Research Blog

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

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

Sticky post

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

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

Emily Levy, an almost-PhD in Duke Biology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Post by Cydney Livingston, Class of 2022

LowCostomy: the Low-Cost Colostomy Bag for Africa

Sticky post

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. 

Prototype of the LowCostomy bag

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

Opening the Black Box: Duke Researchers Discuss Bias in AI

Sticky post

Artificial intelligence has not only inherited many of the strongest capabilities of the human brain, but it has also proven to use them more efficiently and effectively. Object recognition, map navigation, and speech translation are just a few of the many skills that modern AI programs have mastered, and the list will not stop growing anytime soon.

Unfortunately, AI has also magnified one of humanity’s least desirable traits: bias. In recent years, algorithms influenced by bias have often caused more problems than they sought to fix.

When Google’s image recognition AI was found to be classifying some Black people as gorillas in 2015, the only consolation for those affected was that AI is improving at a rapid pace, and thus, incidents of bias would hopefully begin to disappear. Six years later, when Facebook’s AI made virtually the exact same mistake by labeling a video of Black men as “primates,” both tech fanatics and casual observers could see a fundamental flaw in the industry.

Jacky Alciné’s tweet exposing Google’s racist AI algorithm enraged thousands in 2015.


On November 17th, 2021, two hundred Duke Alumni living in all corners of the world – from Pittsburgh to Istanbul and everywhere in between – assembled virtually to learn about the future of algorithms, AI, and bias. The webinar, which was hosted by the Duke Alumni Association’s Forever Learning Institute, gave four esteemed Duke professors a chance to discuss their view of bias in the artificial intelligence world.

Dr. Stacy Tantum, Bell-Rhodes Associate Professor of the Practice of Electrical and Computer Engineering, was the first to mention the instances of racial bias in image classification systems. According to Tantum, early facial recognition did not work well for people of darker skin tones because the underlying training data – observations that inform the model’s learning process – did not have a broad representation of all skin tones. She further echoed the importance of model transparency, noting that if an engineer treats an AI as a “black box” – or a decision-making process that does not need to be explained – then they cannot reasonably assert that the AI is unbiased.

Stacy Tantum, who has introduced case studies on ethics to students in her Intro to Machine Learning Class, echoes the importance of teaching bias in AI classrooms.

While Tantum emphasized the importance of supervision of algorithm generation, Dr. David Hoffman – Steed Family Professor of the Practice of Cybersecurity Policy at the Sanford School of Public Policy – explained the integration of algorithm explainability and privacy. He pointed to the emergence of regulatory legislation in other countries that ensure restrictions, accountability, and supervision of personal data in cybersecurity applications. Said Hoffman, “If we can’t answer the privacy question, we can’t put appropriate controls and protections in place.”

To discuss the implications of blurry privacy regulations, Dr. Manju Puri – J.B. Fuqua Professor of Finance at the Fuqua School of Business – discussed how the big data feeding modern AI algorithms impact each person’s digital footprint. Puri noted that data about a person’s phone usage patterns can be used by banks to decide whether that person should receive a loan. “People who call their mother every day tend to default less, and people who walk the same path every day tend to default less.” She contends that the biggest question is how to behave in a digital world where every action can be used against us.

Dr. Philip Napoli has observed behaviors in the digital world for several years as James R. Shepley Professor of Public Policy at the Sanford School, specifically focusing on self-reinforcing cycles of social media algorithms. He contends that Facebook’s algorithms, in particular, reward content that gets people angry, which motivates news organizations and political parties to post galvanizing content that will swoop through the feeds of millions. His work shows that AI algorithms can not only impact the behaviors of individuals, but also massive organizations.

At the end of the panel, there was one firm point of agreement between all speakers: AI is tremendously powerful. Hoffman even contended that there is a risk associated with not using artificial intelligence, which has proven to be a revolutionary tool in healthcare, finance, and security, among other fields. However, while proven to be immensely impactful, AI is not guaranteed to have a positive impact in all use cases – rather, as shown by failed image recognition platforms and racist healthcare algorithms that impacted millions of Black people, AI can be incredibly harmful.

Thus, while many in the AI community dream of a world where algorithms can be an unquestionable force for good, the underlying technology has a long way to go. What stands between the status quo and that idealistic future is not more data or more code, but less bias in data and code.

Post by Shariar Vaez-Ghaemi, Class of 2025


Junior Alec Morlote Pursues a Love for Biology Via Fruit Flies

Sticky post

As Alec Morlote emphasizes, he’s a Biology major because “I’m really interested in it. I’d definitely be a Biology major whether I was pre-med or not.”

Morlote, a Trinity junior from northern New Jersey, works in the lab of Dr. Pelin Volkan studying the neurobiology of fruit flies. Why fruit flies, of all things? Well, Morlote initially signed up for a research fellowship program during the summer following his freshman year.

Of course, in March of that year, COVID-19 happened, so Morlote ended up postponing his work to this past summer. He got paired with the Volkan lab because he didn’t want to work in an area of research that was very familiar to him.

“I wanted to use research as an opportunity to learn something completely new,” he said. The neurobiology of fruit flies hit the nail on the head.

Alec Morlote

The Volkan Lab is a cell biology and neurobiology lab that studies how social behavior, specifically courting, is affected by stimuli, using fruit flies as a model organism. Morlote’s specific project has to do with olfactory stimuli – the things flies smell. In flies, as he explained, one gene is responsible for courtship behavior in male flies. If you take out the olfactory receptor of the fly, however, that gene won’t be active.

Morlote is interested in seeing how the olfactory receptor is critical to the expression of this gene.

To do this, he has been working on imaging the antennae of flies – work he describes as “cool, but tedious.” It’s incredibly detailed work to pick apart the antenna off of such a tiny creature.  Once isolated, neurotransmitters in the antenna that have been tagged with green fluorescent protein (GFP) light up, thus showing the expression pattern of all cells expressing the neurotransmitter.

Humans clearly don’t have as simplistic a courtship behavior as fruit flies, but the simplicity of the fruit fly makes it an incredibly valuable organism for studying neurobiology. All discoveries in humans initially started with some sort of watered-down version of the human anatomy, whether mice or in this case, fruit flies. Discoveries into the neurobiology and neuroplasticity of fruit flies just might yield significant discoveries into the neurobiology and neuroplasticity of the human brain.

When asked about his favorite and least favorite parts about his research, Morlote laughed.

“I don’t like doing work for three months and getting no results at all,” he remarked in reference to the initial work he started on this summer – but alas, such is the nature of scientific research. But he adds that the best part of research is getting results, any at all. And even no results can mean something.

Morlote’s poster from his summer research

Research was a way for Morlote to narrow his post-graduation plans. He knows now that he wants to pursue an MD, or possibly an MD/PhD. But initially, research was a way for him to see whether this was the path for him at all. When asked why he chose to be pre-med, Morlote said that “it just seemed like the most practical way to apply a love for science.” Biology is the science that he loves the most, and so being pre-med seemed like a no-brainer.

It’s also a family business. Both of Morlote’s parents are doctors, so medicine “is not unfamiliar territory to me.” Being Latin American, both his parents have worked extensively with Latin communities in New Jersey, which is work he hopes to emulate in the future.

Whether or not benchwork stays a part of his life, Morlote knows that he wants his career to involve research somehow. The way he sees it, “you’re doing the bare minimum if you’re just a doctor but you’re not trying to better medicine in some way.” 

Contributing to research just might become his way.

Post by Meghna Datta, Class of 2023

Keeping the Aging Brain Connected With Words and Music

Sticky post

In an era of seemingly endless panaceas for age-based mental decline, navigating through the clutter can be a considerable challenge.

However, a team of Duke researchers, led by cognitive neuroscientist Edna Andrews, PhD, think they may have found a robust and long-term solution to countering this decline and preventing pathologies in an aging brain. Their approach does not require an invasive procedure or some pharmacological intervention, just a good ear, some sheet music, and maybe an instrument or two.

Dr. Edna Andrews, pictured in 2017. (Photo by Megan Mendenhall/Duke Photography)

In early 2021, Andrews and her team published one of the first studies to look at musicianship’s impact in building cognitive brain reserve. Cognitive brain reserve, simply put, is a way to qualify the resilience of the brain in the face of various pathologies. High levels of cognitive reserve can help stave off dementia, Parkinson’s disease or multiple sclerosis for years on end. These levels are quantified through structural measurements of gray matter and white matter in the brain. The white matter may be thought of as the insulated wiring that helps different areas of the brain communicate.

In this particular study, Andrews’ team focused on measurements of white matter integrity through an advanced MRI technique known as diffusion tensor imaging, to see what shape it is in.

Previous neuroimaging studies have revealed that normal aging leads to a decrease in white matter integrity across the brain. Over the past fifteen years, however, researchers have found that complex sensory-motor activities may be able to slow down and even reverse the loss of white matter integrity. The two most robust examples of complex sensory-motor activities are multilingualism and musicianship.

Andrews has long been fascinated by the brain and languages. In 2014, she published one of the seminal texts in the field of cognitive neurolinguistics where she laid the groundwork for a new neuroscience model of language. Around the same time, she published the first and to-date only longitudinal fMRI study of second language acquisition. Her findings, built upon decades of research in cognitive neuroscience and linguistics, served as the foundation for her popular FOCUS course: Neuroscience/Human Language.

Dr. Andrews’ 2014 book. Published by Cambridge University Press

In more recent years, she has shifted her research focus to understanding the impact of musicianship on cognitive brain reserve. Invigorated by her lived experience as a professional musician and composer, she wanted to see whether lifelong musicianship could increase white matter integrity as one ages. She and her team hypothesized that musicianship would increase white matter integrity in certain fiber tracts related to the act of music-making

To accomplish this goal, she and her team scanned the brains of eight different musicians ranging in age from 20 years to 67 years old. These musicians dedicated an average of three hours per day to practice and had gained years’ worth of performance experience. After participants were placed into the MRI machine, the researchers used diffusion tensor imaging to calculate fractional antisotropy (FA) values for certain white matter fiber tracts. A higher FA value meant higher integrity and, consequently, higher cognitive brain reserve. Andrews and her team chose to observe FA values in two fiber tracts, the superior longitudinal fasciculus (SLF) and the uncinate fasciculus (UF), based on their relevance to musicianship in previous studies.

Relative location of subcortical white matter fiber tracts (lateral view). Image from Wikipedia

Previous studies of the two fiber tracts in non-musicians found that their integrity decreased with age. In other words, the older the participants, the lower their white matter integrity in these regions. After analyzing the anisotropy values via linear regression, they observed a clear positive correlation between age and fractional anisotropy in both fiber tracts. These trends were visible in both tracts of both the left and right hemispheres of the brain. Such an observation substantiated their hypothesis, suggesting that highly proficient musicianship can increase cognitive brain reserve as one ages.

These findings expand the existing literature of lifestyle changes that can improve brain health beyond diet and exercise. Though more demanding, neurological changes resulting from the acquisition and maintenance of language and music capabilities have the potential to endure longer into the life cycle.

Andrews is one of the strongest advocates of lifelong learning, not solely for the satisfaction it brings about, but also for the tangible impact it can have on cognitive brain reserve. Picking up a new language or a new instrument should not be pursuits confined to the young child.

It appears, then, that the kindest way to treat the brain is to throw something new at it. A little bit of practice couldn’t hurt either.

Post by Vibhav Nandagiri, Class of 2025

The Most Important 26 Hours of My First Term at Duke

Sticky post

As any first-year will tell you, the scramble for joining new clubs can be a daunting one. As the dust settled from the Involvement Fair, I looked at the fistful of flyers overflowing from my desk. One of these flyers stood out to me in particular: Student Collaborative on Health Policy (SCOHP). The program, backed by the Duke Margolis Center for Health Policy, seeks to educate, serve, and research within the Duke and Durham community regarding the social, economic, and political determinants of health care.

The Four Committees of SCOHP

Intrigued, I ventured to the Social Sciences building the following Sunday afternoon for their inaugural GBM. The event was lively, filled with a dizzying number of avenues for involvement. One such avenue that was the SCOHP-organized Health Policy Case Competition, advertised as a two-day team sprint to develop and pitch solutions to a pressing health care problem. The prizes were handsome: $1,000 for 1st place, $500 for 2nd place, and $250 for 3rd place, courtesy of the Margolis Center and RTI International. Furthermore, participants would be given access to mentors and industry leaders with vast experience in the area of public health.

Six teams, each consisting of three to five members, participated in the case-writing festivities. On Friday, September 10 at 5:00 PM, the case document was released. Our task: to develop a five-year plan aimed at increasing the screening for human papillomavirus (HPV) in either Malawi, South Africa, or Eswatini via a novel imaging technology known as microbeads. A considerably complex task given the vast number of social, institutional, and political barriers lying between the new technology and the women who needed it the most, not to mention the potential for HPV developing into cervical cancer if left undetected and untreated.

The Case Competition Title Document

Our team, Team J, assumed the role of a local NGO partnering with the Eswatini government. The preliminary hours of the competition were spent sifting through a sea of research. We read reviews of tissue imaging technology, feasibility studies on drug distribution networks, and mathematical projections of healthcare costs. At once invigorating and ceaselessly frustrating, the process of developing a comprehensive solution required significant mental and physical rearrangement. The nine hours following the release of the case were spent in a variety of popular campus study spots, from Bostock to Rubenstein Library, The Coffeehouse to dorm common rooms. In the early morning hours, our plan had finally begun to take shape.

A meager five hours of rest separated Day One of the competition from Day Two. After a night of brainstorming and research, we were left with three hours to finalize our five-minute proposals before a hard 12:00 PM deadline. As the deadline approached, we changed into our best attire from the clavicle up (the marvels of Zoom) and sat down. For the next hour and change, ideas flowed thickly and quickly; eager and persuasive tones emanating from our screens, tense silence as the judges moved into breakout rooms for deliberation.

The top three teams, Team J included, were selected for a final presentation round. The guidelines for this round: strengthen the argument, lengthen the presentation. We were in the final stretch. What followed was two hours of remarkably focused work, the likes of which I had never experienced in a team setting. As we sat down for the deciding presentation of the competition, I felt an immense sense of pride, not only in our solution, but also in our twenty-six hour transformations from perplexed receivers to confident presenters. This confidence and breadth of knowledge was visible in all three teams over the course of their fifteen-minute presentations and subsequent five-minute Q&A’s.

Team J’s Final Round Presentation Over Zoom

As the clock struck 7:00 PM on Saturday, September 11, the judges had submitted their verdict, at which point the teams turned towards the screen with rapt attention. The SCOHP organizers began reading the final standings. In what was described as an extremely close decision for the judges, Team J ended up winning first place. Battling the equally powerful forces of disbelief and sleep deprivation, we let out a collective breath. It was all over.

At the time of the competition, I had yet to complete a month at Duke. I didn’t know it then, but those twenty-six hours would end up being some of the most impactful in my first semester. The competition offered an entirely different approach to learning, one that was grounded in interdisciplinary inquiry and effective collaboration. And to think–it all started with a flyer buried underneath many other flyers.

Post by Vibhav Nandagiri, Class of 2025

Decentralized Finance and the Power of Smart Contracts

Sticky post

When people use apps or services like Netflix, Instagram, Amazon, etc. they sign, or rather virtually accept, digital user agreements. Digital agreements have been around since the 1990s. These agreements are written and enforced by the institutions that create these services and products. However, in certain conditions, these systems fail and these digital or service-level agreements can be breached, causing people to feel robbed. 

A recent example of this is the Robinhood scandal that occurred in mid-2021. Essentially, people came together and all wanted to buy the same stock. However, Robinhood ended up restricting buying, citing issues with volatile stock and regulatory agreements. As a result, they ended up paying $70 million dollars in fines for system outages and misleading customers. And individual customers were left feeling robbed. This was partially the result of centralization and Robinhood having full control over the platform as well as enforcing the digital agreement.

Zak Ayesh Presenting on Chainlink
and Decentralized Smart Contracts

Zak Ayesh, a developer advocate at Chainlink recently came to Duke to talk about decentralized Smart Contracts that could solve many of the problems with current centralized digital agreements and traditional paper contracts as well. 

What makes smart contracts unique is that they programmatically implement a series of if-then rules without the need for a third-party human interaction. While currently these are primarily being used on blockchains, they were actually created by computer scientist Nick Szabo in 1994. Most smart contracts now run on blockchains because it allows them to remain decentralized and transparent. If unfamiliar with blockchain refer to my previous article here. 

Smart contracts are self-executing contracts with the terms of the agreement being directly written into computer code.

Zak Ayesh

There are several benefits to decentralized contracts. The first is transparency. Because every action on a blockchain is recorded and publicly available, the enforcement of smart contracts is unavoidably built-in. Next is trust minimization and guaranteed execution. With smart contracts, there is reduced counterparty risk — that’s the probability one party involved in a transaction or agreement might default on its contractual obligation because neither party has control of the agreement’s execution or enforcement. Lastly, they are more efficient due to automation. Operating on blockchains allows for cheaper and more frictionless transactions than traditional alternatives. For instance, the complexities of cross-border remittances involving multiple jurisdictions and sets of legal compliances can be simplified through coded automation in smart contracts.

Dr. Campbell Harvey, a J. Paul Sticht Professor of International Business at Fuqua, has done considerable research on smart contracts as well, culminating in the publication of a book, DeFi and the Future of Finance which was released in the fall of 2021.

In the book, Dr. Harvey explores the role smart contracts play in decentralized finance and how Ethereum and other smart contract platforms give rise to the ability for decentralized application or dApp. Additionally, smart contracts can only exist as long as the chain or platform they live on exists. However, because these platforms are decentralized, they remove the need for a third party to mediate the agreement. Harvey quickly realized how beneficial this could be in finance, specifically decentralized finance or DeFi where third-party companies, like banks, mediate agreements at a high price.  

“Because it costs no more at an organization level to provide services to a customer with $100 or $100 million in assets, DeFi proponents believe that all meaningful financial infrastructure will be replaced by smart contracts which can provide more value to a larger group of users,” Harvey explains in the book

Beyond improving efficiency, this also creates greater accessibility to financial services. Smart contracts provide a foundation for DeFi by eliminating the middleman through publicly traceable coded agreements. However, the transition will not be completely seamless and Harvey also investigates the risks associated with smart contracts and advancements that need to be made for them to be fully scalable.

Ultimately, there is a smart contract connectivity problem. Essentially, smart contracts are unable to connect with external systems, data feeds, application programming interfaces (APIs), existing payment systems, or any other off-chain resource on their own. This is something called the Oracle Problem which Chainlink is looking to solve.

Harvey explains that when a smart contract is facilitating an exchange between two tokens, it determines the price by comparing exchange rates with another similar contract on the same chain. The other smart contract is therefore acting as a price oracle, meaning it is providing external price information. However, there are many opportunities to exploit this such as purchasing large amounts on one oracle exchange in order to alter the price and then go on to purchase even more on a different exchange in the opposite direction. This allows for capitalization on price movement by manipulating the information the oracle communicates to other smart contracts or exchanges. 

That being said, smart contracts are being used heavily, and Pratt senior Manmit Singh has been developing them since his freshman year along with some of his peers in the Duke Blockchain Lab. One of his most exciting projects involved developing smart contracts for cryptocurrency-based energy trading on the Ethereum Virtual Machine allowing for a more seamless way to develop energy units.

One example of how this could be used outside of the crypto world is insurance. Currently, when people get into a car accident it takes months or even a year to evaluate the accident and release compensation. In the future, there could be sensors placed on cars connected to smart contracts that immediately evaluate the damage and payout.

Decentralization allows us to avoid using intermediaries and simply connect people to people or people to information as opposed to first connecting people to institutions that can then connect them to something else. This also allows for fault tolerance: if one blockchain goes down, the entire system does not go down with it. Additionally, because there is no central source controlling the system, it is very difficult to gain control of thus protecting against attack resistance and collusion resistance. While risks like the oracle problem need to be further explored, the world and importance of DeFi, as well as smart contracts, is only growing.

And as Ayesh put it, “This is the future.”

Post by Anna Gotskind, Class of 2022

New Blogger Velda Wang: My Two Loves

Sticky post

Hello! My name is Velda Wang, and by an unspoken rule, I also have to tell you what year I am, where I’m from, and my major. And who am I to break the rules? I am a first-year student from Atlanta, and I am thinking about majoring in neuroscience. 

My love for scientific research was sparked by participating in the 6th grade science fair. My friend and I took our goal of determining whether orange juice or Gatorade had more electrolytes quite seriously (surprise! It’s orange juice). For the first time, I was directing my own learning. The scientific method was our creed. Designing the experiment was like navigating with only a map–we knew the final destination but we had to explore which steps to take to reach that destination. Sometimes we went down the wrong path and had to backtrack, but these detours taught us a lot nonetheless. Collecting data was like viewing beautiful scenery along the way–both are exciting and help make the journey worth it. 

Image taken from Prevention.com

Our nervous anticipation from the prospect of having to present our experiment in front of judges led us to color-coordinate our outfits a week in advance and write a script for our presentation. However, on the day of the science fair, as more judges approached us, the nervousness turned into excitement and adrenaline, and we soon deviated from the script to add other interesting observations and background information. Though we conducted the experiment on the kitchen table in my house, it was enough of a taste of the research process to know that I wanted more.   

I could also spend hours reading and listening to stories. One of my favorite books of all time is When Breath Becomes Air by the late neurosurgeon Paul Kalanithi. 

Image taken from Amazon.com

In the book, Kalanithi shares how literature and neuroscience are both avenues to understand the meaning of life and the human condition because literature is written by people who have had rich life experiences about people who go through rich life experiences and the brain is directly related to our every thought, feeling, and action. The book opened up my eyes to the power of words in connecting people and understanding life. It is with this realization that I came into college with a goal: get better at writing (and also study neuroscience!).

The Duke Research Blog combines my two loves, and I am incredibly excited to bring you stories about fascinating research happening right here at Duke. I am grateful for the opportunity to grow as a writer and to be able to help make science communication a little more accessible for you.

Hope to see you again soon!    

By Velda Wang, Class of 2025

Science Behind the Scenes: Get To Know a Zebrafish Lab Technician

Sticky post

It’s 7:30 a.m. on a Sunday morning, and Mark McDonough is making a very familiar journey through a very unfamiliar mode. With the light rain pelting down on his gelled hair, he’s walking the 2-mile trek from East Campus to West Campus. The C1 doesn’t run until 8:30 a.m. on weekends, and his job is simply too important to wait for Duke-provided transportation.

Since his third week as a freshman, Mark has held the position of Lab Technician at the Duke University School of Medicine Zebrafish Core Facilities. Through the job, which he earned via the university’s work-study program, Mark has had the opportunity to make his college experience more affordable while completing the behind-the-scenes work that keeps the university’s labs running.

Upon arriving at work every morning, Mark spends anywhere from thirty minutes to an hour cleaning the filters on the fish tanks, after which he removes feces and inserts food. These three tasks are just a microcosm of his duties as a lab technician, but without them, a majority of his assigned fish would die before their biological characteristics could be fully measured.

As a freshman, Mark McDonough (pictured) has had the opportunity to work in a lab that does cutting-edge research.

Mark’s day-to-day responsibilities are similar to those of many lab technicians. Hundreds of Duke’s affiliated research labs make use of living subjects and biological specimens which must be sheltered, fed, and closely monitored. Without the presence of lab technicians, studies involving these subjects could lead to inconsequential or misleading results.

Mark’s supervisor, Z-Core Facilities Manager Karina Olivieri, fully understands the importance of the three lab technicians in her five zebrafish facilities. Says Olivieri, technicians ensure the “health of the fish and quality of their water so that researchers can collect measurements and make valuable insights.” As the demand for zebrafish grows on Duke’s campus, she expects the number of lab technician roles to grow as well. This trend will likely not be unique to Duke.

The zebrafish’s see-through embryo, rapid life cycle, and well-documented genome make it a “model organism” for biological experiments.

Nationwide, demand for lab technicians has accelerated in many of the largest research corporations and academic institutions. According to the Foundation for Biomedical Research, almost every U.S. drug must pass through animal testing in order to reach FDA approval, meaning that larger amounts of living specimens must be preserved as the pharmaceutical industry grows. The rising presence of these experimental subjects may be why the Bureau of Labor Statistics reports that lab technician roles are increasing at a rate of 11%, which beats the national average for STEM occupations.

Though lab technicians don’t present work at prestigious conferences or see their names printed at the top of cutting-edge research articles, their work is pivotal for ensuring that innovative research can be conducted at Duke and beyond. So in the unlikely event that you recognize a passing stranger as a lab technician, make sure to thank them for their service to the Duke community. They keep the university’s vibrant research scene – and its fish – thriving.

Post by Shariar Vaez-Ghaemi, class of 2025

Blake Fauskee and the ‘Little Typos’ of Fern DNA

Blake Fauskee, third-year Biology PhD student, 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.

Blake Fauskee, third-year Biology PhD student

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.

An image of different ferns.

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.

Page 1 of 87

Powered by WordPress & Theme by Anders Norén