have”

By Sophie Cox

On March 27, 2024

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

Filmmaker Ashley Hillard and cinematographer Alan Dunkin in Yellowstone. Photo by Hillard.

“I have been interested in storytelling and the environment since my earliest memories,” says Ashley Hillard, a documentary filmmaker with an interest in wildlife management and conservation practices in the United States.

Hillard has a background in film, largely with production companies, talent agencies, and independent projects on the side, but she later shifted into climate tech recruitment. Now she is pursuing an environmental leadership Masters in Environmental Management degree at Duke while working on documentary projects. She is also a Communications Assistant Intern in the Duke Environmental Law and Policy Clinic.

She has been working on a film called “Coexistence,” a documentary that spotlights North American species and wildlife management practices. Hillard got the idea for the project when she noticed that U.S.-based researchers often choose to study species in other countries, perhaps “because it’s easier to go over and say ‘Why don’t you try this?’ rather than having to deal with issues in your backyard.”

“We need to pay attention to our own backyards,” Hillard emphasizes. “The hope,” she says, is “more laws and policies and values change along with behaviors as we become more informed and more aware.” She also believes that “local efforts can usually go further.” Part of her goal in creating films about conservation is to help viewers realize that “individuals can be part of change.” Films and other forms of storytelling can inform people about specific species and conservation efforts, but Hillard hopes her work can help shift perspectives more broadly as well. Effective conservation is often “a social attitudes and values issue,” Hillard says. “There needs to be a shift in how we view the environment.”

An American bison that Hillard saw while filming in Yellowstone.
Photo by Hillard.

Shifting baseline syndrome is the idea that people’s expectations of how nature should look reflect their own experiences rather than an accurate picture of the natural state of landscapes, flora, fauna, and wildlife abundance. Our understanding of what nature “normally” looks like changes over generations and is skewed by the societies and time periods we inhabit. The more we damage our environments, the less we collectively remember what they looked like before—and the less motivated we may be to restore them to a condition most of us can’t remember.

When humans and wildlife come into conflict, our perceptions of how nature “should” be can matter tremendously. Gray wolves were recently delisted from the Endangered Species list, then re-listed in most places—both were controversial decisions—but their numbers are far lower than they were historically. Still, some think there are too many wolves. In the Western U.S., gray wolf conservation efforts often clash with the desires of ranchers and and hunters, who may view higher wolf populations as a threat to livestock or game animals like deer and elk. But some of these hunters and ranchers, Hillard says, “are real conservationists doing amazing work,” and she thinks they should get more attention.

While creating the film, Hillard has tried to capture the complexities of wildlife conservation. It’s not as simple as “They’re bad, they’re good, and this is how we solve it,” Hillard says.

There are different ideas about how conservation efforts should be conducted and which animals should be protected in the first place. The dominant approach to wildlife management in the U.S., Hillard says, is rooted in the idea that there are “good” species that people can use and “bad” species that people don’t like to live with, such as wolves and other predators. “This perspective,” she says, “came over with colonists.” She mentions Little Red Riding Hood and the Big Bad Wolf; the stories we tell about animals can reflect societal attitudes toward them. Many indigenous peoples, meanwhile, have traditionally viewed all species as kin. This “cultural aspect” affects people’s willingness to coexist with species like wolves, which in turn affects our conservation practices.

A gray wolf at the Grizzly and Wolf Discovery Center in Yellowstone.
Photo by Alan Dunkin, provided by Hillard.

In this country, very few people are killed by wildlife—about 700 annually, according to one review that counted deaths from bites, wildlife-vehicle collisions, and zoonotic diseases. Car accidents, on the other hand, are more than 60 times more deadly, killing about 43,000 people in the U.S. per year. “We have a certain acceptance of how we die,” Hillard says. “There are a number of things that kill people with much higher percentages [than deaths from wildlife] that we… accept as day-to-day,” but we don’t tend to hear calls to eliminate cars from society, while an animal that harms a human is often given a death sentence. Hillard thinks media in general should be more careful about how they share stories about wildlife, especially negative encounters. If stories focus only on rare but tragic incidents, it can distort perceptions of species and “feed into that doom loop.”

Films, Hillard says, can inspire people “to look at things differently and see things from different perspectives.” Storytelling is also a way of communicating scientific information and encouraging action. Hillard feels that some stories about environmental issues are told in a one-sided, black-and-white way, but the nuances of these problems are important. “Finding those complexities and working through them… and then trying to craft stories around that to share with the public so they can make more informed decisions” is part of the goal of Hillard’s films.

“Coexistence” focuses on well-known, often controversial species like red wolves and mountain lions. “Familiarity and awareness of a species can contribute to interest in protecting them,” Hillard says. Such species are sometimes referred to as charismatic megafauna and can be viewed as ambassadors for conservation or umbrella species whose protection helps other wildlife as well. But Hillard has concerns about the term charismatic megafauna. “It diminishes a species’s value and reduces them to ‘cute’ so you no longer see them as an intrinsic part of an ecosystem,” she says. She believes it’s important to emphasize protection of entire ecosystems, not just specific species within them.

A Mexican gray wolf pup at the California Wolf Center. The Mexican gray wolf is a gray wolf subspecies.
Photo by Hillard.

Hillard hopes that her films inspire more awareness of and interest in environmental issues. “There’s a lot of pressure to get it right,” she says. And storytelling can have its own issues when it comes to presenting accurate information. “Information can be left out or shaped in a way to make it more compelling,” Hillard acknowledges. She feels that many wildlife films focus first on scenery and animals, then discuss conservation issues at the end. But “Coexistence” is “very much focused on the issues.” It is expected to be released by early 2025.

“I strive to tell impactful stories in creative ways that are more upbeat in tone,” Hillard says. She believes it’s important for people to be aware of the challenges facing wildlife, but she also wants to inspire hope and the belief that individual actions can matter. “To feel powerless can make you feel hopeless, and there is a lot to be hopeful for,” she says. “But there needs to be a shift in how we view the environment.”

One major problem she sees is our consumerist, materialistic society. “We’re kind of consuming ourselves off the planet,” Hillard says. “How do you change behaviors within a society that’s so hyper-consumptive?”

Films and other forms of storytelling can make scientific information more accessible. “Communicating is that bridge to getting people to care, to understand it, to learn about it,” Hillard says. “Without communication, science studies and research may be siloed in academia.” When we lack accurate and accessible information, we may rely on “‘I heard someone say something about that thing’” rather than science to inform our understanding of issues.

Along with providing accurate information, Hillard wants to encourage “a view of mutualism with other species” and raise questions like “How can we be better neighbors to nonhuman species?”

Ultimately, she wants viewers to recognize that “biodiversity is essential, and it’s not a nice-to-have.”

Hillard at Lands End Lookout in San Francisco.
Photo credit Alan Dunkin, provided by Hillard.

Post by Sophie Cox, Class of 2025

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

An Ode to Refrigerated Insects

By Sophie Cox

On November 7, 2023

In Animals

Imagine lying on your back, legs flailing, unable to flip yourself over. To make matters worse, there is a rope attached to your head that you can’t remove. Meanwhile, a giant is prodding at you with a long metal stick, and you can’t figure out if she’s trying to hurt you or help you.

Earlier this semester, I was that giant.

A tiny insect on its back under a microscope. Note the strand of lint caught on its beak.

I was in the entomology lab in the basement of the biology building on a Friday night, photographing insects under a microscope. One of them, so tiny that I could barely see it with the naked eye, had ended up on its back with its beak-like mouth caught on a miniscule thread of lint. I was using a pin to try to remove the lint, but my efforts were dragging the insect haphazardly across the leaf it was on, and I gave up out of fear of hurting it. Under the microscope, the insect’s situation was dramatic and hard to watch, but when I walked to the Duke Gardens later that night to release it, it was just a dark speck in my palm.

A candy-striped leafhopper viewed through a microscope.

Photographing insects for the entomology class I am taking this semester gives me perspective on a world that operates on a smaller scale, with obstacles humans don’t have to contend with—like pieces of lint ensnaring our mouths. But in order to photograph insects, I need them to stay reasonably still. Fred Nijhout, Ph.D., who teaches the entomology course, taught us that you can keep live insects in a refrigerator temporarily, which doesn’t kill them but slows their metabolism down significantly, making them easier to photograph. In the past few months, I have spent many hours with refrigerated insects.

As much as I love insects, I was terrified of this class. I thought it would require making a physical insect collection—which, in turn, would require me to kill insects, and I simply didn’t think I’d be able to do that. Fortunately, there was an option to create a photography collection with living insects instead, which is why I’ve spent so much time catching, photographing, and releasing insects over the past several weeks. We need to collect or photograph twelve insect orders and twenty families, which has led to some unusual situations — like sheer delight upon finding a termite or cockroach. (Both represent orders that, until recently, I didn’t have in my collection.)

The first insect I refrigerated was a tiny lace bug I found wandering across my pants one afternoon. I coaxed it onto my hand and ran to my dorm to get a vial. (I have since learned to keep small containers with me nearly everywhere I go.) I put the lace bug inside the vial and stuck it in the common room refrigerator overnight, wrapped discreetly in a plastic bag. I had serious misgivings. Could such a small creature really survive an entire night in a refrigerator? And what if someone found it and threw it away? The next morning, I retrieved it with much apprehension. The insect wasn’t moving. It seemed somehow lighter, more desiccated, and I was certain it was dead. What had I done?

A lace bug, the first insect I refrigerated. I didn’t notice the intricate structures protruding from its body until I saw it under a microscope.

I brought the lace bug to class and put it back in the refrigerator. Later that day, Nijhout showed me how to photograph it with the microscope camera. It remained motionless while we maneuvered it this way and that. But then, just as we were about to take another picture, one of its tiny antennae wiggled. It was alive. After all those hours in the refrigerator, it was still alive. I won’t soon forget that wiggling antenna. It felt miraculous in the most literal sense of the word.

Watching a refrigerated insect “wake back up” never ceases to amaze me. When a butterfly that was lying on its side suddenly flaps its wings and rights itself, or a curled-up damselfly begins to twitch after several minutes of total stillness, or a lace bug regains the ability to wiggle an antenna, I always feel like I am witnessing something remarkable. But my favorite part of the whole process might be what happens next.

After I’ve finished photographing an insect, I always try to release it, ideally wherever I found it. It is always a relief to put them back where they belong, alive and moving and hopefully unharmed. But it can be hard to let them go. Spending enough time with one creature, any creature, turns it into an individual, and once you’ve become acquainted with an individual, it’s hard not to care what happens to it. After I release an insect, I will never know its fate. But if cooperating with refrigeration and photography is the insects’ part of the deal, then releasing them afterward is mine.

An ailanthus webworm moth eating mango syrup with its straw-like proboscis.

Sometimes, I make more literal deals with the insects. One day, I caught an ailanthus webworm moth, a bright orange insect with black and white markings, and it kept reviving before I could get a good picture. Each time I relegated it back to the refrigerator, I felt worse and worse. So I put the moth back in the fridge one more time, promising that it would be the last, and walked to the dining hall, where I squirted mango syrup onto a napkin. I tried to be subtle so no one would ask me why I was putting it on a napkin instead of in a cup of iced tea. Oh, I’m just feeding the refrigerated moth in the insect lab. Nothing unusual. Have a great day! Back in the lab, I dabbed some syrup onto the back of my notebook and offered it to the moth, partly as a reward for its patience, partly to assuage my own guilt, and partly as a last-ditch attempt to keep the moth still while I photographed it. The moth became completely focused on lapping up the syrup, but I had failed to account for its feeding process, an exuberant dance that was anything but still. Nevertheless, a deal is a deal—that moth wasn’t going back in the fridge. I walked across campus to the spot where I’d found it, and it kept eating the sugary treat the whole time. For once, my photography subject didn’t seem eager to leave.

At Nijhout’s suggestion, I left this beetle at room temperature overnight, in a jar with some water droplets, instead of refrigerating it.

The mango syrup retrieval mission probably isn’t the strangest thing I’ve done in pursuit of insects. One morning, I was standing outside in the pouring rain, already soaked and so no longer remotely concerned about getting wetter, and holding my arms above my head in an awkward position while I tried to remove the slippery cap from an insect container in order to catch a candy-striped leafhopper perched on a leaf above me.

Another time, our class was on a field trip on the Al Buehler Trail when I spotted a dainty insect almost floating through the sun-dappled swamp. Nijhout identified it as a phantom crane fly, and when I failed to catch it in a dignified manner from the boardwalk, I jumped into the mud and swooped my net, successfully capturing the cranefly. Back in the lab the next day, I found that the phantom crane fly revived even faster than the ailanthus webworm moth, seeming to regain full movement within moments of exiting the refrigerator. I snapped pictures using a lens that attaches to my phone, but just as I was about to return it to its container to release it, it drifted into the air, and—like a phantom—it disappeared. I never found it again.

A phantom crane fly, which revived almost instantly despite repeated refrigerations.

Duke does not assign an Ethical Inquiry code to the entomology class, but I feel I have done more ethical inquiry in this class than any other. Is photography a worthy reason to risk an insect’s life? Is accidentally releasing a phantom crane fly in a dark room without food or water any better than killing it outright? Is killing insects an essential part of entomology? If so, when is it justified, and when is it not?

In class, we have learned about a series of groundbreaking experiments that strike me as twisted. In one, Stefan Kopec “ligated” caterpillars by tying a very tight string around them to see if either half would still molt. Spoiler: yes, the front half containing the brain. If you cut the brain out of the head and transplant it to the abdomen, then the back half will molt instead. Conclusion: the brain is essential for molting, but it doesn’t need to be attached to the rest of the nervous system. Another experiment involved scientists cutting cecropia moth cocoons in half with a razor blade and sealing each half with wax, followed by more brain transplantation (in this case, a transplanted brain does not make the back half emerge from the cocoon—unless you also transplant a piece of the thoracic gland). Yet another involved beheading two insects and attaching their necks with a capillary tube to see if injecting a hormone into one will prompt the other to molt as well (yes, it will). I hate even imagining these experiments, and I can’t picture myself ever performing them.

My apparent inability to kill insects even in the name of science might become a real problem if I want to study entomology after college. But when I question the value of certain experiments or feel guilty for refrigerating an insect, I am not acting as a scientist. I am acting as an older version of the fourth grader who watched in distress as her classmate ripped caterpillars’ heads off or the eighth grader staring at a circle of kids surrounding a beautiful cecropia moth, distraught from just imagining that someone might hurt it. (The moth was fine—the teacher got one of the kids to agree to protect it. I was not—she sent me to the bathroom to calm down and then sent my friend to check on me.)

At times, I take this concern for the hypothetical suffering of other beings entirely too far. In a cell biology lab this semester, our TA explained that the E. coli bacteria we were working with had had a very rough day: they’d gone through a process that left holes in their membrane, then been put on ice to prevent those holes from completely destroying them. Clearly feeling bad for bacteria is not a recipe for success, but wanting to minimize insects’ suffering seems more justifiable. There seems to be an important distinction between a child pulling caterpillars’ heads off for fun and a scientist tying strings around a caterpillar to answer specific scientific questions. But is the pursuit of knowledge alone enough of a justification for killing the creatures we study? I would have an easier time justifying an experiment that kills insects to advance human medicine or insect conservation.

Ultimately, the morality of killing insects may depend on a question we can never answer: “What does it feel like to be an insect?” I would not want to be shut in a refrigerator for several hours, prodded with a pin, or cut in half with a razor blade, so how can I justify doing that to an insect? I torture myself repeatedly with these thought experiments, but there is a glaring problem with my “golden rule” line of reasoning: I am not an insect. How can I imagine how refrigeration feels to a creature that can slow its metabolism to just 1%, as we learned in class? Perhaps my mom is right when she encourages me to think of these insect-chilling sessions as akin to medically induced comas or periods of peaceful rest rather than sustained torture sessions.

A lacewing in the refrigerator. Since it kept trying to fly away when I took it out, I stuck my head in the refrigerator to take pictures, and the lacewing and I seemed to reach a detente. Later that evening, before it got cold like a refrigerator outside, I let it go.

Where is the line between science and torture? On the flip side, where is the line between anthropomorphizing animals (problematic in science) and giving them the benefit of the doubt when it comes to sentience and capacity to feel pain? It’s not just our experience of the world, our umwelt, that is different from that of insects. We also have entirely different survival strategies. Humans are a K-selected species; we have few offspring but invest heavily into the survival of each individual. Insects, meanwhile, are r-selected; they have many babies, often hundreds or thousands, and many of them will die. If one lace bug can lay hundreds of eggs and many butterflies and moths live only a matter of days, then killing or saving a few insects probably has a negligible impact on the species as a whole. There are other initiatives, like reducing pesticide use, planting native flowers, and mowing lawns less frequently, that can benefit insects on a much larger scale. But the time and effort I spend keeping my refrigerated insects alive was never about protecting a species. It has always been about protecting an individual.

A particularly tiny insect, viewed under a microscope next to part of a pin.

At first, my tendency to get attached to insects made it very difficult for me to justify refrigerating them. But seeing tiny creatures under a microscope is a powerful, intoxicating thrill. Maybe refrigeration is a fair compromise, a way to observe insects without killing them and to keep them safe until I let them go.

A previously refrigerated beetle about to be released back at the Duke Pond.

Post by Sophie Cox, Class of 2025

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