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

Category: Field Research Page 1 of 14

Vernal, Ephemeral, Spring Beauty by Any Other Name

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Nicki Cagle, Ph.D., with perfoliate bellwort, an ephemeral forest plant also known as wild oats (Uvularia perfoliata).

“Ephemeral” is one of my favorite words. It conjures up images of vernal pools and fireflies and flowers in spring. It comes from ephēmeros, a Greek word meaning “lasting a day.” English initially used it in a scientific sense, to refer to fevers and then in reference to short-lived organisms like flowers or insects. Today “ephemeral” is most often used to describe anything fleeting or short-lived.

The term “spring ephemeral,” for instance, refers to flowers that are visible for only a short time each spring before they disappear.

Nicki Cagle, Ph.D, a senior lecturer in the Nicholas School of the Environment, led a spring ephemeral workshop in the Korstian Division of Duke Forest on a Friday afternoon in late March. The workshop was hosted by DSER, the Duke student chapter of the Society for Ecological Restoration. We focused on identifying herbaceous plant species and families, particularly spring ephemerals.

“Spring ephemerals are perennials that emerge early in the spring and then grow, reproduce, and disappear from the surface of the forest floor in just a few short weeks,” Cagle explains. We also found several species that aren’t technically ephemerals but still bloom in early spring — before the tree canopy emerges and plunges the floor into shade.

Oxalis violacea, a species of wood sorrel.

The first plant Cagle points out is Oxalis violacea, a type of wood sorrel. “This particular species will have purple flowers,” she says. The genus name, Oxalis, refers to the plant’s oxalic acid content. “You can nibble on it,” but “you don’t want to nibble on it too much.” Oxalic acid, which is also found in common foods like spinach, gives the leaves a pleasant, lemony taste, but it can cause problems if eaten in excess.

Common bluet (Houstonia caerulea).

When we come across a patch of lovely, pale violet flowers with yellow centers, Cagle challenges the workshop participants to determine which family it belongs to. She offers two options: Rubiaceae, a large family that often has either opposite or whorled leaves and four to five petals and which includes familiar plants like coffee, or Violaceae, a very small plant family whose members “tend to have everything in fives” (like petals, stamens, and sepals) and often have basal leaves. Answer: Rubiaceae. This particular species is Houstonia caerulea, the common bluet. Its yellow centers help distinguish it from related species like the summer bluet, tiny bluet, and purple bluet. If anything, Cagle says, the plant’s presence is “an indicator of disturbance,” but it’s still good to have around.

Here’s the little brown jug (Hexastylis arifolia).

Next we come across two species in the Hexastylis genus. They are sometimes called wild ginger, but the name is misleading. Hexastylis species are not related to the ginger you buy in the store, which is in a completely different family. Hexastylis is, however, in the same family as the Asarum genus, which Cagle thinks of as “proper” wild ginger. Asarum and Hexastylis have traditionally been used as food and medicine, but they also contain toxins. According to Cagle, they belong to “one of the few plant families that have fossilized remains in the United States,” even dating back to the late Cretaceous Period.

The two species we see are Hexastylis arifolia, the little brown jug, and Hexastylis minor which looks similar but “tends to have a much more rounded form.” Like many spring ephemerals, Hexastylis is often dispersed by ants. The seeds have elaiosomes, fatty deposits that ants find attractive.

“We have a lot of different violets of varying origins” in this area. According to Cagle, this one is likely to be a common blue violet, Viola sororia.

There’s a patch of violets near the Hexastylis plants. “We have a lot of different violets… of varying origins” around here, Cagle says. Many of the native species have both a purple form and a variety that’s white with purple striping. Other species in the violet family come in different colors altogether, and Cagle says many of those are of European origin.

The Johnny-jump-up pansy, for instance, can have “funkier colors,” like yellow or pinkish purple and is native to Europe and Asia. Violets can be hard to identify. Some species are distinguished mainly by characteristics like the lobes (projections in leaves with gaps between them) or the hairiness of the leaves. The bird’s foot violet and wood violet, for example, “tend to have really deep lobes.”

Cagle says the violet we’re looking at is likely the common blue violet, characterized by smooth leaves and petals, purple or purple-and-white flowers, and rounded or slightly arrow-shaped leaves.

The Cranefly orchid (Tipularia discolor) reproduces later in the year. The purple on the bottom of the leaves, and sometimes on the top as well (see right), helps protect the plant from sunlight and herbivores.

The orchid family, Orchidaceae, is one of the largest families of flowering plants in the world. Many of its members are tropical, including the Vanilla genus, but “we do have a number of native orchids” here as well, including yellow and pink lady’s slipper orchids, putty-root, and the cranefly orchid.

The cranefly orchid, Tipularia discolor, isn’t yet in bloom, but we come across the leaves several times on our walk. According to Cagle, Tipularia discolor “isn’t actually a spring ephemeral” because it reproduces later in the year. However, “it’s ephemeral in its own way,” the leaves disappear by the time it flowers. Cagle says the plant’s scientific name can remind you what to look for: “‘Tip-’ because you’re going to tip this leaf over” to look at the underside and “discolor” because the leaves are a striking purple underneath. Some of the ones we see are purple on top as well. Cagle explains that the purple coloration serves as sunscreen and protection from critters that eat plants.

The plant gets its common name (and its scientific genus name, interestingly) from its delicate flowers, which are supposed to resemble craneflies. When the plant blooms, “the flowers are so delicate and so subtle that most of the time you miss them.” Pollinators like Noctuid moths, on the other hand, find the flowers easily and often. Cranefly orchids even have “specialized seed structures” that “get fused onto insects [such as the moths]… and carried off.”

Rue anemone (Thalictrum thalictroides or Anemonella thalictroides).
Cagle with giant chickweed (Stellaria pubera).

The rue anemone, unlike the cranefly orchid, is a true spring ephemeral. It belongs to a more “primitive” family and has lots of petals in a spiral arrangement. The species is also known as windflower “because they flutter and dance as the breeze comes through.” Cagle mentions that the plant is “usually pollinated by flies and little bees” and serves as an important food source for insects in early spring. But “how do these even exist” in a forest with so many plant-eating deer? Many spring ephemerals, Cagle explains, have “some really potent toxins” that protect them from large herbivores.

We stop briefly to examine perfoliate bellwort, also known as wild oats (Uvularia perfoliata), and giant (or star) chickweed. Chickweed is in the pink family, named not for the color but because “the petals… [look] as if they’re cut by ‘pinking shears,’” which have saw-toothed blades that leave notches in fabric.

Trout lily (Erythronium umbilicatum). According to Cagle, “No spring ephemeral walk is actually complete without finding some trout lilies.”

Near the end of our walk, we find several trout lilies. That’s fortunate. “No spring ephemeral walk is actually complete without finding some trout lilies,” Cagle says.

Unsurprisingly, trout lilies belong to the lily family. “Their flower structure,” Cagle says, “is very symmetrical” with three petals and three sepals. In trout lilies, the sepals resemble petals, too. This particular species is Erythronium umbilicatum. The species name, umbilicatum, refers to its “really long peduncle,” or flower stalk, which “allows the seed to actually touch the ground.” The seed is dimpled, Cagle says, “like a little belly button.” The name “trout lily,” meanwhile, refers to the mottled pattern on the leaves.

Spring beauty (Claytonia virginica), “a quintessential spring ephemeral.”

At the base of a tree near a small river, Cagle points out a flower called spring beauty (Claytonia virginica), “a quintessential spring ephemeral.” Some flowers, like the common bluet we saw earlier, thrive in disturbed areas, but plants like the spring beauty need rich, undisturbed habitat. That makes them good indicator species, species that can help scientists gauge environmental conditions and habitat quality. When a natural area is being restored, for example, scientists can measure restoration progress by comparing the “restoration site” to an undisturbed “reference site.”

According to Cagle, the spring beauty is pollinated by “bee flies… flies that kind of look like bees.” After pollination, the flowers turn pink. Cagle says this is common among ephemerals. One theory is that the color change signifies which flowers have already been pollinated, but others think it’s just a result of senescence, or aging.

Spring beauties are also “photonastic,” meaning they open and close in response to changing light conditions. “There is some evidence that the Iroquois would eat this plant in order to prevent conception,” Cagle says, but today the plant—like many spring ephemerals—is under protection in some areas. Human activities, sadly, have contributed to the decline of too many spring ephemerals.

Alum root (Heuchera americana) near the end of the walk. According to Cagle, its roots can be used “to form mordant for dyes.” Members of the Saxifrage family, which includes alum root, often have five petals, five sepals, and five stamens.

Not all of the plants we saw are spring ephemerals. Some, although they bloom in early spring, “wouldn’t technically be considered ephemeral because their leaves stick around even if their blooms don’t last long.” True ephemerals, on the other hand, “are plants that just seem to disappear off the face of the planet (or the forest floor) after a few weeks,” Cagle says. Only three of the species we found during the workshop are true ephemerals: the windflower, trout lily, and spring beauty. However, these aren’t the only spring ephemerals found in the area. Cagle’s personal favorite is bloodroot, with its “bright white petals” and pollen “that looks like it’s glowing.”

Next time you’re in the woods, keep your eyes out for ephemerals and other early spring flowers, but look quickly. They won’t be here for long.

By Sophie Cox

Post and Photos by Sophie Cox, Class of 2025

Kinsie Huggins: the Future Doctor Who Could Shot-Put

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From shot-putting, to helping conduct two research studies, to being selected for a cardiology conference, meet: Kinsie Huggins. She is from Houston, Texas, currently majoring in Biology and minoring in Psychology with a Pre-Med track here at Duke. With such a simple description, one can already see how bright her future is!

“I want to be a pediatrician and work with kids,” Huggins says. “When I was younger, I lived in Kansas, and in my area, there were no black pediatricians. My mother decided to go far to find one and I really bonded with my pediatrician. One day, I made a pact with her in that I would become a pediatrician too so that I can also inspire other little girls like me of my color and other minority groups.”

Having such a passion to let African-American and minority voices be heard, Huggins is also part of the United Black Athletes, using her shot-put platform to make sure these voices are heard in the athletics department.

And while she may be a top-notch sportswoman, she is also just as impressive when it comes to her studies and research. One of her projects focuses on the field of nephrology – the study of kidneys and kidney disease. She and a pediatric nephrologist are currently working on studying rare kidney diseases and the differences in DNA correlating to these diseases.

Kinsie is also a researcher at GRID (Genomics Race Identity Difference), which studies the sickle cell trait in the NCAA. With the sudden deaths of college athletes from periods of over-exhaustion during conditioning, there has been a rise in attention of sickle cell trait and its impact on athletes. At first, the NCAA implemented a policy that made it mandatory for college athletes to get tested for sickle cell in 2010, but some were wary about the lack of scientific validity in such claims. Now, the NCAA has funded GRID to conduct such research.

The difference of Normal red blood cell and sickle cell (CDC).

 “We are analyzing the policy (athletes need to be tested for sickle cell), interviewing athletes in check-ups, and looking at data to see if the policy is working out for athletes and their performance/health,” Huggins explains.

With such an impressive profile, it doesn’t go without saying that Huggins didn’t go unnoticed. The American College of Cardiology (ACC) select high school and college students interested in the field of medicine and have them attend a conference in Washington D.C. to hear about research presentations, groundbreaking results of late-breaking clinical trials, and lectures in the field. Having worked hard, Huggins was selected to be part of the Youth Scholars program from the ACC and was invited to the conference on April 2-4. 

Let’s wish Kinsie the best of luck at the conference and on her future research!

Post by Camila Cordero, Class of 2025

Measuring What Climate Change Does, Not Just Whether It’s Happening

Duke has a goal of being a “climate university,” Nicholas School of Environment Dean Toddi Steelman said in introducing a panel discussion on Climate Change Science during Research Week. She said it’s a vision in which the university’s focus on climate informs every aspect of its mission, from education and operations to community partnerships – and, of course, research.

Five Duke climate scientists spoke on the Feb. 1 panel, all remotely. (View the Discussion.)

Jim Clark, professor of statistical science at the Nicholas School, described our planet’s climate as a “moving target” when it comes to understanding its impact on biodiversity. Complex connections exist between species, like a “system of interactions” between each other, that responds to climate change.

Our understanding of this system is limited by population data collection like the Breeding Bird Survey and the USDA Forest Inventory & Analysis — projects that lack “co-located monitoring of multiple species groups,” Clark said. Such measures fail to capture the relationships between species.

Professor James Clark

Instead, Clark advocates moving away from static models like these population measurements and towards the question of “How does change in the whole community respond to the environment and other species?” In order to understand our dynamic climate, we need an equally dynamic conception of biodiversity, he argued.

Marc Jeuland, associate professor of public policy and global health, and leader of the Sustainable Energy Researchers Initiative (SETI), talked about the “deep inequities” in energy access across rural parts of developing regions and the prospect of accomplishing “a just and sustainable energy transition” of their energy sources.

He thinks the transition can be accomplished with existing sustainable energy technologies like wind and solar.

The problem has two main parts, he said. First is the lack of clean cooking energy, with 2.6 billion humans dependent on solid fuels (wood and charcoal) and polluting stoves. The second is the lack of electricity and electrical services, with 760 million people going without and millions more lacking reliable service, he said.

Professor Marc Jeuland

Jeuland said there is an urgent need to reallocate resources to spread climate solution technologies in these parts of the world.

Jeuland and his SETI team tirelessly investigate how to overcome energy poverty and the populations they affect most – primarily in Africa and Southern Asia – to understand the feasibility and tradeoffs with the adoption of increased access to alternative fuels.

Emily Bernhardt, the James B. Duke distinguished professor of biogeochemistry in the Nicholas School and chair of Duke Biology, addressed the question of how climate change and sea level rise will impact coastal communities and ecosystems.

She said we don’t really have to wait to see what will happen: predominantly low-income communities along the coast are already suffering the consequences of sea water and extreme weather events. But she said the regions’ struggles remain unsolved and underrepresented because they lack the economic and political power to affect change.

Professor Emily Bernhardt

Whenever an event like a hurricane occurs, coastal plain communities are susceptible to storm surges that introduce salt into freshwater environment – leading to sometimes catastrophic, often long-lasting impacts on existing ecosystems, Bernhardt said.

Bernhardt and hundreds of other scientists along the United States coast are working together on something she called “convergence research” that seeks solutions for coastal and other vulnerable communities. It’s called the Saltwater Intrusion and Sea Level Rise (SWISLR) Research Coordinating Network. 

Betsy Albright, associate professor of environmental science and policy, and Brian McAdoo, associate professor of earth and climate science, shared their zoom-hosting duties.

They talked about social justice and social science in mitigating the impact of climate change. Their work examines the role of local communities and governments in disaster recovery and how they can work to create systems to manage aid and other resources as extreme weather events become more common.

As with most climate issues, marginalized communities are disproportionately impacted by these events, they said. Albright and McAdoo are searching for ways to help these regions create the capacity to respond and become more resilient to future events.

Professor Elizabeth Albright
Professor Brian McAdoo

The climate crisis is arguably the greatest challenge of this generation, but this esteemed panel brought much-needed attention to the obstacles facing every aspect of the world of climate science research and how their research is working to overcome them.

Post by Nhu Bui, Class of 2024

The Mind Behind Muser

Biology professor Sheila Patek remembers when she was an undergraduate, petrified as she waded through the world of academia in search of a research position. Knocking on door after door, Patek promised herself that if she was able to enter that world of research, she was going to change it; she was going to help students find opportunities and shift the rigid, exclusionary culture of academia.

Years later, Professor Patek was able to keep her promise. She created Muser, a website to connect students to research opportunities in an effort “to achieve accessible, transparent, equitable, and multidisciplinary research experiences for students and mentors.”

Patek first began this effort as a faculty member at the University of Massachusetts, where she found few efficient pathways for undergraduates to find research opportunities. Patek had grown accustomed to being at UC Berkeley, where they utilized a fully integrated system known as the Undergraduate Research Apprentice Program. The University of Massachusetts was more reminiscent of Patek’s own undergrad experience, and it was there that she and her colleagues began working on the first version of Muser’s software. This is the version that she brought with her when she came to Duke.

Here, we’re lucky to have a slew of resources — DukeList, the Undergraduate Research Support Office, Bass Connections — that are intended to help students pursue research. However, Patek says that Muser distinguishes itself by being specifically designed to address the many barriers that still prevent students from pursuing research — from a lack of support and resources to racial and gender biases. 

Team Muser: (from left) Sheila Patek, Founder; Sonali Sanjay, Co-Student Leader; Katherine Wang, Co-Student Leader; Theo Cai, Duke Undergrad Muser Director and Nowicki Fellow (Credit: Ben Schelling)

One way Muser does this is by making all initial applications anonymous. Patek mentions studies that have found that things like the race and gender connotation of names have significant influence on who gets a position; for example, when given CVs that are identical except for the gender of the names, faculty are more likely to rate the male CVs higher. From the mentor side of Muser, research leads see students’ personal statements first, then must formally review the applications if they wish to view all the information the student has provided — including their names. Patek notes that it has surprised and perhaps frustrated many mentors, but it’s a feature for the benefit of students; it allows them to first be heard without the preconceptions attached to something like their name.

On the flip side, Muser tries to keep things as transparent as possible for students (although anonymous mentors are in the works). There are set timelines — called “rounds” — in which mentors post positions and students apply then hear back. With most other forums for research like DukeList, students are expected to check in and apply constantly — not even knowing if they will get a response. Muser solves this through these rounds, as well as a unique “star” system: mentors that actually review every application get a gold star, visible to students applying. 

So far, over three thousand (3000) undergraduates have used the software, and Patek estimates that in 2021, 20% of Duke undergraduates had, at some point, held a research position thanks to Muser. She also boasts the diversity of research leads that have become involved with Muser; it features professors, graduate students, and lab managers alike as mentors, who represent a better gender and diversity balance than academia as a whole. But as much progress has been made, Patek’s ultimate dream would be for every project in every department to be posted on Muser, available for undergraduates who don’t have to worry about being denied because of bigotry or ignored altogether. 

“The culture of academia is fundamentally opaque to everyone not in it,” Patek notes, but she and the Muser team are doing everything they can to change that. The newest version of Muser’s software open source on GitHub and available for free — has recently been adopted by Harvey Mudd College and the University of Massachusetts, and Patek expresses her hope for the idea to spread nationwide. 

Universities that have adopted Muser

The website used to be called MUSER — an acronym meaning Matching Undergraduates to Science and Engineering Research — but nowadays, it’s known simply as “Muser.” I’ve been told that the rebranding is a play on words, referencing the Muses of Greek and Roman mythology who oversaw the full range of arts and sciences, to represent all thinkers. 

The next round of Muser for Summer 2022 research positions opens on February 19. Mentors can post opportunities NOW, until February 18. For more information, visit the website and check out this fantastic article introducing Muser.

Introducing Muser – A Better Way to Find Student Research

An effortlessly simple research platform where Duke students and Duke research projects can connect? Yes, please!

If you are anything like me, Duke University’s incredible research opportunities were extremely enticing when considering this school. One of the top 10 research institutions in the United States, Duke University’s research community spends over 1 billion dollars annually to fund its projects, which includes notable research facilities like the Duke Center for Human Genetics, the Duke Cancer Institute, the Duke Center for AIDS Research, and the Duke Human Vaccine Institute.

However, the amount of opportunity in this area can be overwhelming to approach, and as a student you often have no clue where to start.

Summer undergraduate research in cancer biology at the Duke University School of Medicine.

That’s where Muser comes in.

Duke introduces: Muser.com

Muser is a website created by Sheila Patek, a Duke biology professor who used grant money from the National Science Foundation to create a more equitable and straightforward way to connect undergraduates with professors with research opportunities. The resource allows researchers to post ongoing research positions with a direct application through the website.

Muser can sort research projects by compensation, hours, year, and project category, simplifying Duke’s incredibly complex research community by a lot.

“Muser posts research projects in 4 rounds throughout the year, a Fall round (August), a late Fall round for Spring projects (October/November), a Spring round for Summer projects (February/March), and a Spring round for Fall projects (March/April),” according to its website. Muser makes it easy to accommodate research positions into the part of your semester that works with your busy schedule.

I connected with some Duke students who have found success with the growing research platform, and though their interests were diverse, the success was all-encompassing.

“My experience with my Muser Project for the summer of 2021 was great overall,” said Elaijah Lapay, class of 2025. “It was essentially a history research assistantship helping a professor in the history department conduct research on elderly and eldercare in North Carolina. I was able to go to the NC State archives as well as archives across eastern North Carolina to really dive into the question of treatment of the elderly during the 20th century.”

Lapay’s research is so fruitful that the professor, James Chappel, the Gilhuly Family Associate Professor of History, is continuing to pursue this project for the rest of the school year. “I truly felt one-of-a-kind… I definitely feel like I’ve learned a lot and it’s sparked a passion in me for geriatrics and eldercare.”

A look inside Dr. Laurie Sanders’s lab here at Duke University.

“I got the chance to work in the Sanders lab under principal investigator Dr. Laurie Sanders and post-doctorate Dr.Claudia Gonzalez-Hunt!” said Shreya Goel, class of 2025. This lab was the first to link a genetic mutation to mitochondrial DNA damage which was ultimately discovered to be a marker for sporadic Parkinson’s disease.

“I get to work with human cells to induce and track mitochondrial and nuclear DNA mutations to determine their effect on the progression of the cell cycle,” Goel said. Her research position is making a difference and it allows her to gain tangible experience in a field she is passionate about.

The success stories are copious, and the opportunity that this platform has brought to prodigious students like these is without question.

At a billion-dollar research school, understanding where to begin can be intimidating. Muser alleviates these worries by connecting researchers and students through an accessible platform.

Have more questions? Visit Muser’s FAQ page to get more information and get into contact with one of Muser’s staff.

Post by Skylar Hughes
Class of 2025

Finding the Tipping Point for Coastal Wetlands

Cypress swamp, eastern North Carolina. Photo by Steve Anderson, Duke

DURHAM, N.C. — The Albemarle-Pamlico Peninsula covers more than 2,000 square miles on the North Carolina coastal plain, a vast expanse of forested swamps and tea-colored creeks. Many people would probably avoid this place, whose dense thickets of cane and shrubs and waterlogged soils can slow a hike to a crawl.

“It’s hard fieldwork,” says Duke researcher Steve Anderson. “It gets really dense and scratchy. That, plus the heat and humidity mixed with the smell of sulfur and the ticks and the poison ivy; it just kind of adds up.”

But to Anderson and colleagues from Duke and North Carolina State University, these bottomlands are more than impenetrable marsh and muck and mosquitoes. They’re also a barometer of change.

Researchers surveying plants in Alligator River National Wildlife Refuge in 2016. Photo by Mathew Stillwagon, North Carolina State University

Most of the area they study lies a mere two to three feet above sea level, which exposes it to surges of ocean water — 400 times saltier than freshwater — driven inland by storms and rising seas. The salt deposits left behind when these waters recede build up year after year, until eventually they become too much for some plants to cope with.

Trudging in hip waders through stunted shrubs and rotting tree stumps, Anderson snaps a picture with his phone of a carpet of partridge berry trailing along the forest floor. In some parts of the peninsula, he says, the soils are becoming so salty that plants like these can no longer reproduce or are dying off entirely.

Along the North Carolina coast, understory plants such as this partridge berry (left) are quickly ceding ground to species such as this bigleaf marsh-elder (right) as the soils become too salty for them to thrive. Credit: Steve Anderson

In a recent study the team, led by professors Justin Wright and Emily Bernhardt of Duke, and Marcelo Ardón of NC State, surveyed some 112 understory plants in the region, making note of where they were found and how abundant they were in relation to salt levels in the soil.

The researchers identified a ‘tipping point,’ around 265 parts per million sodium, where even tiny changes in salinity can set off disproportionately large changes in the plants that live there.

Above this critical threshold, the makeup of the marsh floor suddenly shifts, as plants such as wax myrtle, swamp bay and pennywort are taken over by rushes, reeds and other plants that can better tolerate salty soils.

Certain dwindling plants could be an early warning sign that salt is poisoning inland waters, researchers say. Credit: Steve Anderson

The hope is that monitoring indicator species like these could help researchers spot the early warning signs of salt stress, Anderson says.

This research was supported by grants from the National Science Foundation (DEB1713435, DEB 1713502, and Coastal SEES Collaborative Research Award Grant No. 1426802).

CITATION: “Salinity Thresholds for Understory Plants in Coastal Wetlands,” Anderson, S. M., E. A. Ury, P. J. Taillie, E. A. Ungberg, C. E. Moorman, B. Poulter, M. Ardón, E. S. Bernhardt, and J. P. Wright. Plant Ecology, Nov. 24, 2021. DOI: 10.1007/s11258-021-01209-2.

Salt is poisoning the soils past a point of no return for some marsh plants; one team is trying to pinpoint the early warning signs. By Steve Anderson.

A Conversation with Emily Levy, Soon-to-Be Biology PhD

Emily Levy studies how the physical and social environments that baboons experience affect their physiology and life outcomes. The Massachusetts native, who works under advisor Susan Alberts (PhD), is in the final year of her Biology PhD and will defend her thesis later this Spring.

Though Duke’s in-person classes have been delayed until next week, I caught up with Levy over Zoom. The wall of her home office displays a fascinating Russian map of Chicago from the cold war era that shows bridges with their weight capacity. Levy tells me that she had no idea how her husband, who is from Evanston, found the map.

Emily Levy, an almost-PhD in Duke Biology

Levy’s research stems from the Amboseli Baboon Research Project – a nearly 50-year-old, ongoing study of wild baboons in Kenya. Duke’s Alberts has been studying these baboons for over 35 years and is a renowned primatologist involved with the project. Alberts’ lab collaborates with field researchers in Kenya to receive data and samples that are imperative to much of their work.

“Something that I really appreciate about Susan and the way she runs the lab is that she starts first-year grad students on a starter project,” Levy told me. Following a discussion about Levy’s interests, this project led to her first work on dominance rank, stress levels, and what this means physiologically for baboons. Levy also “poked around” at how scientists study dominance rank and found that the methods used for assessing rank “matter a lot.”

In her more recent project, Levy is trying to figure out what early life environments mean for adulthood in baboons. “So, we know that baboons that experience a really harsh early life, if they survive to adulthood, have really, really reduced lifespans as adults – like half as long – as baboons that had no adverse events,” Levy said.

“I’m focusing on two hypotheses to get at what might be happening under the skin that could have something to do with longer term effects on health and mortality.” One hypothesis is that a tough early life environment, especially nutritional stress, could stunt baboon growth and impinge adult activities like foraging or maintaining dominance rank. The other hypothesis proposes that early life adversity disrupts immune development, leading to an immune system that is either always inflamed or produces an overpowering inflammatory response when a baboon does get sick.

The second hypothesis is one that has been supported by human research, but Levy’s preliminary results “are the exact opposite.” This highlights one facet of the importance of her research: Its implications and parallels to human health and mortality. But Levy says her research is also “cool because it’s just cool” and appreciates what her work may add to basic science beyond human application.

In her journey to Duke, Levy said that she “tried a few ways of studying” animals before arriving at the work she conducts now.  Levy, who really liked animals, enjoyed time outside, and was “hooked on biology” in high school, began her undergraduate career at Williams College with this in mind. “In college, I took biology and neuroscience and then took animal behavior my sophomore year and was like Oooo, this is cool!,” Levy exclaimed with a big smile on her face, “And it felt sort of light-bulby.”

Along the journey to her PhD, Levy studied plants and insect pollinators and spent a few weeks in Madagascar in a tent filled with fleas. Though Levy said that these experiences of field work became “one of my favorite things about my job,” they also helped shape her trajectory as a scientist as she figured out which model systems and research questions “did and did not spark her joy.”

It was during her undergraduate thesis assessing social behavior in rats that she felt a strong “click” for studying social behavior in animals. Taking a couple years to work in a clinical research lab that conducted work on autism in humans, Levy enjoyed working on research to aid in special needs people. “But pretty quickly,” Levy said, “I was like, Alright, I don’t want to study humans for my whole life.”

“I’d basically been crossing things off my list up until this point,” Levy continued, “I now knew I wanted to study social animal behavior in non-human animals.” In her year away from research, Levy worked as an outdoor educator in Wyoming while she applied to grad school with this study plan in mind. Her time in Jackson Hole, Wyoming narrowed her interests even more, pushing her towards behavioral ecology because of her observation of an amazing, unbroken natural ecosystem.

Levy says she ultimately ended up at Duke because “the Baboon Project is amazing,” “Susan Alberts is amazing,” and “the Duke Biology Department is really wonderful.”

While Levy enjoys working with Alberts and mentoring undergraduates, as well as using grant writing as a “fun way to develop really exciting ideas and hypotheses,” she also shared some of her frustrations with me. “Science is very slow — often, not always — and a project from start to finish takes a long time. And the publication process is so long. I struggle with that pace sometimes” Additionally, as someone who was raised to never take herself too seriously, Levy also said that she has felt a lot of pressure in grad school to take herself more seriously than she should as part of academic culture.

Levy loves teaching and her hope is to become a faculty member at a small liberal arts college or undergraduate institution following a post-doc, for which she is currently in the application process. Through this future work, Levy aspires to “bring undergrads through the scientific process.”

In her time away from the lab and science, Emily is an avid baker. “One of my goals in grad school has been to acknowledge and own what I am good at, and I know I am good at baking,” Levy said with a grin. Chocolate chip cookies are her specialty.

If she could give any aspiring science PhDs a word of advice, Levy offered that you should have fun and “pay attention to the non-intellectual, as well as intellectual, things that you enjoy most.” As exemplified by her path to figuring out what exactly it was in science that inspired her, Levy says not to worry as much about figuring out where you are going, and when, but reaping the lessons and insights of the experiences along the way.

Post by Cydney Livingston, Class of 2022

Building a Just Foundation for Our Energy Transition

Swine Country Documentary Project

As conversations about the energy transition away from fossil fuels become increasingly important (and time-sensitive), some experts in environmental policy aren’t just worried about the conversations themselves. They’re worried about who has a seat at the table — and who doesn’t. 

Sherri White-Williams

On November 8, at “Building a Just Foundation for Our Energy Transition,” a few of these experts — Sherri White-Williamson, Environmental Justice Policy Director at the NC Conservation Network; Josh McClenney, the North Carolina Field Coordinator at Appalachian Voices; and J. Spenser Darden, the Assistant Dean for Diversity and Inclusion at Duke’s Sanford School of Public Policy — spoke about this and other issues. Thomas Klug, a Research Associate at the Duke Energy Access Project, moderated the panel, which was put together by the Sanford Energy & Environment Club.

Klug asked the panelists to define what a “just transition” really means in the context of the panelists’ work, and whether it differs from a diverse and inclusive transition.

J. Spenser Darden

McClenney answered that a just transition entails recognizing that Black, brown, and indigenous communities, as well as low socio-economic status individuals, have historically faced the worst effects of fossil fuel economies. Living in the “physical and economic traction zones,” they’re the ones that lose jobs — like coal miners, in the case of McClenney’s work with Appalachian Voices. 

However, where a diverse and inclusive transition involves “getting people to the table,” just policies will actually reflect the conversations had at the table. An unjust transition, McClenney said, is one where “people clap themselves on the back for doing such a great job having these diverse, inclusive discussions — then make policies that work against their participants.” Ensuring inclusion for communities that have historically been excluded is important, but it’s equally important to make sure the resulting policies are actually inclusive.

Josh McClenney

White-Williams agreed with McClenney — inclusion should never end at “checking the box.” The goal should be to incorporate the input of marginalized voices into resulting policy. White-Williams also added that fairness, while not necessarily guaranteed by diversity and inclusivity, is a key part of a just energy transition. 

Spenser stressed the need to move away from “extractive, colonial” ways of thinking about energy and who makes up society, and to instead incorporate indigenous ways of thinking. He stated that diversity and inclusion is reactive: people realize flaws in the way they’ve built something and try to address it later by incorporating new elements. A just system, on the other hand, is built to be “for and by” communities that have been excluded from the very start.

Klug asked the panelists to recount some of the ways they’ve seen organizations, utilities, and decision makers putting the processes required for a just transition into practice.

McClenney spoke of revelations from the onset of COVID-19 in March 2020. Preventing utility shutoffs became critically important: people were losing jobs or forced to stay at home. They couldn’t come up with the money to pay their utility bills. While fighting utility shutoffs with Appalachian Voices, he saw a group of Knoxville organizations, including Knoxville Water and Energy for All, bringing attention to the fact that the shutoffs were not just a COVID problem. For some Black and brown communities, McClenney said, “keeping the lights on had always been an issue.” These grassroot groups’ advocacy expanded beyond the pandemic: they wanted energy and water recognized as human rights.

Klug asked the panelists how they feel about President Joe Biden’s performance with regard to just transitions in the energy sector — specifically, his January executive orders and recent bipartisan $1.2 trillion infrastructure bill

White-Williams cited a major concern with Biden’s policies: they don’t give enough attention to rural issues. In Sampson county here in North Carolina, massive hog farms overwhelmingly surround communities of color. North Carolina’s new Farm Act will allow Smithfield Foods to build a system to trap methane from hog waste to be processed and eventually used as renewable electricity. But residents living near hog farms already experience toxic water, unbearable stench, and heightened risk of other diseases, and this system would likely make the problem even worse. It’s a textbook example of an unjust energy transition. That’s why environmental and civil rights organizations have asked the EPA to intervene — to no avail, at least thus far. (White-Williams is featured in this article about the current state of affairs.) “Rural America is suffering,” White-Williams said. She wants to see federal agencies using their power to ensure a just energy transition.

McClenney echoed White-Williams’ concern about hog farms, adding that deaths have resulted from providing workers with limited information about the conditions they would be working in — especially those who don’t speak English and whose undocumented status puts them in a vulnerable position. 

On a different note, he thinks Biden’s expansions to Broadband and clean water are a step in the right direction. He stated that with North Carolina’s House Bill 951, which requires the Utilities Commission to cut emissions by 70% by 2030 (even more ambitious than Biden’s executive order, which seeks to cut US emissions in half by 2030), “there are opportunities right now to effect positive change — we just have to do a good job.” It’s about how we get to that carbon reduction goal.

Klug asked how people at universities — faculty, students, and staff alike — can contribute to this work in policy and in advocacy.

White-Williams told the audience to recognize that “having a degree does not make you an expert when you walk into these communities.” Community members have lived experience: they can tell policymakers and activists what they need, not the other way around. Change should be a partnership, and so should research: “Academics have a research question before they’ve even spoken to anyone.” Instead, “listen and learn from the people who have been there all their lives.”

Spenser invited the audience to think about “who the real experts are” in unique and different ways. Institutions like Duke are often separate from the communities they inhabit, serving as a sort of beacon on the hill. “We need to invert this paradigm,” he said.

McClenney added to Spenser’s criticism of schools like Duke, who “throw food out every day and hold dorm rooms empty during the summer while people go hungry and unhoused.” What’s needed is a fundamental reimagination of the university’s relationship to the community it inhabits. He also added to White-Williams’ point about research: it can be merely “another type of extraction” if not carried out in a just manner.

Klug asked the panelists whether we need to assess the impacts of energy policy differently through the lens of research.

McClenney flagged the words “affordability” and “reliability” in energy research, asking the audience to consider who that applies to. Affordability is not just about how rates compare to New York City or California, but whether someone has to forego insulin or go hungry in order to make a payment. By thinking through these words and what they really mean, we can “begin to understand impacts on a deeper level.”

Spenser implored researchers to use an intersectional lens: instead of considering economic impact and efficiency in isolation, to consider the way in which policies “contribute or ameliorate historic disparities.” In order to truly measure impact, efficacy, and outcome, researchers must be “historically aware and community invested.”

White-Williams agreed with McClenney and Spenser, asking researchers to consider whether policies are a “band-aid or a true fix.” She cited North Carolina’s Weatherization Assistance Program, which allocates tens of millions of dollars toward fixing “patched-up” homes that may have serious underlying problems. She wonders whether it may be better to simply spend the money on programs to place people in housing that is “actually livable.”

Klug opened the panel to questions. One audience member asked the panelists what concrete steps they recommend in order to “harness the power of diversity.”

White-Williams reiterated the importance of working with impacted communities, stressing the need for local leaders who can serve as experts on the needs of the community. Elected officials might “sacrifice the needs of these communities for some other interest,” but local advocates can apply pressure where needed.

Spenser pushed back on the question, stating that instead of urgency and speed, “we need to commit to a longer process” — honoring historical legacies and “spending time helping people understand what the conversation is.” 

“Environmental policy isn’t sexy,” Spenser concluded. (“Except,” he added, “for pipelines.”)

Maybe not. But it’s important that it gets made — and that it gets made justly.

Post by Zella Hanson

250,000-Year-Old Child Adds to the Mystery of Our Human Origins

Based on the small size of Leti’s skull and on the combination of baby teeth and unerupted adult teeth, researchers estimate that the Homo naledi child would have been 4-6 years old.

Look at the palm of your hand and spread your fingers wide. Now imagine squeezing your body through a gap narrower than the distance between the tip of your thumb and the tip your pinkie finger. Let’s make this a bit worse: the gap is in complete darkness, its walls are rough stone, and all you have is a tiny headlamp. Ok, now that you are there, all you have to do is carefully find and recover dime-sized fragments of an invaluable treasure.

That’s how researchers recovered the first Homo naledi child’s skull ever to be found.

The finding was revealed this week in two papers published in the journal PaleoAnthropology by an international team of 21 researchers.

Homo naledi are possibly our most mysterious long-lost cousins. They are an ancient human relative that lived in what is now South Africa, approximately 350 to 250 thousand years ago. They were first discovered in the Rising Star Cave system in 2013, in a research expedition led by Lee Berger, Professor and chair of Palaeo-Anthropology and Director of the Centre for Exploration of the Deep Human Journey at the University of Witwatersand.

The research team, which includes Steven Churchill, professor of evolutionary anthropology at Duke, named the child Leti (pronounced Let-e), after the Setswana word “letimela” meaning “the lost one”.

Leti was found in one of the previously unexplored narrow fissures that radiate from Rising Star’s known chambers. His resting site was a 15 cm wide and 80 cm long gap where only the smallest (and bravest) of explorers could fit.

Explorer Becca Peixoto wedges herself between cave rock walls to get to Leti’s skull.

Marina Elliot, lead author of the first paper and one of the explorers to first discover Homo naledi, said in a press conference that excavating Leti’s remains required explorers to wedge themselves practically upside down between two rock walls.

Finding yet another fossil in a prolific site may not seem groundbreaking, but finding a child’s skull is a major achievement. First of all, children’s bones are thin and fragile, and rarely withstand the test of time.

Second, finding a child’s skull gives researchers a precious glimpse into the development of Homo naledi.

“A child’s skull allows us to study how Homo naledi grew and developed, and how their growth rate and schedule compares to other hominid species, and to our own,” Churchill said.

In addition to skull fragments, researchers also recovered two worn baby teeth and four unworn adult teeth that were yet to erupt. These findings show that Leti would have been between four and six years old at the time of her or his death.

Based on similarities between the soil of the fissure where Leti was found and the better-known areas of the cave, Tebogo Makhubela, senior lecturer of Geology at the University of Johannesburg and author of the papers, estimated that Leti has been hidden in Rising Star for over 250,000years.

The discovery of Leti’s skull also deepens the mystery of how Homo naledi’s remains ended up in such a deep, dark, and treacherous cave.

Berger’s team had previously hypothesized that the first 15 Homo naledi individuals found in Rising Star had been disposed there by their own species, as a burial. This hypothesis created an uproar: could a small-brained hominin from over 300,000years ago bury their dead, just like we do?

Leti’s skull was found on a small shelf at the back of the cave’s fissure. No other bones were found, suggesting that Leti’s head may have been deliberately placed there. Leti, as well as all other Homo naledi fossils ever found, showed no evidence of being dragged by predators, carried by water, or tumbled around in any other way.

“Those were social individuals. Seeing one of their own being picked apart by animals could have been very distressing,” Churchill said. “Purposeful disposal of their bodies still seems like the most likely explanation.”

Berger is undeterred by nay-sayers. “This is science,” Berger said at a press conference. “We will continue testing and challenging our hypotheses with every piece of data that we get.”

The researchers hope that other teams around the world will study Leti and other Homo naledi fossils. To that end, Leti’s skull was CT-scanned, and its scans can be downloaded from Morphosource, an open access repository of museum specimens’ 3D scans hosted at Duke University.

Leti will probably not be the last treasure to come out of Rising Star’s spider web of narrow passages.

“I can’t wait to go back to South Africa and see what else is waiting for us in that cave,” said Juliet Brophy, Professor of Geography and Anthropology at Louisiana State University and lead author of the paper describing Leti’s skull.

“This finding makes us remember that exploration is always worth doing,” said Elliot, who is a researcher at Simon Fraser University and Witwatersand University. “There is a lot still out there to be found”.

The Rising Star cave system is known for being extremely dangerous to explore.

Elliot et al. was funded by the National Geographic Society, the Lyda Hill Foundation, the South African National Research Foundation, and the Gauteng Provincial Government, for funding the discovery, recovery and ongoing analyses of the material. Additional support was provided by ARC (DP140104282).

Brophy et al. was funded by the National Geographic Society, the Lyda Hill Foundation, the South African National Research Foundation, the South African Centre for Excellence in Palaeosciences, The University of the Witwatersrand, the Vilas Trust, the Fulbright Scholar Program, Louisiana State University, North Carolina State University, the Texas A&M University College of Liberal Arts Seed Grant program and the Texas A&M College of Liberal Arts Cornerstone Faculty Fellowship.

Citations:

“Expanded Explorations of the Dinaledi Subsystem, Rising Star Cave System, South Africa.” Marina C. Elliot,Tebogo V. Makhubela, Juliet K. Brophy, Steven E. Churchill, Becca Peixoto, Elen M. Feuerriegel, Hannah Morris, Rick Hunter, Steven Tucker, Dirk Van Rooyen, Maropeng Ramalepa, Mathabela Tsikoane,Ashley Kruger, Carl Spander, Jan Kramers, Eric Roberts, Paul H.G.M. Dirks,John Hawks,Lee R. Berger. PaleoAnthropology, November 2021. DOI: https://doi.org/10.48738/2021.iss1.68.

“Immature Hominin Craniodental Remains From a New Localityin the Rising Star Cave System, South Africa.” Juliet K. Brophy, Marina C. Elliot, Darryl J. De Ruiter, Debra R. Bolter, Steven E. Churchill, Christopher S. Walker, John Hawks, Lee Berger. PaleoAnthropology, November 2021, DOI: https://doi.org/10.48738/2021.iss1.64.

By Marie-Claire Chelini
By Marie-Claire Chelini

In the World Capital of Vanilla Production, Nearly Three out of Four Farmers Say They Don’t Have Enough to Eat

A new study investigates why and what they can do about it

Madagascar, famous for its lemurs, is home to almost 26 million people. Despite the cultural and natural riches, Madagascar is one of the poorest countries in the world. Over 70% of Malagasy people are farmers, and food security is a constant challenge. Rice is the most important food crop, but lately an internationally-prized crop has taken center stage: vanilla. Most of the world’s best quality vanilla comes from Madagascar. While most Malagasy farmers live on less than $2 per day, selling vanilla can make some farmers rich beyond their dreams, though these profits come with a price, and a new study illustrates it is not enough to overcome food insecurity.

In a paper published June 25, 2021 in the journal Food Security, a team of scientists collaborating between Duke University and in Madagascar set out to investigate the links between natural resource use, farming practices, socioeconomics, and food security. Their recently published article in the journal Food Security details intricate interactions between household demographics, farming productivity, and the likelihood of experiencing food shortages.

Vanilla beans, Wikimedia Commons

The team interviewed almost 400 people in three remote rural villages in an area known as the SAVA region, an acronym for the four main towns in the region: Sambava, Andapa, Vohemar, and Antalaha. The Duke University Lemur Center has been operating conservation and research activities in the SAVA region for 10 years. By partnering with local scientists, the team was able to fine-tune the way they captured data on farming practices and food security. Both of the Malagasy partners are preparing graduate degrees and expanding their research to lead the next generation of local scientists.

Farmers harvesting the rice fields in Madagascar. Credit: Wikimedia Commons.

The international research team found that a significant proportion of respondents (up to 76%) reported that they experienced times during which did not have adequate access to food during the previous three years. The most common cause that they reported was small land size; most respondents estimated they owned less than 4 hectares of land (<10 acres), and traditional farming practices including the use of fire to clear the land are reducing yields and leading to widespread erosion. The positive side is that the more productive the farm, especially in terms of rice and vanilla harvests, the lower the probability of food insecurity. There was an interaction between rice and vanilla harvests, such that those farmers that produced the most rice had the lowest probability of food insecurity, even when compared to farmers who grew more vanilla but less rice. Though vanilla can bring in a higher price than rice, there are several factors that make vanilla an unpredictable crop.

The vanilla market is subject to extreme volatility, with prices varying by an order of magnitude from year to year. Vanilla is also a labor- and time-intensive crop; it requires specific growing conditions of soil, humidity, and shade, it takes at least 3 years from planting to the first crop. Without the natural pollinators in its home range of Mexico, Malagasy vanilla requires hand pollination by the farmers, and whole crops can be devastated by natural disasters like disease outbreaks and cyclones. Further, the high price of vanilla brings with it ‘hot spending,’ resulting in cycles of boom and bust for impoverished farmers. Because of the high price, vanilla is often stolen, which leads farmers to spend weeks in their fields guarding the vanilla from thieves before harvesting. It also leads to early harvests, before the vanilla beans have completely ripened, which degrades the quality of the final products and can exacerbate price volatility.

In addition to the effects of farming productivity on the probability of food insecurity, the research revealed that household demographics, specifically the number of people living in the household, had an interactive effect with land size. Those farmers that had larger household sizes (up to 10 in this sample) had a higher probability of experiencing food insecurity than smaller households, but only if they had small landholdings. Those larger families that had larger landholdings had the lowest food insecurity. These trends have been documented in many similar settings, in which larger landholdings require more labor, and family labor is crucial to achieving food sovereignty.

The results have important implications for sustainable development in this system.  The team found that greater rice and vanilla productivity can significantly reduce food insecurity. Therefore, a greater emphasis on training in sustainable, and regenerative, practices is necessary. There is momentum in this direction, with new national-level initiatives to improve rice production and increase farmers’ resilience to climate change. Further, many international aid organizations and NGOs operating in Madagascar are already training farmers in new, regenerative agriculture techniques. The Duke Lemur Center is partnering with the local university in the SAVA region to develop extension services in regenerative agriculture techniques that can increase food production while also preserving and even increasing biodiversity. With a grant from the General Mills, the Duke Lemur Center is developing training modules and conducting workshops with over 200 farmers to increase the adoption of regenerative agriculture techniques.

Further, at government levels, improved land tenure and infrastructure for securing land rights is needed because farmers perceive that the greatest cause of food insecurity is their small landholdings. Due to the current land tenure infrastructure, securing deeds and titles to land is largely inaccessible to rural farmers. This can lead to conflicts over land rights, feelings of insecurity, and little motivation to invest in more long-term sustainable farming strategies (e.g., agroforestry). By improving the ability of farmers to secure titles to their land, as well as access agricultural extension services, farmers may be able to increase food security and productivity, as well as increased legal recognition and protection.

To move forward as a global society, we must seek to achieve the United Nation (UN) Sustainable Development Goals (SDGs). One of the SDGs is Goal #2, Zero Hunger. There are almost one billion people in the world who do not have adequate access to enough safe and nutritious food. This must change if we expect to develop sustainably in the future. Focusing on some of the hardest cases, Madagascar stands out as a country with high rates of childhood malnutrition, prevalence of anemia, and poverty. This year, more than one million people are negatively impacted by a three-year drought that has resulted in mass famine and a serious need for external aid. Sadly, these tragedies occur in one of the most biodiverse places on earth, where 80-90% of the species are found no where else on earth. This paradox results in a clash between natural resource conservation and human wellbeing.

Achieving the UN’s SDGs will not be easy; in fact, we are falling far short of our targets after the first decade. The next ten years will determine if we meet these goals or not, and our collective actions as a global society will dictate whether we transform our society for a sustainable future or continue with the self-destructive path we have been following. Further research and interventions are still needed to conserve biodiversity and improve human livelihoods.

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