Category: Students Page 8 of 42

Jason Dinh’s research career began unintentionally with a semester at Duke’s Marine Lab. A current fourth-year PhD candidate in Duke’s Biology Department, Dinh ventured to the Marine Lab for a mental reset in the spring of his sophomore year as a Duke undergraduate. “While I was there, I realized that people can just get paid to ask questions about how the world works,” Dinh told me, “And I really didn’t know that was a thing that you could do.” Maybe this is what I want to do, he thought.

Jason Dinh, fourth-year PhD candidate in Duke Biology Department

Dinh spent his remaining undergraduate summers investigating the impacts of soundscapes on oyster and fish larvae development. Now, he studies snapping shrimp – a small oceanic species that is “one of the biggest sound producers in the ocean,” bested only by toothed whales.

Dinh first became aware of snapping shrimp during his undergraduate research. He told me that you can find snapping shrimp “basically anywhere, from the equator up to Virginia or maybe North Carolina.” While conducting research on ocean sounds and oyster and fish larvae, Dinh noticed the frequent snapping sounds of the snapping shrimp when he placed underwater microphones. “We didn’t really know what they were doing,” Dinh said.

An image of a species of snapping shrimp like Dinh works with.

The male snapping shrimp is asymmetrical with one very large claw and one that is regular-sized. The large claw has a tiny hook on the end and when the shrimp clamps down or “snaps” the claw, the top half latches into the bottom, shooting out an air bubble at sixty miles per hour that “essentially boils the water behind it,” producing the loud snapping noise in its wake. When many shrimp are snapping at once, it sounds almost like the frying grease when cooking bacon, Dinh tells me. (Click here to watch a video of the snapping shrimp in action.)

At first, researchers suspected the bubble from the snap was a means of stunning prey, but “It turns out that snapping shrimp also fight each other,” Dinh said. And when fighting, male snapping shrimp shoot the air bubbles at one another. The bigger the shrimp’s body size, the larger the snapping claw and the louder the snapping sound.

An image of two snapping shrimp facing off.

Going into his PhD, Dinh wanted to continue his undergraduate work in acoustics and figure out novel ways animals were producing sounds. His investigation of the snapping shrimp took him in new directions, however. Through his projects, Dinh has conducted work on the costs and benefits that keep the claw size as an honest indicator of shrimp size in competitions and approached a plethora of questions from the physiological and physical mechanisms of sending and assessing snaps, up to the evolutionary implications of the sexual selection for claw size.

“I don’t think I really knew I wanted to do research until right before I applied for grad school,” Dinh said at the beginning of our conversation. He remembers being a child curious about nature and bringing in “hundreds of cicadas” and “random critters into the house.” A few decades later and his research is centered on living creatures, which is both a rewarding and tricky process.

“Live animals are going to do what live animals want to do,” Dinh stated simply. “One thing my advisor always tells us is that you don’t get to tell the animal what to do, it tells you what you are going to do.” This has certainly held true for Dinh. While he has had many detailed and well-planned experimental ideas, he says he’s ultimately ended up doing what the “animals told him they were willing and happy to do in the lab.” However, along the way Dinh basks in the “joys in tiny discoveries in the process of research.”

I asked Dinh how he ended up at Duke in the first place and why he chose to stick around for his PhD. “So I ended up at Duke for undergrad because I really liked basketball, which is a really bad reason to choose a school.” But ultimately, this choice “paid off really well because my first year was the last year we won the National Championship,” Dinh said. He traveled to Indianapolis for the event which he says was the “best basketball game of [his] life.”

Dinh decided to do his PhD at Duke because of how deeply he admires his advisor, Sheila Patek (PhD), as a scientist. “I think she’s just a wonderful, passionate, passionate defender of basic science and just doing science because more knowledge is good for society,” Dinh elaborated, “Sheila’s also a staunch and fearless advocate for her students.” Though Dinh considers himself an “outlier” in the lab – primarily a behavioral ecologist in a lab of researchers investigating biomechanics – the way that Patek approaches science is the way that he wants to approach science as well.

Like Alice falling down the rabbit hole in *Alice in Wonderland,* Dinh compares the diving explorations of science as being a “professional rabbit holer.” Science consists of picking questions further and further apart and leaning into research findings to tunnel into topics.

“I feel like science is being a professional rabbit holer,” Dinh stated. While Dinh is on the pursuit of the weapon size and fighting strategies of snapping shrimp, he doesn’t know exactly where he wants to head next, following the completion of his PhD. Like the snapping shrimp that collect information about their opponents to make an informed decision about engaging in fights, Dinh says he is conducting a sort of Bayesian method of his own. He’s assessing his experiences as he goes and sorting out the right next step for him.

A fan of the meditative art of writing, long morning walks with his dog, and reality TV, Dinh appreciates being “on the frontier of what we know” and is sure to let his deep-rooted curiosity about the natural world continue to guide him.

What is The Duke Summer Experiences Database?

By Sophie Cox

On February 21, 2022

In Computers/Technology, Data, Faculty, Students

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.

Post by Sophie Cox, Class of 2025

2019 Duke Grad Founds Cryptocurrency Startup Fei Protocol

By Anna Gotskind

On February 21, 2022

In Artificial Intelligence, Computers/Technology, Students

As cryptocurrency gains popularity, people continue to question “How and where can these tokens be used?” A November 2021 study by Pew Research reported that 86% of Americans claimed to have heard about cryptocurrency and 16% say they personally have invested in, traded, or otherwise used it.

Despite this, there are still very few places where one can make purchases directly using crypto. This means that in order to use cryptocurrency, people must first convert it back to US dollars, which can cost a lot due to transaction fees. Additionally, the exchange rate between any given crypto token and USD changes by the second, resulting in a lack of price stability.

(If you are unfamiliar with cryptocurrency or transaction (gas) fees please refer to my prior article here.)

Duke Alum, Joey Santoro, sensed this gap and saw an opportunity. Santoro graduated from Duke in 2019 with a major in Computer Science. There needed to be a volatility-free token with a stable valuation (i.e. matching the USD), to move between the worlds of crypto and fiat currency. This is also known as a stablecoin. While several were already in existence, Santoro wanted to create a more scalable and decentralized one.

Thus, in December of 2020, Joey founded the Fei Protocol. Fei is a stablecoin in Ethereum native decentralized finance (DeFi). Stablecoins are a type of token that aids in maintaining a liquid market by pegging the token’s value to the USD. Fei is able to achieve this through various stability mechanisms. Stablecoins can be used for real-life transactions while still benefiting from instant processing and the security of cryptocurrency payments.

When asked why he chose to work in crypto as opposed to Machine Learning (ML) or Artificial Intelligence (AI) Joey explained that it came down to how much impact he could have.

“The barrier for making an avenue of innovation in crypto is so much lower than something like a machine learning. Higher risk, higher reward.”
joey santoro

Santoro did not come to Duke with the plan of founding a web3 DeFi protocol. In fact, when he matriculated he was actually pre-med and originally only took CS 101 because it was a pre-requisite for the Neuroscience major.

However, it did not take long for Joey to realize he wanted to work in the crypto space. In his second semester, he joined the Duke Blockchain Lab and ended up teaching a blockchain course in his junior and senior years.

Because decentralized finance is still so new, no one completely knows what they are doing, which creates considerable opportunities for innovation. Additionally, because the crypto space is decentralized, it is inherently collaborative and community-driven.

“Being able to write code that’s immediately interoperable with dozens of financial protocols is the coolest thing ever,” Santoro said

Joey argues anyone can become an expert in a particular area in crypto in a couple of months. He said economists and mechanism designers are increasingly moving into the crypto space.

When the Fei Protocol launched in 2020 it was the height of a bull market for crypto and there was heavy demand for a decentralized stablecoin. While there were several other stablecoins in existence, USDC and tether were the most popular and they were both centralized, meaning they were owned by companies.

“What so important to me and why I do this is because I want people to be able to do whatever they want with their money.”
JOey santoro

The demand for a decentralized stablecoin created excitement around Feio but also a highly compressed timescale. The Fei Protocol ended up having the largest token launch for an Ethereum DeFi protocol in history, raising $1.25B. However, when it launched, the peg broke due to issues with the incentive mechanism and bugs in the code.

Santoro recalled the surreal and challenging experience of watching the protocol he spent countless weeks working on fall apart before his eyes. However, his team and investors decided to stick it through and try to salvage what they had built. It took over a month just to fix everything that had gone wrong. In the meantime, people were threatening Santoro and his team.

While the Fei protocol faced challenges while launching, Joey and his team were able to adapt, learn from their mistakes, and come back stronger. They recently conducted a multi-billion-dollar merge with Rari Capital and launched Fei version2 (V2).

Additionally, this is the first multi-billion dollar merger in DeFi meaning that the decision to merge was voted on by members of the respective Decentralized Autonomous Organizations (DAOs). This is a huge milestone in the world of DeFi and sets a precedent for the potential of decentralized business operations.

Joey Santoro Presenting at the ETHDenver Convention

Moving forward Joey explained, “I’m obsessed with simplicity now; I still move fast but more carefully.”

Post by Anna Gotskind, Class of 2022

The Mind Behind Muser

By Nhu Bui

On February 14, 2022

In Computers/Technology, Faculty, Field Research, Students

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.

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.

Ethereum: What are Transaction Fees and How are They Determined?

By Anna Gotskind

On February 2, 2022

In Computers/Technology, Data, Engineering, Students

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?

Essentially, there is a finite amount of Bitcoin, 21 million to be exact. Bitcoin miners run complex computer rigs to solve intricate and complicated puzzles in order to confirm groups of bitcoin transactions called blocks. Once a block is mined, the miner is rewarded with bitcoin.

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.

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.
William Zhao ’23, student researcher

This research paper was recognized by Vitalik Buterin, one of the co-founders of Ethereum.

Remembrance of Wordles Past

By Sophie Cox

On February 1, 2022

In Computers/Technology, Data, Students

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.

Writing this story was dangerous. Before, I was only vaguely aware of the existence of Wordle, a wildly popular online word game created by Josh Wardle and recently bought by the New York Times. Now I can’t stop playing it. The objective of the game sounds deceptively simple: try to guess the right five-letter word in six attempts or fewer.

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.

Introducing Muser – A Better Way to Find Student Research

By Skylar Hughes

On January 26, 2022

In Field Research, Genetics/Genomics, History, Science Communication & Education, Students

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.

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.

Blake Fauskee and the ‘Little Typos’ of Fern DNA

By Cydney Livingston

On January 21, 2022

In Biology, Genetics/Genomics, Students

Blake Fauskee, third-year Biology PhD student, initially pitched his graduate project to advisor Kathleen Pryer (Ph.D.) as an undergrad.

Fauskee, who researches RNA editing sites in ferns, told me about the project that he’s been working on for the last several years. His research could push back against the idea that DNA is the end-all, be-all molecule for encoding life as we know it.

Fauskee broke down RNA editing for me. “RNA editing is this extra step in the whole central dogma, the whole gene expression process, that happens in plant organellar DNA,” he said. This process takes place in plant mitochondrial and chloroplast genomes.

Fauskee uses a lot of metaphors to describe his work, which I find both helpful and admirable. Science can often be dense and lack feasible connections to processes that most of us are familiar with. “Basically, in [plant] DNA, there are little typos almost. The wrong nucleotide is encoded at certain spots. When those genes are going to be expressed, they get turned into RNA and then other proteins from the nucleus come in and find the little typos so that in the end you get the correct protein.”

This image shows a simplified diagram of how RNA editing works.

Fauskee calls RNA editing an “interesting and strange process” that neither animals nor humans have. His work attempts to study the evolution of this process, the patterns of RNA editing, and why it came to be. He uses DNA and RNA sequence data and the help of computational tools to do his work. He explains that when sequencing DNA, you can think of the fragmented base pairs “as little puzzle pieces.”

“So, I take all those little puzzle pieces and try to put back together the chloroplast genome, which is about 150,000 base pairs. It’s like a thousand-piece puzzle.”

Next, he figures out where the fern’s gene sequences are on the DNA strands, making use of genomic databases that contain known genomes. He then aligns RNA sequences to the genes he has mapped. Fauskee looks for the “typos” or “little differences” between the DNA and RNA: “That’s how we find the RNA editing sites.” Finally, he evaluates how the proteins would be changed by the typos in the DNA if the RNA was not edited after being transcribed.

“So, a lot of these fern genes will have a STOP codon right in the middle, which is really, really bad if you don’t fix because you are only going to get half a protein,” Fauskee said. STOP codons signal to the protein-building ribosomes that the protein is finished once it reads this portion of the RNA. Fauskee explained that these types of errors are the ones would expect organisms to lose, but it turns out they are the ones that are conserved in ferns. “Is there an extra function there? Is it helpful? Is it adaptive?” Fauskee asked.

Comparative analyses between fern species are important. By looking at whether there are common editing sites and common amino acid changes, Fauskee says, “we’re trying to understand if certain editing sites may be advantageous and what kinds of fluctuation we see between certain types of changes.”

Fauskee underscored the importance of his work. “RNA editing is a really interesting process that kind of undermines what I learned in molecular biology…They always tell you DNA is the bedrock, it’s the be-all, end-all. But what happens when the DNA is wrong? What’s the other added layer on this?”

Simply put, Fauskee, says that because of RNA editing, “We have to rethink central dogma a little bit.” In some plants, 10% of all their gene products contribute to RNA editing, Fauskee tells me. “That’s a big chunk and that’s got to be important,” Fauskee said, “Why would evolution keep such a burden going?”

Biology’s central dogma is the idea that DNA is transcribed into RNA and then translated into proteins. RNA editing adds an extra step before translation and protein production.

There may also be implications for how RNA editing sites affect the way that genetic relationships are mapped through phylogenetics. If differences between the DNA of different species at RNA editing sites, this could be misleading. Though the DNA indicates a change in base pair, RNA editing could lead to the same output in protein despite the seeming change. “If you took [RNA editing] into account,” Fauskee says, “does it give you a different answer?”

Fauskee studies ferns because of the amount of editing sites found in these plants. While flowering plants have lost editing sites over time, ferns have not. “For RNA editing, you can look at all angiosperms (flowering plants) and for the whole chloroplast genome, they might have 30-50 RNA editing sites. When you get into ferns, that number jumps up to 300-500 and I am trying to understand why.”

Botanical science first captured Fauskee’s interest while he completed his undergraduate degree in his home state at the University of Minnesota Duluth (UMD). As a sophomore at UMD, Fauskee was taken under the wing of Amanda Grusz (Ph.D.). Grusz received her PhD in biology from Duke and worked under Pryer during her own time at the university. “I’m like my advisor’s academic grandson, which is kind of funny.” Clara Howell, who is part of Fauskee’s PhD cohort and who I spoke with last Fall, is also an academic grandchild in her own lab.

Being an “academic grandson” has worked out well for Fauskee. His key advice to me for any person considering a PhD, “Make sure your advisor is not someone you just admire as a scientist, but as a person.” On a day-to-day basis, Fauskee says that advisor Katheen Pryer “is pretty hands off” but is also “one of the most supportive people ever. I’m pretty much the driver of my own ship. If I am falling off the road, she’ll push me back on the road, but she’ll give me freedom to swerve around on that road.”

Fauskee also emphasized a piece of wisdom that Pryer passed down to him. “If whatever you’ve got going on is working and everyone else is doing something different, who cares?” he said.

Though Fauskee says that “lab work can be frustrating,” getting his long analyses to run after wrangling lots of data is very rewarding. Fauskee, who does not have a background in coding or computer languages, likes to “tell people that [his] floor of biology combined is one competent coder.” When he’s not stealing bits of his biology neighbor’s code, Fauskee loves to attend Duke Basketball games and is a fan of the television show Survivor.

Post by Cydney Livingston, Class of 2022

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

By Cydney Livingston

On January 14, 2022

In Animals, Biology, Field Research, Students

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.

Images from *Scientific American’s* article about the Amboseli Baboon Research Project.

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.”

Images of Emily Levy conducting field work. On right, Levy is conducting field work in the Amboseli National Park in Southern Kenya.

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*

LowCostomy: the Low-Cost Colostomy Bag for Africa

By Camila Cordero

On January 11, 2022

In Biology, Biomedical Engineering, Cancer, Engineering, Environment/Sustainability, Global Health, Medicine, Students

It’s common for a Pratt engineering student like me to be surrounded by incredible individuals who work hard on their revolutionary projects. I am always in awe when I speak to my peers about their designs and processes.

So, I couldn’t help but talk to sophomore Joanna Peng about her project: LowCostomy.

Rising from the EGR101 class during her freshman year, the project is about building a low-cost colostomy bag — a device that collects excrement outside the patient after they’ve had their colon removed in surgery. Her device is intended for use in under-resourced Sub-Saharan Africa.

“The rates in colorectal cancer are rising in Africa, making this a global health issue,” Peng says. “This is a project to promote health care equality.”

The solution? Multiple plastic bags with recycled cloth and water bottles attached, and a beeswax buffer.

“We had to meet two criteria: it had to be low cost; our max being five cents. And the second criteria was that it had to be environmentally friendly. We decided to make this bag out of recycled materials,” Peng says.

For now, the team’s device has succeeded in all of their testing phases. From using their professor’s dog feces for odor testing, to running around Duke with the device wrapped around them for stability testing, the team now look forward to improving their device and testing procedures.

“We are now looking into clinical testing with the beeswax buffer to see whether or not it truly is comfortable and doesn’t cause other health problems,” Peng explains.

_{Poster with details of the team’s testing and procedures}

Peng’s group have worked long hours on their design, which didn’t go unnoticed by the National Institutes of Health (NIH). Out of the five prizes they give to university students to continue their research, the NIH awarded Peng and her peers a $15,000 prize for cancer device building. She is planning to use the money on clinical testing to take a step closer to their goal of bringing their device to Africa.

Peng shows an example of the beeswax port buffer (above). The design team of Amy Guan, Alanna Manfredini, Joanna Peng, and Darienne Rogers (L-R).

“All of us are still fiercely passionate about this project, so I’m excited,” Peng says. “There have been very few teams that have gotten this far, so we are in this no-man’s land where we are on our own.”

She and her team continue with their research in their EGR102 class, working diligently so that their ideas can become a reality and help those in need.

Post by Camila Cordero, Class of 2025

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