A Duke team looks at the math behind COVID’s waves as new coronavirus variants continue to emerge.Credit: @ink-drop
DURHAM, N.C. — First it was Alpha. Then Delta. Now Omicron and its alphabet soup of subvariants. In the three years since the coronavirus pandemic started, every few months or so a new strain seems to go around, only to be outdone by the next one.
If the constant rise and fall of new coronavirus variants has left you feeling dizzy, you’re not alone. But where most people see a pandemic roller coaster, one Duke team sees a mathematical pattern.
In a new study, a group of students led by Duke mathematician Rick Durrett studied the calculus behind the pandemic’s waves.
Published Nov. 2022 in the journal Proceedings of the National Academy of Sciences, their study got its start as part of an 8-week summer research program called DOmath, now known as Math+, which brings undergraduates together to collaborate on a faculty-led project.
Their mission: to build and analyze simple mathematical models to understand the spread of COVID-19 as one strain after another popped up and then rose to outcompete the others.
In an interview about their research, project manager and Duke Ph.D. student Hwai-Ray Tung pointed to a squiggly line showing the number of confirmed COVID cases per capita in the U.S. between January 2020 and October 2022.
The COVID-19 pandemic has unfolded in waves. Adapted from The New York Times, July 18, 2022
“You can see very distinct humps,” Tung said.
The COVID pandemic has unfolded in a series of surges and lulls — spikes in infection followed by downturns in case counts.
The ups and downs are partly explained by factors such as behavior, relaxation of public policies, and waning immunity from vaccines. But much of the roller coaster has been driven by changes to the coronavirus itself.
All viruses change over time, evolving mutations in their genetic makeup as they spread and replicate. Most mutations are harmless, but every so often some of them give the virus an edge: Enabling it to break into cells more easily than other strains, better evade immunity from vaccines and past infection, or make more copies of itself in order to spread more effectively.
Take the Delta variant, for example. When it first started going around in the U.S. in May 2021, it was responsible for just 1% of COVID cases. But thanks to mutations that helped the virus evade antibodies and infect cells more easily, it quickly tore across the country. Within two months it had outcompeted all the other variants and rose to the top spot, causing 94% of new infections.
“The natural question to ask is: What’s going on with the transition between these different variants?” Tung said.
For their study the team developed a simple epidemic model called an SIR model, which uses differential equations to compute the spread of disease over time.
SIR models work by categorizing individuals as either susceptible to getting sick, currently infected, or recovered. The team modified this model to have two types of infected individuals and two types of recovered individuals, one for each of two circulating strains.
The model assumes that each infectious person spreads the virus to a certain number of new people per day (while sparing others), and that, each day, a certain fraction of the currently infected group recovers.
In the study, the team applied the SIR model to data from a database called GISAID, which contains SARS-CoV-2 virus sequences from the pandemic. By looking at the coronavirus’s genetic code, researchers can tell which variants are causing infection.
Study co-author Jenny Huang ’23 pointed to a series of S-shaped curves showing the fraction of infections due to each strain from one week to the next, from January 2021 to June 2022.
When they plotted the data as points on a graph, they found that it followed a logistic differential equation as each new variant emerged, rose steeply, and — within six to 10 weeks — quickly displaced its predecessors, only to be taken over later by even more aggressive or contagious strains.
Durrett said it’s the mathematical equivalent of something biologists call a selective sweep, when natural selection increases a variant’s frequency from low to high, until nearly everyone getting stick is infected with the same strain.
“I’ve been interested in epidemic modeling since the end of freshman year when COVID started,” said Huang, a senior who plans to pursue a Ph.D. in statistics next year with support from a prestigious Quad Fellowship.
They’re not all typical math majors, Durrett said of his team. Co-author Sofia Hletko, ’25, was a walk-on to the rowing team. Laura Boyle ’24 was a Cameron Crazie.
For some team members it was their first experience with mathematical research: “I came in having no idea what a differential equation was,” Boyle said. “And by the end, I was the person in the group explaining that part of our presentation to everyone.”
Boyle says one question she keeps getting asked is: what about the next COVID surge?
“It’s very hard to say what will happen,” Boyle said.
The teams says their research can’t predict future waves. Part of the reason is the scanty data on the actual number of infections.
Countries have dialed back on their surveillance testing, and fewer places are doing the genomic sequencing necessary to identify different strains.
“We don’t know the nature of future mutations,” Durrett said. “Changes in people’s behavior will have a significant impact too.”
“The point of this paper wasn’t to predict; rather it was to explain why the waves were occurring,” Huang said. “We were trying to explain a complicated phenomenon in a simple way.”
This research was supported by a grant from the National Science Foundation (DMS 1809967) and by Duke’s Department of Mathematics.
CITATION: “Selective Sweeps in SARS-CoV-2 Variant Competition,” Laura Boyle, Sofia Hletko, Jenny Huang, June Lee, Gaurav Pallod, Hwai-Ray Tung, and Richard Durrett. Proceedings of the National Academy of Sciences, Nov. 3, 2022. DOI: 10.1073/pnas.2213879119.
DURHAM, N.C. — English professor Charlotte Sussman doesn’t get much time in her role as department chair to work on her latest book project, an edited collection of essays on migration in and out of Europe.
“At least not during daylight hours,” Sussman said.
But a recent workshop brought a welcome change to that. Sussman was one of 22 faculty who gathered Dec. 13 for an end-of-semester writing retreat hosted by the Duke Faculty Write Program.
Duke faculty and staff gather for an end-of-semester writing retreat.
Most of them know all too well the burnout faculty and students face at the end of the semester. But for a few precious hours, they hit pause on the constant onslaught of emails, meetings, grading and other duties to work alongside fellow writers.
The participants sat elbow-to-elbow around small tables in a sunlit room at the Duke Integrative Medicine Center. Some scribbled on pads of paper; others peered over their laptops.
Each person used the time to focus on a specific writing project. Sussman aimed to tackle an introduction for her 34-essay collection. Others spent the day working on a grant application, a book chapter, a course proposal, a conference presentation.
Jennifer Ahern-Dodson, Ph.D.
“We have so many negative associations with writing because there’s always something more to do,” said associate professor of the practice Jennifer Ahern-Dodson, who directs the program. “I want to change the way people experience writing.”
Ahern-Dodson encouraged the group to break their projects into small, specific tasks as they worked toward their goals. It might be reading a journal article, drafting an outline, organizing some notes, even just creating or finding a file.
After a brief workshop, she kicked off a 60-minute writing session. “Now we write!” she said.
The retreat is the latest installment in a series that Ahern-Dodson has been leading for over 10 years. In a typical week, most of these scholars wouldn’t find themselves in the same room. There were faculty and administrators from fields as diverse as history, African and African American Studies, law, psychology, classics, biostatistics. New hires sitting alongside senior scholars with decades at Duke.
Peggy Nicholson, J.D., Clinical Professor of Law, writing alongside colleagues from across campus
“I really like the diversity of the group,” said Carolyn Lee, Professor of the Practice of Asian and Middle Eastern Studies. “It’s a supportive environment without any judgement. They all have the same goal: they want to get some writing done.”
Sussman said such Faculty Write program get-togethers have been “indispensable” to bringing some of her writing projects over the finish line.
Participants say the program not only fosters productivity, but also a sense of connection and belonging. Take Cecilia Márquez, assistant professor in the Duke History Department. She joined the Duke faculty in 2019, but within months the world went into COVID-19 lockdown.
“This was my way to meet colleagues,” said Márquez, who has since started a writing group for Latinx scholars as an offshoot.
The writing retreats are free for participants, thanks to funding from the Office of the Dean of Trinity College of Arts and Sciences and the Thompson Writing Program. Participants enjoy lunch, coaching and community in what’s normally a solitary activity.
“I appreciate the culture of collaboration,” said David Landes, who came to Duke this year as Assistant Professor of the Practice in Duke’s Thompson Writing Program. “In the humanities our work is intensely individualized.”
Assistant Professor of Biostatistics & Bioinformatics Hwanhee Hong (left) and Adam Rosenblatt, Associate Professor of the Practice in International Comparative Studies (right)
Retreats are one of many forms of support offered by the Faculty Write program: there are also writing groups and workshops on topics such as balancing teaching and scholarship or managing large research projects.
“One of the distinguishing features of Faculty Write is the community that extends beyond one event,” Ahern-Dodson said. “Many retreats are reunions.”
After two hours of writing, Ahern-Dodson prompted the group to take a break. Some got up to stretch or grab a snack; others stepped outside to chat or stroll through the center’s labyrinth at the edge of Duke Forest.
It’s more than just dedicated writing time, Ahern-Dodson said. It’s also “learning how to work with the time they have.”
The retreats offer tips from behavioral psychology, writing studies, and other disciplines on time management, motivation, working with reader feedback, and other topics.
As they wrap up the last writing session of the day, Ahern-Dodson talks about how to keep momentum.
“Slow-downs and writing block are normal,” Ahern-Dodson said. Maybe how you wrote before isn’t working anymore, or you’re in a rut. Perhaps you’re not sure how to move forward, or maybe writing simply feels like a slog.
“There are some things you could try to get unstuck,” Ahern-Dodson said. Consider changing up your routine: when and where you write, or how long each writing session lasts.
“Protect your writing time as you would any other meeting,” Ahern-Dodson said.
Sharing weekly goals and accomplishments with other people can help too, she added.
“Celebrate each win.”
Ultimately, Ahern-Dodson says, the focus is not on productivity but on meaning, progress and satisfaction over time.
“It’s all about building a sustainable writing practice,” she said.
Ahern-Dodson leads an end-of-semester writing retreat for Duke scholars.
Coming soon: On Friday, Jan. 27 from 12-1 p.m., join Vice Provost for Faculty Advancement Abbas Benmamoun for a conversation about how writing works for him as a scholar and administrator. In person in Rubenstein Library 249 (Carpenter Fletcher Room)
Get Involved: Faculty and staff are invited to sign up for writing groups for spring 2023 here.
The healthcare industry and academic medicine are excited about the potential for artificial intelligence — really clever computers — to make our care better and more efficient.
The students from Duke’s Health Data Science (HDS) and AI Health Data Science Fellowship who presented their work at the 2022 Duke AI Health Poster Showcase on Dec. 6 did an excellent job explaining their research findings to someone like me, who knows very little about artificial intelligence and how it works. Here’s what I learned:
Artificial intelligence is a way of training computer systems to complete complex tasks that ordinarily require human thinking, like visual categorization, language translation, and decision-making. Several different forms of artificial intelligence were presented that do healthcare-related things like sorting images of kidney cells, measuring the angles of a joint, or classifying brain injury in CT scans.
Talking to the researchers made it clear that this technology is mainly intended to be supplemental to experts by saving them time or providing clinical decision support.
Meet Researcher Akhil Ambekar
Akhil standing next to his poster “Glomerular Segmentation and Classification Pipeline Using NEPTUNE Whole Slide Images”
Akhil Ambekar and team developed a pipeline to automate the classification of glomerulosclerosis, or scarring of the filtering part of the kidneys, using microscopic biopsy images. Conventionally, this kind of classification is done by a pathologist. It is time-consuming and limited in terms of accuracy and reproducibility of observations. This AI model was trained by providing it with many questions and corresponding answers so that it could learn how to correctly answer questions. A real pathologist oversaw this work, ensuring that the computer’s training was accurate.
Akil’s findings suggest that this is a feasible approach for machine classification of glomerulosclerosis. I asked him how this research might be used in medicine and learned that a program like this could save expert pathologists a lot of time.
What was Akhil’s favorite part of this project? Engaging in research, experimenting with Python and running different models, trying to find what works best.
Meet Researcher Irene Tanner
Irene Tanner and her poster, “Developing a Deep Learning Pipeline to Measure the Hip-Knee-Ankle Angle in Full Leg Radiographs”
The research Irene Tanner and her team have done aims to develop a deep learning-based pipeline to calculate hip-knee-ankle angles from full leg x-rays. This work is currently in progress, but preliminary results suggest the model can precisely identify points needed to calculate the angles of hip to knee to ankle. In the future, this algorithm could be applied to predict outcomes like pain and physical function after a patient has a joint replacement surgery.
What was Irene’s favorite part of this project? Developing a relationship with mentor, Dr. Maggie Horn, who she said provided endless support whenever help was needed.
Meet Researcher Brian Lerner
Brian Lerner and his poster, “Using Deep Learning to Classify Traumatic Brain Injury in CT Scans”
Brian Lerner and his team investigated the application of deep learning to standardize and sharpen diagnoses of traumatic brain injury (TBI) from Computerized Tomography (CT) scans of the brain. Preliminary findings suggest that the model used (simple slice) is likely not sufficient to capture the patterns in the data. However, future directions for this work might examine how the model could be improved. Through this project, Brian had the opportunity to shadow a neurologist in the ER and speculated upon many possibilities for the use of this research in the field.
What was Brian’s favorite part of this project? Shadowing neurosurgeon Dr. Syed Adil at Duke Hospital and learning what the real-world needs for this science are.
Many congratulations to all who presented at this year’s AI Health Poster Showcase, including the many not featured in this article. A big thanks for helping me to learn about how AI Health research might be transformative in answering difficult problems in medicine and population health.
Saxicolous lichens (lichens that grow on stones) from the Namib Desert, and finger lichen, Dactylina arctica (bottom left insert), common in the Arctic, on display in Dr. Jolanta Miadlikowska’s office. The orange color on some of the lichen comes from metabolites, or secondary chemicals produced by different lichen species. The finger lichen is hollow.
Lichens are everywhere—grayish-green patches on tree bark on the Duke campus, rough orange crusts on desert rocks, even in the Antarctic tundra. They are “pioneer species,” often the first living things to return to barren, desolate places after an extreme disturbance like a lava flow. They can withstand extreme conditions and survive where nearly nothing else can. But what exactly are lichens, and why does Duke have 160,000 of them in little envelopes? I reached out to Dr. Jolanta Miadlikowska and Dr. Scott LaGreca, two lichen researchers at Duke, to learn more.
Dr. Jolanta Miadlikowska looking at lichen specimens under a dissecting microscope. The pale, stringy lichen on the brown bag is whiteworm lichen (Thamnolia vermicularis), used to make “snow tea” in parts of China.
According to Miadlikowska, a senior researcher, lab manager, and lichenologist in the Lutzoni Lab (and one of the Instructors B for the Bio201 Gateway course) at Duke, lichens are “obligate symbiotic associations,” meaning they are composed of two or more organisms that need each other. All lichens represent a symbiotic relationship between a fungus (the “mycobiont”) and either an alga or a cyanobacterium or both (the “photobiont”). They aren’t just cohabiting; they rely on each other for survival. The mycobiont builds the thallus, which gives lichen its structure. The photobiont, on the other hand, isn’t visible—but it is important: it provides “food” for the lichen and can sometimes affect the lichen’s color. The name of a lichen species refers to its fungal partner, whereas the photobiont has its own name.
Lichen viewed through a dissecting microscope. The black speckles visible on some of the orange lichen lobes are a “lichenicolous” fungus that can grow on top of lichen. There are also “endolichenic fungi… very complex fungal communities that live inside lichen,” Miadlikowska says. “We don’t see them, but they are there. And they are very interesting.”
Unlike plants, fungi can’t perform photosynthesis, so they have to find other ways to feed themselves. Many fungi, like mushrooms and bread mold, are saprotrophs, meaning they get nutrients from organic matter in their environment. (The word “saprotroph” comes from Greek and literally means “rotten nourishment.”) But the fungi in lichens, Miadlikowska says, “found another way of getting the sugar—because it’s all about the sugar—by associating with an organism that can do photosynthesis.” More often than not, that organism is a type of green algae, but it can also be a photosynthetic bacterium (cyanobacteria, also called blue-green algae). It is still unclear how the mycobiont finds the matching photobiont if both partners are not dispersed together. Maybe the fungal spores (very small fungal reproductive unit) “will just sit and wait” until the right photobiont partner comes along. (How romantic.) Some mycobionts are specialists that “can only associate with a few or a single partner—a ‘species’ of Nostoc [a cyanobacterium; we still don’t know how many species of symbiotic and free-living Nostoc are out there and how to recognize them], for example,” but many are generalists with more flexible preferences.
Two species of foliose (leaf-like) lichens from the genus Peltigera. In the species on the left (P. canina), the only photobiont is a cyanobacterium from the genus Nostoc, making it an example of bi-membered symbiosis. In the species on the right (P.aphthosa), on the other hand, the primary photobiont is a green alga (which is why the thallus is so green when wet). In this case, Nostoc is a secondary photobiont contained only in the cephalodia—the dark, wart-like structures on the surface. With two photobionts plus the mycobiont, this is an example of tri-membered symbiosis.
Lichens are classified based on their overall thallus shape. They can be foliose (leaf-like), fruticose (shrubby), or crustose (forming a crust on rocks or other surfaces). Lichens that grow on trees are epiphytic, while those that live on rocks are saxicolous; lichens that live on top of mosses are muscicolous, and ground-dwelling lichens are terricolous. Much of Miadlikowska’s research is on a group of cyanolichens (lichens with cyanobacteria partners) from the genus Peltigera. She works on the systematics and evolution of this group using morphology-, anatomy-, and chemistry-based methods and molecular phylogenetic tools. She is also part of a team exploring biodiversity, ecological rules, and biogeographical patterns in cryptic fungal communities associated with lichens and plants (endolichenic and endophytic fungi). She has been involved in multiple ongoing NSF-funded projects and also helping graduate students Ian, Carlos, Shannon, and Diego in their dissertation research. She spent last summer collecting lichens with Carlos and Shannon and collaborators in Alberta, Canada and Alaska. If you walk in the sub basement of the Bio Sciences building where Bio201 and Bio202 labs are located, check out the amazing photos of lichens (taken by Thomas Barlow, former Duke undergraduate) displayed along the walls! Notice Peltigera species, including some new to science, described by the Duke lichen team.
Lichens have value beyond the realm of research, too. “In traditional medicine, lichens have a lot of use,” Miadlikowska says. Aside from medicinal uses, they have also been used to dye fabric and kill wolves. Some are edible. Miadlikowska herself has eaten them several times. She had salad in China that was made with leafy lichens (the taste, she says, came mostly from soy sauce and rice vinegar, but “the texture was coming from the lichen.”). In Quebec, she drank tea made with native plants and lichens, and in Scandinavia, she tried candied Cetraria islandica lichen (she mostly tasted the sugar and a bit of bitterness, but once again, the lichen’s texture was apparent).
In today’s changing world, lichens have another use as well, as “bioindicators to monitor the quality of the air.” Most lichens can’t tolerate air pollution, which is why “in big cities… when you look at the trees, there are almost no lichens. The bark is just naked.” Lichen-covered trees, then, can be a very good sign, though the type of lichen matters, too. “The most sensitive lichens are the shrubby ones… like Usnea,” Miadlikowska says. Some lichens, on the other hand, “are able to survive in anthropogenic places, and they just take over.” Even on “artificial substrates like concrete, you often see lichens.” Along with being very sensitive to poor air quality, lichens also accumulate pollutants, which makes them useful for monitoring deposition of metals and radioactive materials in the environment.
Dr. Scott LaGreca with some of the 160,000 lichen specimens in Duke’s herbarium.
LaGreca, like Miadlikoska, is a lichenologist. His research primarily concerns systematics, evolution and chemistry of the genus Ramalina. He’s particularly interested in “species-level relationships.” While he specializes in lichens now, LaGreca was a botany major in college. He’d always been interested in plants, in part because they’re so different from animals—a whole different “way of being,” as he puts it. He used to take himself on botany walks in high school, and he never lost his passion for learning the names of different species. “Everything has a name,” he says. “Everything out there has a name.” Those names aren’t always well-known. “Some people are plant-blind, as they call it…. They don’t know maples from oaks.” In college he also became interested in other organisms traditionally studied by botanists—like fungi. When he took a class on fungi, he became intrigued by lichens he saw on field trips. His professor was more interested in mushrooms, but LaGreca wanted to learn more, so he specialized in lichens during grad school at Duke, and now lichens are central to his job. He researches them, offers help with identification to other scientists, and is the collections manager for the lichens in the W.L. and C.F. Culberson Lichen Herbarium—all 160,000 of them.
The Duke Herbarium was founded in 1921 by Dr. Hugo Blomquist. It contains more than 825,000 specimens of vascular and nonvascular plants, algae, fungi, and, of course, lichens. Some of those specimens are “type” specimens, meaning they represent species new to science. A type specimen essentially becomes the prototype for its species and “the ultimate arbiter of whether something is species X or not.” But how are lichens identified, anyway?
Lichenologists can consider morphology, habitat, and other traits, but thanks to Dr. Chicita Culberson, who was a chemist and adjunct professor at Duke before her retirement, they have another crucial tool available as well. Culbertson created a game-changing technique to identify lichens using their chemicals, or metabolites, which are often species-specific and thus diagnostic for identification purposes. That technique, still used over fifty years later, is a form of thin-layer chromatography. The process, as LaGreca explains, involves putting extracts from lichen specimens—both the specimens you’re trying to identify and “controls,” or known samples of probable species matches—on silica-backed glass plates. The plates are then immersed in solvents, and the chemicals in the lichens travel up the paper. After the plates have dried, you can look at them under UV light to see if any spots are fluorescing. Then you spray the plates with acid and “bake it for a couple hours.” By the end of the process, the spots of lichen chemicals should be visible even without UV light. If a lichen sample has traveled the same distance up the paper as the control specimen, and if it has a similar color, it’s a match. If not, you can repeat the process with other possible matches until you establish your specimen’s chemistry and, from there, its identity. Culberson’s method helped standardize lichen identification. Her husband also worked with lichens and was a director of the Duke Gardens.
Thin-layer chromatography plates in Dr. LaGreca’s office. The technique, created by Dr. Chicita Culberson, helps scientists identify lichens by comparing their chemical composition to samples of known identity. Each plate was spotted with extracts from different lichen specimens, and then each was immersed in a different solvent, after which the chemicals in the extracts travel up the plate . Each lichen chemical travels a characteristic distance (called the “Rf value”) in each solvent. Here, the sample in column 1 on the rightmost panel matches the control sample in column 2 in terms of distance traveled up the page, indicating that they’re the same species. The sample in column 4, on the other hand, didn’t travel as far as the one in column 5 and has a different color. Therefore, those chemicals (and species) do not match.
LaGreca shows me a workroom devoted to organisms that are cryptogamic, a word meaning “hidden gametes, or hidden sex.” It’s a catch-all term for non-flowering organisms that “zoologists didn’t want to study,” like non-flowering plants, algae, and fungi. It’s here that new lichen samples are processed. The walls of the workroom are adorned with brightly colored lichen posters, plus an ominous sign warning that “Unattended children will be given an espresso and a free puppy.” Tucked away on a shelf, hiding between binders of official-looking documents, is a thin science fiction novel called “Trouble with Lichen” by John Wyndham.
The Culberson Lichen Herbarium itself is a large room lined with rows of cabinets filled with stacks upon stacks of folders and boxes of meticulously organized lichen samples. A few shelves are devoted to lichen-themed books with titles like Lichens De France and Natural History of the Danish Lichens.
Each lichen specimen is stored in an archival (acid-free) paper packet, with a label that says who collected it, where, and on what date. (“They’re very forgiving,” says LaGreca. “You can put them in a paper bag in the field, and then prepare the specimen and its label years later.”) Each voucher is “a record of a particular species growing in a particular place at a particular time.” Information about each specimen is also uploaded to an online database, which makes Duke’s collection widely accessible. Sometimes, scientists from other institutions find themselves in need of physical specimens. They’re in luck, because Duke’s lichen collection is “like a library.” The herbarium fields loan requests and trades samples with herbaria at museums and universities across the globe. (“It’s kind of like exchanging Christmas presents,” says LaGreca. “The herbarium community is a very generous community.”)
Duke’s lichen collection functions like a library in some ways, loaning specimens to other scientists and trading specimens with institutions around the world.
Meticulous records of species, whether in databases of lichens or birds or “pickled fish,” are invaluable. They’re useful for investigating trends over time, like tracking the spread of invasive species or changes in species’ geographic distributions due to climate change. For example, some lichen species that were historically recorded on high peaks in North Carolina and elsewhere are “no longer there” thanks to global warming—mountain summits aren’t as cold as they used to be. Similarly, Henry David Thoreau collected flowering plants at Walden Pond more than 150 years ago, and his samples are still providing valuable information. By comparing them to present-day plants in the same location, scientists can see that flowering times have shifted earlier due to global warming. So why does Duke have tens of thousands of dried lichen samples? “It comes down to the reproducibility of science,” LaGreca says. “A big part of the scientific method is being able to reproduce another researcher’s results by following their methodology. By depositing voucher specimens generated from research projects in herbaria like ours, future workers can verify the results” of such research projects. For example, scientists at other institutions will sometimes borrow Duke’s herbarium specimens to verify that “the species identification is what the label says it is.” Online databases and physical species collections like the herbarium at Duke aren’t just useful for scientists today. They’re preserving data that will still be valuable hundreds of years from now.
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!
“Crypto is scaling so quickly but security systems are still the same as they were in 2013.” Those are the words of Daniel Chong, a recent Duke student whose new startup aims to change that.
One of the largest challenges within cryptocurrency is security. The most impactful application of cryptocurrency thus far is decentralized finance (DeFi). DeFi eliminates intermediaries by allowing people and businesses to conduct financial transactions through blockchain technology as opposed to working through banks or other corporations. However, as a result, people are personally responsible for securing their assets.
When engaging with cryptocurrency people generally use a trading platform and a wallet. Cryptocurrency trading platforms like Coinbase, Binance, and Crypto.com allow people to buy and sell cryptocurrencies using USD or other cryptocurrencies. However, in order to use crypto, one must transfer some of it into a wallet.
As with conventional currency, crypto wallets are not required in order to use cryptocurrency but they allow individuals to store their tokens in one place, easily retrieve them and send it to other individuals or organizations (i.e. buying non-fungible tokens). Some of the most popular wallets include Coinbase wallet, Metamask, and Electrum.
Screenshot of a Metamask Wallet
These wallets are not only password-protected but provide each user with a seed phrase or a series of words generated by one’s cryptocurrency wallet. This phrase, like a password, provides access to the crypto associated with that wallet.
An example seed phrase
The catch is, if an individual gets locked out of their wallet and cannot remember or does not have access to their seed phrase, all of their money will be lost. This is a major problem in the space and people have lost millions of dollars to lost seed phrases and inaccessible wallets. In fact, 20% of all existing Bitcoin tokens have been misplaced.
Furthermore, in the past, it was already hard enough to secure one’s crypto wallets but now people have several wallets, each with their own unique seed phrase and passcodes making it all the more difficult.In the Fall of 2020, Daniel Chong, a Duke first-year at the time, identified this wallet security problem.
“Crypto is scaling so quickly but security systems are still the same as they were in 2013.”
Daniel Chong
Having grown up in Las Vegas, Chong was used to fast-paced environments and unique challenges. During high school, Chong started coding as a hobby.
“I just wanted to build something,” he explained
The first project he built was a website for a research paper he had in his high school psychology class. In 2018 Chong was introduced to solidity, a programming language that’s main purpose is to develop smart contracts for the Ethereum blockchain. If you are unfamiliar with blockchain, please refer to my previous article here.
Chong matriculated to Duke during a period of transition, the Fall of 2020. As a result of being sent home due to COVID-19 in the Spring and having to shift to online meetings, many on-campus clubs were struggling. Early on Chong met Manmit Singh, a Junior at the time and the President of the Duke Blockchain Lab.
Even though Chong was only a first-year, he had experience coding in solidity and ended up aiding Singh in revamping Duke Blockchain Lab so students could continue engaging with and learning about blockchain despite the pandemic. Additionally, he ran a virtual course on web3 and solidity development for other club members.
Despite the fact that Chong was attending classes, involved in clubs, and working part-time, he began talking to his brother Noah who was a senior at Georgia Tech about once again, building something.
After working on building a security solution for crypto wallets for about a year, Chong and his brother received venture capital funding for their startup Harpie: a simple crypto protection plan that scales with you.
Chong explained that venture capitalists are very excited about crypto right now, especially back in November of 2021 when crypto was in a bull market and bitcoin was at a market high of 60,000.
Harpie is a web app that allows users to connect all of their wallets to individualized protection plans. This means that if you have a Harpie protection plan and someone hacks your wallet or you get locked out, you can go to the Harpie web app and transfer your funds from the unusable wallet to a new one.
Additionally, users are able to choose the degree of security their Harpie account has. Users can regain access to their fund via email, phone, or (personal recommendation) 2-factor authentication. Ultimately, for $8.99/month you can protect as many wallets, with any sum of funds, as you want.
Why Harpie is a better backup Solution
After working for just over a year, Harpie launched on February 14th, 2022. The next weekend Chong and his brother headed to ETHDenver, the largest Ethereum conference, to promote Harpie and compete in the Hackathon. For those who are unfamiliar, hackathons are competitive, sprint-like events where computer programmers and others are involved in software development work to build something over a condensed period of time.
Over 10,000 people participated in the ETHDenver hackathon in person and over 30,000 participated virtually for over $1 million in bounties and prizes, as well as up to $2 million in investment capital.
While the teams had 36 hours to build a project, Chong and his brother managed to build there’s in 4-5 hours. They did this by quickly creating a front-runner bot/flash bot to help people avoid getting hacked by detecting and halting transactions to unauthorized addresses.
The brothers not only successfully built the bot but also placed top 10 in the overall hackathon and had the opportunity to present their project.
While presenting, Chong also received questions from Vitalik Buterin, the founder of Ethereum. He explained this as a very “nerve-wracking experience” and added that Buterin asked very technical questions such as what the miners’ extractable value would be.
Chong and his brother (left) onstage with Vitalik Buterin (right) presenting at ETHDenver
In the future, Chong would be open to entering more hackathons but right now is more interested in growing his startup. Currently, Chong is taking time off from school to focus on Harpie and to, ultimately, revolutionize security systems as they relate to online assets.
Graphics courtesy of Catherine Angst, Director of Communications in the Division of Experiential Education at Duke University.
Pre-pandemic, Duke undergraduates looking for a good summer experience might have seen something good at an in-person fair or maybe heard about an opportunity from a favorite professor. But there was a lot of luck involved.
Now, thanks to the Duke Summer Experiences database, which launched in late January, undergrads can view a variety of summer opportunities in one centralized place. They can search by area of interest, type of program, program cost, year in school, and several other filters.
“Duke Summer Experiences is a resource for all of Duke,” says Catherine Angst, Director of Communications in the Division of Experiential Education, “because it’s an easily searchable, permanent database that allows people to select the features of an opportunity that are important to them.”
Angst explains that the new database is “an evolution of the Duke summer opportunities fair and the ‘Keep Exploring’ project.”
In previous years, Duke organized an in-person fair with representatives from various summer programs. During the pandemic, the “Keep Exploring” project was created to “[provide] students with summer opportunities and mentorship during a time when not a lot of traditional opportunities were operating because of COVID.” The two programs joined forces, she said, and ultimately expanded into the Duke Summer Experiences website.
By aggregating opportunities into one place, the database should increase awareness and access for summer programs.
Dean Sarah Russell, Director of the Undergraduate Research Support Office, thinks this might be especially valuable for research opportunities, which she says tend to be less publicized. “Previously,” she says, “students might know about DukeEngage, GEO, or summer courses, but would have to rely on word of mouth or, if they were lucky, a tip from faculty or advisors to find out about smaller, lesser-known programs.”
Ms. Leigh Ann Muth-Waring, Assistant Director in Employer Relations at the Career Center, sees similar benefits to the new database: “Prior to the website’s creation, students had to actively search for information about summer programs by contacting individual departments on campus,” sometimes causing students to miss deadlines. The Duke Summer Experiences website, on the other hand, provides easy-to-navigate and up-to-date information.
Another goal of the Duke Summer Experiences database, Ms. Angst says, is to “build a community of practice where administrators can share best practices, resources, and lessons learned.”
Dr. Karen Weber, Executive Director of the Office of University Scholars and Fellows, hopes this will “enable administrators across campus to collaborate more effectively together and improve programmatic outcomes.” For instance, “They can communicate on shared initiatives, such as developing successful recruitment and marketing strategies, creating student applications, editing participation agreements, addressing student and administrative issues, engaging with faculty, and assessing programs.”
Along with making summer opportunities easier to find and encouraging administrative collaboration, Duke Summer Experiences is also beta-testing a new application process that would allow students to use one application to apply for multiple opportunities at once. Muth-Waring said the Duke Experiences Application “allows the student to complete one questionnaire with general information (name, major, etc.) which then can be used to apply to multiple Duke-sponsored summer programs.” It also provides links to other programs students might be interested in.
Ms. Angst also sees the new application system as a valuable tool. She hopes that it will reduce “application fatigue” among students looking for summer opportunities.
The Career Center is already using the new application platform for their summer Internship Funding Program, which encourages participation in unpaid or low-paying summer internships by providing financial support to students. According to Ms. Muth-Waring, the new application system “has helped us streamline our program’s application process so that it is easier and less burdensome for students.” Streamlining the process of finding summer opportunities is a major goal of the Summer Experiences website as well. Ultimately, Ms. Muth-Waring says, “both the Duke Summer Experiences Database and the Duke Experiences Application are creating an easier way for students to learn about and apply to university-sponsored summer programs, research opportunities, internships, and funding sources.” For students seeking summer opportunities through Duke, the Summer Experiences website can make the process easier.
One of downtown Durham’s most memorable landmarks, the Chesterfield building looks like it was aesthetically designed to maintain the country’s morale during World War II. On the former cigarette factory’s roof rests a brilliant red sign that’s visible from miles away:
But don’t mistake the building’s quaint exterior for antiquity: the Chesterfield Building is home to one of the nation’s most powerful quantum computers. Managed by the Duke Quantum Center, the computer is part of Duke’s effort to bolster the Scalable Quantum Computing Laboratory (SQLab).
On February 2nd, the lab’s director – Christopher Monroe – joined engineering professor Michael Reiter and English professor Charlotte Sussman in a Research Week panel to discuss the growing presence of computation at Duke and in research institutions across the country. (View the panel.)
Chris Monroe
Monroe opened by detailing the significance of quantum computing in the modern world. He explained that quantum mechanics are governed by two golden rules: first, that quantum objects are waves and can be in superposition, and second, that the first rule only applies when said objects are not being measured.
The direct impact of quantum mechanics is that electrons can be in two orbits at the same time, which revolutionizes computing. Quantum computers factor numbers exponentially faster than classical computers, converge to more desirable solutions in optimization problems and have been shown to bolster research in fields like biomolecular modeling.
Still, Monroe insists that the future reach of quantum computing is beyond anyone’s current understanding. Says Monroe, “quantum computing is an entirely new way of dealing with information, so we don’t know all the application areas it will touch.” What we do know, he says, is that quantum computers are poised to take over where conventional computers and Moore’s Law leave off.
While Monroe discussed computing innovations, Michael Reiter – James B. Duke Professor of Computer Science and Electrical and Computer Engineering – demonstrated the importance of keeping computing systems safe. By pointing to the 2010 Stuxnet virus, a series of cyberattacks against Iranian nuclear centrifuges, and the 2017 Equifax Data Breach, which stole the records of 148 million people, Dr. Reiter provided evidence to show that modern data systems are vulnerable and attractive targets for cyber warfare.
Michael Reiter
To show the interdisciplinary responsibilities associated with the nation’s cybersecurity needs, Reiter posed two questions to the audience. First, what market interventions are appropriate to achieve more accountability for negligence in cybersecurity defenses? Second, what are the rules of war as it relates to cyber warfare and terrorism?
After Reiter’s presentation, Charlotte Sussman transitioned the conversation from the digital world to the maritime world. A professor of English at Duke, Sussman has always been interested in ways to both memorialize and understand the middle passage, the route slave trading ships took across the Atlantic from Africa to the Americas. Through the University’s Bass Connections and Data+ research programs, she and a group of students were able to approach this problem through the unlikely lens of data science.
Sussman explained that her Data+ team used large databases to find which areas of the Atlantic Ocean had the highest mortality rates during the slave trade, while the Bass Connections team looked at a single journey to understand one young migrant’s path to the bottom of the sea.
Professor Sussman (second from right), and the Bass Connections/Data+ Team.
Monroe, Reiter, and Sussman all showed that the applications of computing are growing without bound. Both the responsibility to improve computing infrastructures and the ability to leverage computing resources are rapidly expanding to new fields, from medicine and optimization to cybersecurity and history.
With so many exciting paths for growth, one point is clear about the future of computing: it will outperform anyone’s wildest expectations. Be prepared to find computing in academia, business, government, and other settings that require advanced information.
Many of these areas, like the Chesterfield Building, will probably see the impact of computing before you know it.
By now most people have heard of Bitcoin, the first form of decentralized cryptocurrency which was created in 2009 and popularized in 2011. However, these novel tokens did not just appear out of thin air, they had to be mined. But what does this mean?
On 3 January 2009, the bitcoin network came into existence after the founder, Satoshi Nakamoto, mined the genesis block of bitcoin (block number 0), and received a reward of 50 bitcoins. The rewards for Bitcoin mining are reduced by half roughly every four years due to its scarcity. Currently, miners are rewarded 6.25 Bitcoins for every block. Additionally, when a transaction is approved via mining, it is added to a block which is then added to the Bitcoin blockchain. A blockchain is an immutable, decentralized, and transparent computer network that acts as a publicly available ledger. For more information please reference my previous article here.
Not all tokens are mined, however, the most popular or widely used ones, Bitcoin and Ethereum are. Today, we will be focusing on the Ethereum Blockchain using ETH tokens.
Similar to Bitcoin, ETH is also mined by solving complex puzzles in order to confirm and verify blockchain transactions. However, ETH miners are paid in ETH, not bitcoin. In addition to receiving the ETH from mining, miners are also paid through transaction fees called gas.
Transaction fees are determined by a Transaction fee mechanism (TFM), a key component of blockchain protocol. However, there has yet to be an empirical study on the real-world impact of TFMs. Recently, a study out of Duke and Peking University evaluated the effect of EIP-1559, the first TFM to abandon the traditional first-price auction paradigm.
Every transaction or smart contract executed on the Ethereum blockchain requires gas. If you are unfamiliar with smart contracts please reference my previous article here.
“Gas is a unit of measurement for the amount of computational effort required to execute a specific on-network operation”
William Zhao ’23, Student researcher
However, the price of gas is constantly changing in response to how many others are trying to make transactions on the blockchain. Gas prices are typically denoted in GWEI or a billionth of an ETH ( 0.000000001 ETH). For context as of February 1st, 2022 at 1:17 ET, ETH is worth $2778.50 USD per token.
When an ETH transaction is placed it is not immediately completed and resides in a memory pool or “Mempool.” These are smaller databases of unconfirmed or pending transactions. Prior to the EIP-1559 update, the Ethereum TFM centered around the first-price auction paradigm.
Mempool
Conceptually, the first-price auction paradigm is fairly simple. Essentially every time a transaction is made there is an accompanying gas bid. Crypto wallets like Metamask or Coinbase Wallet provide suggested gas bids for users but still allow them to alter the bid. This is because transaction verification priority is determined by the miner and thus given to whoever bids the most. Once a transaction is verified it is added to the miner’s block and then to the blockchain. As a result, some users would offer unnecessarily high gas fees in order for their transaction to skip the line and be quickly processed thus creating major delays for others.
There were several problems under this previous TFM including long wait times for verification, extremely high gas and unpredictable prices, as well as inefficiencies around block size and consensus security. Recent research examined the causal effect of EIP-1559 on blockchain transaction fee dynamics, transaction waiting time, and security. They found that while the transaction mechanism became even more complex it did also become more efficient.
EIP-1559 improves user experience by reducing users’ waiting times, improving fee estimation, and mitigating intra-block difference of gas price paid (which is more important for miners). However, EIP-1559 did not have a large impact on gas fee reduction or consensus security. In addition, they found that when ETH’s price is more volatile, the waiting time is significantly higher.
Figure 8: Distributions of median waiting time. Users experience a much lower transaction waiting time following EIP-1559.
Ultimately, while user experience improved, scalability issues held the TFM from having a larger effect on important components like gas prices.
“If you can only hold a certain amount of transactions that’s a hard cap on development, however, high gas prices are a scalability issue not a mechanism design issue.
Devang Thakkar, a fourth-year PhD candidate at Duke University, recently created an archive for Wordle that gives users unlimited access to past Wordle games. Gray tiles indicate letters not found anywhere in the correct word, yellow indicates letters that are in the word but not in the right place, and green indicates correctly placed letters.
Thanks to Devang Thakkar, a fourth-year PhD student in Computational Biology and Bioinformatics at Duke, the 200+ Wordle games released before I discovered its charms are readily accessible online. So now I’m making up for lost time.
Thakkar recently spent a weekend building an archive of every Wordle game in existence. You can play them in any order. You can start at the beginning. You can start with today’s Wordle and work backward. You can sit down and play eight in a row. Just hypothetically, of course.
Devang Thakkar became hooked on Wordle when his roommate introduced it to him, but he wanted a way to access old Wordles as well. First, he experimented with manually changing the date on his browser to trick the computer into showing him old Wordles. However, his browser gave him an error message if he tried to go back more than fourteen days. To get around that, Mr. Thakkar wrote a Python script using a Python library called Selenium, which allowed him “to basically go back as much as you want.”
Thakkar combined his own data with an open-source Wordle project called WordMaster created by Katherine Peterson. With an open-source project, Thakkar says, “You put your work out there, and then someone else adds to it.”
Devang Thakkar at the 2020 Data Through Design exhibition in New York. Photograph courtesy of Devang Thakkar.
Whereas WordMaster randomly generates new five-letter words, Thakkar’s archive provides access to “official” Wordle games from the past. While there were many random Wordle generators already in existence, it was the usage of the official Wordle list and the ability to go back to a particular Wordle that set this archive apart. Thakkar also added features like the ability to share your answers with others and an option that lets users access Wordle games in a random order.
Thakkar tells me the project was “just for fun.” “I was bored… so I was like, ‘let’s make something!’” he says. Nevertheless, “That is essentially what I do for my work as well; I write code.” In the Dave Lab, Devang Thakkar uses sequencing data to study the origins of different types of lymphomas.
In his free time, Devang Thakkar enjoys woodworking and metalworking. Pictured here are two of his projects, a wooden bowl and his own dining room table. Photographs courtesy of Devang Thakkar.
When he’s not working or making Wordle archives, Devang Thakkar can often be found in Duke’s Innovation Co-Lab, where he enjoys woodworking and metalworking. His projects range from creations intended as gifts, like a laptop stand and beer caddy, to his own dining room table. Thakkar says the hobby, being very different from his normal work, helps him maintain work-life balance.
The Wordle project, on the other hand, required coding skills Thakkar uses daily. “This is just like work for me, but for fun.” He enjoys graphic design and board games and has “a special affection for board games with words.”
As for the Wordle archive, Mr. Thakkar says he never expected it to become so popular. He thought it would mostly be used by his friends, but the archive quickly accumulated millions of weekly users. “People keep sending me screenshots of their friends sending them this website,” he says.
Meanwhile, I’ve started noticing Wordle references everywhere. Just after I spoke to Thakkar about his project, I happened to stumble across a link to BRDL, a delightful Wordle spinoff that uses four-letter birding codes instead of words. By blind luck, I guessed the right code on my second try: AMGO, American goldfinch. A few days later, I overheard two students talking about the daily Wordle. Clearly, I’m not the only one who’s become hooked on the game. Fortunately for everyone who is, Devang Thakkar’s Wordle archive, which he called “Remembrance of Wordles Past,” offers unlimited access.
