Category: Guest Post Page 2 of 12

Duke Scientists Studying the Shape of COVID Things to Come

On April 27, 2020

In Biology, Faculty, Genetics/Genomics, Guest Post, Immunology, Medicine

The novel coronavirus pandemic has now resulted in more than 3 million confirmed cases globally and is pushing scientists to share ideas quickly and figure out the best ways to collaborate and contribute to solutions.

SARS-CoV-2 surface proteins illustrated by We Are Covert, via Wikimedia Commons

Recently, Duke researchers across the School of Medicine came together for an online symposium consisting of several short presentations to summarize the latest of what is known about the novel coronavirus, SARS-CoV-2.

This daylong event was organized by faculty in the Department of Molecular Genetics and Microbiology and researchers from different fields to share what they know about the virus and immunity to guide vaccine design. This conference highlighted the myriad new research pathways that Duke researchers are launching to better understand this pandemic virus.

One neat area of research is understanding viral processes within cells to identify steps at which antivirals may block the virus. Stacy Horner’s Laboratory studies how RNA viruses replicate inside human cells. By figuring out how viruses and cells interact at the molecular level, Horner can inform development of antivirals and strategies to block viral replication. Antivirals stop infections by preventing the virus from generating more of copies of itself and spreading to other cells. This controls damage to our cells and allows the immune system to catch up and clear the infection.

At the symposium, Horner explained how the SARS-CoV viral genome consists of 29,891 ribonucleotides, which are the building blocks of the RNA strand. The viral genome contains 14 areas where the RNA code can be transcribed into shorter RNA sequences for viral protein production. Though each RNA transcript generally contains the code for a single protein, this virus is intriguing in that it uses RNA tricks to code for up to 27 proteins. Horner highlighted two interesting ways that SARS-CoV packs in additional proteins to produce all the necessary components for its replication and assembly into new viral progeny.

The first way is through slippery sequences on the RNA genome of the virus. A ribosome is a machine inside the cell that runs along a string of RNA to translate its code into proteins that have various functions. Each set of 3 ribonucleotides forms one amino acid, a building block of proteins. In turn, a string of amino acids assembles into a distinct structure that gives rise to a functional protein.

One way that SARS-CoV-2 packs in additional proteins is with regions of its RNA genome that make the ribosome machinery slip back by one ribonucleotide. Once the ribosome gets offset it reads a new grouping of 3 ribonucleotides and creates a different amino acid for the same RNA sequence. In this way, SARS-CoV-2 makes multiple proteins from the same piece of RNA and maximizes space on its genome for additional viral proteins.

An example of an RNA ‘hairpin’ structure, which might fool a ribosome to jump across the sequence rather than reading around the little cul de sac. (Ben Moore, via Wikimedia Commons)

Secondly, the RNA genome of SARS-CoV-2 has regions where the single strand of RNA twists over itself and connects with another segment of RNA farther along the code to form a new protein. These folds create structures that look like diverse trees made of repetitive hairpin-like shapes. If the ribosome runs into a fold, it can hop from one spot in the RNA to another disjoint piece and attach a new string of amino acids instead of the ones directly ahead of it on the linear RNA sequence. This is another way the SARS-CoV-2 packs in extra proteins with the same piece of RNA.

Horner said a step-by-step understanding of what the virus needs to survive at each step of its replication cycle will allow us to design molecules that are able to block these crucial steps.

Indeed, shapes of molecules can determine their function inside the cell. Three Duke teams are pursuing detailed investigation of SARS-CoV-2 protein structures that might guide development of complementarily shaped molecules that can serve as drugs by interfering with viral processes inside cells.

Some Duke faculty who participated in the virtual viral conference. (L-R from, top) Stacy Horner, Nick Heaton, Micah Luftig, Sallie Permar, Ed Miao and Georgia Tomaras. (image: Tulika Singh)

For example the laboratory of Hashim Al-Hashimi, develops computational models to predict the diversity of structures produced by these tree-like RNA folds to identify possible targets for new therapeutics. Currently, the Laboratories of Nicholas Heaton and Claire Smith are teaming up to identify novel restriction factors inside cells that can stop SARS-CoV-2.

However, it is not just the structures of viral components expressed inside the cells that matter, but also those on the outside of a virus particle. In Latin, corona means a crown or garland, and coronaviruses have been named for their distinctive crown-like spikes that envelop each virus particle. The viral protein that forms this corona is aptly named the “Spike” protein.

This Spike protein on the viral surface connects with a human cell surface protein (Angiotensin-converting enzyme 2, abbreviated as ACE2) to allow the virus to enter our cells and cause an infection. Heaton proposed that molecules designed to block this contact, by blocking either the human cell surface protein or the viral Spike protein, should also be tested as possible therapies.

One promising type of molecule to block this interaction is an antibody. Antibodies are “Y” shaped molecules that are developed as part of the immune response in the body by the second week of coronavirus infection. These molecules can detect viral proteins, bind with them, and prevent viruses from entering cells. Unlike several other components on our immune defense, antibodies are shaped to specifically latch on to one type of virus. Teams of scientists at Duke led by Dr. Sallie Permar, Dr. Georgia Tomaras, and Dr. Genevieve Fouda are working to characterize this antibody response to SARS-CoV-2 infection and identify the types of antibodies that confer protection.

Infectious disease specialist Dr. Chris Woods is leading an effort to test whether plasma with antibodies from people who have recovered can prevent severe coronavirus disease in acutely infected patients.

Indeed, there are several intriguing research questions to resolve in the months ahead. Duke scientists are forging new plans for research and actively launching new projects to unravel the mysteries of SARS-CoV-2. With Duke laboratory scientists rolling up their sleeves and gowning up to conduct research on the novel coronavirus, there will be soon be many more vaccine and therapeutic interventions to test.

Guest post by Tulika Singh, MPH, PhD Candidate in the Department of Molecular Genetics and Microbiology (T: @Singh_Tulika)

Students Dance Their Way Out of “AI Bias”

By Guest Post

On March 10, 2020

In Art, Computers/Technology, Engineering, Guest Post, Students

Martin Brooke is no ordinary Engineering professor at Duke University. He teaches computer scientists, engineers, and technology nerds how to dance.

Brooke co-teaches Performance and Technology, an interactive course where students create performance projects and discuss theoretical and historical implications of technologies in performance. In a unique partnership with Thomas DeFrantz, a professor of African and African American Studies and Dance students will design a technology based on “heart,” for example, in order to understand how human expression is embedded in technology. Two weeks later, they’ll interact with motion-sensing, robotic trees that give hugs; and 3D printed hearts that detect colors and match people, sort of like a robotic tinder.

Thomas DeFrantz (left) and Martin Brooke watch their students perform in the Performance and Technology course .

Brooke loves that this class is fun and interactive, but more importantly he loves that this class teaches students how to consider people’s emotions, facial expressions, cultural differences, cultural similarities and interactions when designing new technologies.

Human interface is when a computerized program or device takes input from humans — like an image of a face — and gives an output — like unlocking a phone. In order for these devices to understand human interface, the programmer must first understand how humans express themselves. This means that scientists, programmers, and engineers need to understand a particular school of learning: the humanities. “There are very, very few scientists who do human interface research,” Brooke said.

The students designed a robotic “Tinder” that changes colors when it detects a match.

Brooke also mentioned the importance of understanding human expressions and interactions in order to limit computer bias. Computer bias occurs when a programmer’s prejudiced opinions of others are transferred into the computer products they design. For example, many recent studies have proven that facial recognition software inaccurately identifies black individuals when searching for suspects of a criminal case.

“It turns out one of the biggest problems with technology today is human interface,” Brooke said. “Microsoft found out that they had a motion sensitive Artificial Intelligence that tended to say women, [more often than men], were angry.” Brooke said he didn’t consider the importance of incorporating the arts and humanities into engineering before coming to Duke. He suggested that it can be uncomfortable for some scientists to think and express themselves artistically. “[When] technologists [take Performance and Technology], for example, they are terrified of the performance aspects of it. We have some video of a guy saying, ‘I didn’t realize I was going to have to perform.’ Yeah, that’s what we were actually quite worried about, but in the end, he’s there in the video, doing slow motion running on stage — fully involved, actually performing, and really enjoying it.

Duke has a strong initiative to promote arts and humanities inclusion in science, technology, engineering, and mathematics. Brooke plans to bring Bass Connections, a research program that focuses on public outreach and cross-disciplinary work, to his Performance and Technology class before the end of the semester to demonstrate bias through a program he calls AI Bias In the Age of a Technical Elite.

“You give it someone’s name and it will come up with a movie title, their role, and a synopsis of the movie,” Brooke said. “When I put in my name, which is an English name, it said that the movie I would be in is about a little boy who lives in the English countryside who turns into a monster and terrorizes the town.” This program shows even something as simple as a name can have so much stigma attached to it.

Bass Connections Students working on technology and engineering projects. (From the official Duke page for Bass Connections.)

Brooke’s hope is that his class teaches students to think about technology and human interface. “Hopefully that’s a real benefit to them when they get out actually designing products.”

Guest post by Jordan Anderson, a masters student in Science & Society

Teens Have the Feels About Their Family’s Standing

By Guest Post

On January 7, 2020

In Behavior/Psychology, Global Health, Guest Post, News Release, Students

A study of British twins appearing this week in the Proceedings of the National Academy of Sciences shows that an adolescent’s sense of their own family’s social and economic standing is closely linked to that child’s physical and cognitive health.

In fact, the adolescent’s perception of status was a more powerful predictor of their well-being and readiness for further education than their family’s actual status. The study sample represented the full range of socioeconomic conditions in the U.K.

“Testing how young people’s perceptions related to well-being among twins provided a rare opportunity to control for poverty status as well as environmental and genetic factors shared by children within the same family,” said lead author Joshua Rivenbark, an MD/PhD student in Duke’s Medical School and Sanford School of Public Policy.

Joshua Rivenbark is an MD/PhD student in medicine and policy

“Siblings grew up with equal access to objective resources, but many differed in where they placed their family on the social ladder – which then signaled how well each twin was doing,” Rivenbark said.

Researchers followed 2,232 same-sex twins born in England and Wales in 1994-95 who were part of the Environmental Risk (E-Risk) Longitudinal Twin Study based at King’s College London. Adolescents assessed their family’s social ranking at ages 12 and 18. By late adolescence, these beliefs signaled how well the teen was doing, independent of the family’s access to financial resources, healthcare, adequate nutrition and educational opportunities. This pattern was not seen at age 12.

“The amount of financial resources children have access to is one of the most reliable predictors of their health and life chances,” said Candice Odgers, a professor of psychological science at the University of California, Irvine, who is the senior author of the report. “But these findings show that how young people see their family’s place in a hierarchical system also matters. Their perceptions of social status were an equally good, and often stronger, indicator of how well they were going to do with respect to mental health and social outcomes.”

Study findings also showed that despite growing up in the same family, the twins’ views were not always identical. By age 18, the twin who rated the family’s standing as higher was less likely to be convicted of a crime; was more often educated, employed or in training; and had fewer mental health problems than his or her sibling.

“Studies that experimentally manipulate how young people see their social position would be needed to sort out cause from effect,” Rivenbark said.

The E-Risk study was founded and is co-directed by Duke professors Avshalom Caspi and Terrie Moffitt at King’s College London.

Guest Post by Pat Harriman, UC-Irvine News @UCIPat

Inventing New Ways to Do Brain Surgery

By Guest Post

On January 2, 2020

In Biomedical Engineering, Faculty, Guest Post, Medicine, Neuroscience

This is the sixth and final 2019 post written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Dr. Patrick Codd is the Director of the Duke Brain Tool Laboratory and an Assistant Professor of Neurosurgery at Duke. Working as a neurosurgeon and helping with the research and development of various neurosurgical devices is “a delicate balance,” he said.

Codd currently runs a minimally invasive neurosurgery group. However, at Massachusetts General Hospital, he used to run the trauma section. When asked about which role was more stressful, he stated “they were both pretty stressful” but for different reasons. At Mass General, he was on call for most hours of the day and had to pull long shifts in the operating room. At Duke, he has to juggle surgery, teaching, and research and the development of new technology.

“I didn’t know I was going to be a neurosurgeon until I was in college,” Codd said. Despite all of the interesting specialties he learned about in medical school, he said “it was always neurosurgery that brought me back.”

Currently, he is exclusively conducting cranial surgery.

Neurosurgeon U.S. Air Force Maj Jonathan Forbes,looks through loupes as he performs brain surgery at the Bagram Air Field in Afghanistan, Oct. 10, 2014.

Though Dr. Codd has earned many leadership positions in his career, he said he was never focused on advancement. He simply enjoys working on topics which he loves, such as improving minimally invasive surgical techniques. But being in leadership lets him unite other people who are interested in working towards a common goal in research and development. He has been able to skillfully bring people together from various specialties and help guide them. However, it is difficult to meet everyone’s needs all of the time. What is important for him is to be a leader when he needs to be.

Dr. Codd said there are typically five to eight research papers necessary in to lay the groundwork for every device that is developed. However, some technologies are based on the development of a single paper. He has worked on devices that make surgery more efficient and less minimally invasive and those that help the surgical team work together better. When developing technologies, he tries to keep the original purpose of the devices the same. However, many revisions are made to the initial design plans as requirements from the FDA and other institutions must be met. Ironically, Dr. Codd can’t use the devices he develops in his own operating room because it would be a conflict of interest. Typically other neurosurgeons from across the country will use them instead.

Post by Andrew Bahhouth, NCSSM 2020

Sharing is Caring, But How Does it Start?

By Guest Post

On December 23, 2019

In Behavior/Psychology, Faculty, Guest Post, Students

This is the second of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

As an occasional volunteer at a local children’s museum, I can tell you that children take many different approaches to sharing. Some will happily lend others their favorite toys, while others will burst into tears at the suggestion of giving others a turn in an exhibit.

For Rita Svetlova Ph.D. at the Duke Empathy Development Lab, these behaviors aren’t just passing observations, they are her primary scientific focus. In November, I sat down with Dr. Svetlova to discuss her current research, past investigations, and future plans.

Originally from Russia, Svetlova obtained an M.A. from Lomonosov Moscow State University in Moscow before earning her Ph.D in developmental psychology from the University of Pittsburgh. She later worked as a post-doctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Now at Duke University as an assistant research professor of psychology and neuroscience and the principal investigator in the Empathy Development Lab, Svetlova looks at the development of ‘prosocial’ behavior in children — behaviors such as sharing, empathy, and teamwork.

Svetlova credits her mentor at the University of Pittsburgh, Dr. Celia Brownell, for inspiring her to pursue child psychology and development. “I’ve always been interested in prosociality, but when I was in Russia I actually studied linguistics,” she says. “When I moved to the U.S., I changed paths partly because I’ve always wanted to know more about human psychology. The reason I started studying children is partly because I was interested in it and partly because I met Dr. Brownell. I branched out a little bit, but I generally found it interesting.”

An unsuccessful sharing experience. (From Awkward Family Photos)

Although her passion for childhood development research began in Pittsburgh, Svetlova has embraced her role as a Duke researcher, most recently tackling a scenario that most academically-inclined readers are familiar with — a partner’s failure to perform in a joint-commitment — in a co-authored May 2017 paper titled “Three-Year-Olds’ Reactions to a Partner’s Failure to Perform Her Role in a Joint Commitment.”

In the study, 144 three-year-olds were presented with a common joint commitment scenario: playing a game. For one third of the children, the game ended when their partner defected, while another third of the test group had a partner who didn’t know how to play. The final third of the group saw the game apparatus break. Svetlova looked at how the children’s reactions varied by scenario: protesting defectors, teaching the ignorant partner, and blaming the broken apparatus. The results seem to suggest that three-year-olds have the ability to evaluate intentions in a joint commitment.

Another paper Svetlova co-authored, titled “Three- and 5-Year-Old Childrens’ Understanding of How to Dissolve a Joint Commitment,” compared the reactions of three- and five-year-olds when a puppet left a collaborative game with either permission, prior notification, or suddenly without prior notification. If the puppet left without warning, three-year-old subjects protested more and waited longer for the puppet’s return, but both age groups seemed to understand the agreement implicit in a joint commitment.

These joint commitments are only a small fraction of the questions that Svetlova hopes to address.

“A longitudinal study of prosociality would be amazing,” she says. “What I’m interested in now is the intersection of fairness understanding and in-group/out-group bias. What I am trying to look into is how children understand their in-group members vs. out-group members and whether there’s something we can do to make them more accepting of their out-group members.”

“Another one I am interested in is the neural basis of empathy and prosocial behavior. I haven’t started yet, but I’m planning a couple of studies on looking into the brain mechanisms of empathy in particular,” Svetolova says. “We plan to scan children and adults while experiencing an emotion themselves and compare that brain activation to the brain activation while witnessing someone experiencing an emotion, the question being ‘do we really feel others’ emotions as our own?’”

Svetlova also expressed her interest in the roles that gender, culture, and upbringing play in a child’s development of prosociality.

I had to ask her why teenagers seemed to “regress” in prosociality, seemingly becoming more selfish when compared to their childhood selves.

“I would distinguish between self-centered and selfish,” she assured me. “You are not necessarily selfish, it’s just that during teenagehood you are looking for your place in the world, in the ‘pack.’ That’s why these things become very important, other’s opinions about you and your reputation in this little group, people become very anxious about it, it doesn’t mean that they become selfish all of a sudden or stop being prosocial.” She added, “I believe in the good in people, including teenagers.”

Guest Post by Sellers Hill, NCSSM 2020

How Do You Engineer a Microbial Community?

By Guest Post

On December 20, 2019

In Biology, Engineering, Environment/Sustainability, Faculty, Guest Post, Students

This is the first of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Claudia Gunsch, the Theodore Kennedy distinguished associate professor in the department of civil and environmental engineering, wants to know how to engineer a microbial community. An environmental engineer with a fascination for the world at the micro level, Gunsch takes a unique approach to solving the problem of environmental pollution: She looks to what’s already been done by nature.

Gunsch and her team seek to harness the power of microbes to create living communities capable of degrading contamination in the environment.

“How can you engineer that microbial community so the organisms that degrade the pollutant become enriched?” she asks. “Or — if you’re thinking about dangerous pathogenic organisms — how do you engineer the microbial community so that those organisms become depressed in that particular environment?”

The first step, Gunsch says, is to figure out who’s there. What microbes make up a community? How do these organisms function? Who is doing what? Which organisms are interchangeable? Which prefer to live with one another, and which prefer not living with one another?

“Once we can really start building that kind of framework,” she says, “we can start engineering it for our particular purposes.”

Yet identifying the members of a microbial community is far more difficult than it may seem. Shallow databases coupled with vast variations in microbial communities leave Gunsch and her team with quite a challenge. Gunsch, however, remains optimistic.

“The exciting part is that we have all these technologies where we can sequence all these samples,” she says. “As we become more sophisticated and more people do this type of research, we keep feeding all of this data into these databases. Then we will have more information and one day, we’ll be able to go out and take that sample and know exactly who’s there.”

“Right now, it’s in its infancy,” she says with a smile. “But in the long-term, I have no doubt we will get there.”

Gunsch is currently working on Duke’s Superfund Research Center designing bioremediation technologies for the degradation of polycyclic aromatic hydrocarbon (PAH) contamination. These pollutants are extremely difficult to break down due to their tendency to stick strongly onto soil and sediments. Gunsch and her team are searching for the right microbial community to break these compounds down — all by taking advantage of the innate capabilities of these microorganisms.

A photo montage from Dr. Gunsch’s lab page.

Step one, Gunsch says, has already been completed. She and her team have identified several different organisms capable of degrading PAHs. The next step, she explains, is assembling the microbial communities — taking these organisms and getting them to work together, sometimes even across kingdoms of life. Teamwork at the micro level.

The subsequent challenge, then, is figuring out how these organisms will survive and thrive in the environment they’re placed in, and which microbial seeds will best degrade the contamination when placed in the environment. This technique is known as “precision bioremediation” — similar to precision medicine, it involves finding the right solution in the right amounts to be the most effective in a certain scenario.

“In this particular case, we’re trying to figure out what the right cocktail of microbes we can add to an environment that will lead to the end result that is desired — in this case, PAH degradation,” Gunsch says.

Ultimately, the aim is to reduce pollution and restore ecological health to contaminated environments. A lofty goal, but one within sight. Yet Gunsch sees applications beyond work in the environment — all work dealing with microbes, she says, has the potential to be impacted by this research.

“If we understand how these organisms work together,” she says, “then we can advance our understanding of human health microbiomes as well.”

Post by Emily Yang, NCSSM 2021

Stalking Elusive Ferns Down Under

By Guest Post

On November 11, 2019

In Biology, Field Research, Guest Post, Students

Graduate student Karla Sosa (left) photographs and presses newly collected ferns for later analysis while Ashley Field (in truck) marks the GPS location of the find.

In Queensland, Australia, early March can be 96 degrees Fahrenheit. It’s summer in the Southern Hemisphere, but that’s still pretty hot.

Although hot, dry Australia probably isn’t the first place you’d think to look for ferns, that’s precisely why I’m here and the sole reason we’ve hit the road at 6 a.m. Our schedule for the day: to drive as far south as we can while still letting us come home at the end of the day.

My local colleague, Ashley Field, grew up just the next town over. A skinny, speedy man, he works at James Cook University in Cairns and knows most of northern Queensland like the back of his hand.

Cairns is on the coast at the upper right, where the little green airplane is.

The ferns I’m looking for today are interesting because some species can move from their original home in Australia to the tiny islands in the Pacific. But some cannot. Why? Understanding what makes them different could prove useful in making our crops more resilient to harsh weather, or preventing weeds from spreading.

We’ve been driving for four hours before we turn off onto a dirt road. If you haven’t been to Australia, it’s worth noting that four hours here is unlike any four hours I’ve experienced before. The roads are fairly empty, flat, and straight, meaning you can cover a lot of terrain. Australia is also incredibly big and most of the time you’re travelling through unpopulated landscapes. While it may be only four hours, your mind feels the weight of the distance.

Here’s the one they were looking for!
*Cheilanthes tenuifolia* with lots of little spore babies on the undersides of its leaves.

The dirt road begins to climb into the mountains. We are leaving behind low scrub and big granite rocks that sit on the flat terrain. Ashley knows where we can find the ferns I’m looking for, but he’s never driven this road before. Instead, we’re trusting researchers who came before us. When they explored this area, they took samples of plants that were preserved and stored in museums and universities. By reviewing the carefully labelled collections at these institutions, we can know which places to revisit in hopes of finding the ferns.

Often, however, having been collected before there was GPS, the location information on these samples is not very precise, or the plants may no longer live there, or maybe that area got turned into a parking lot, as happened to me in New Zealand. So, despite careful planning, you may drive five hours one way to come up empty handed.

As we move higher up the mountain, the soil turns redder and sparse eucalyptus forests begin to enclose us. We locate the previous collections coordinates, an area that seems suitable for ferns to grow. We park the truck on the side of the road and get out to look.

We comb 300 feet along the side of the road because these ferns like the edges of forest, and we find nothing. But as we trudge back to the truck, I spot one meager fern hiding behind a creeping vine! It’s high up off the road-cut and I try to scramble up but only manage to pull a muscle in my arm. Ashley is taller, so he climbs partway up a tree and manages to fetch the fern. It’s not the healthiest, only 6 inches tall for a plant that usually grows at least 12 to 14 inches. It’s also not fertile, making it less useful for research, and in pulling it out of the ground, Ashley broke one of its three leaves off. But it’s better than nothing!

This delicate beauty has no name yet. Karla has to compare it to other ferns in the area to know whether it’s just an odd-looking variant or possibly … a new species!

Ashley excels at being a field botanist because he is not one to give up. “We should keep looking,” he says despite the sweat dripping down our faces.

We pile back in and continue up the road. And who could have predicted that just around the bend we would find dozens of tall, healthy looking ferns! There are easily fifty or so plants, each a deep green, the tallest around 12 inches. Many others are at earlier stages of growth, which can be very helpful for scientists in understanding how plants develop. We take four or five plants, enough to leave a sample at the university in Cairns and for the rest to be shipped back to the US. One sample will be kept at Duke, and the others will be distributed amongst other museums and universities as a type of insurance.

The long hours, the uncertainty, and the harsh conditions become small things when you hit a jackpot like this. Plus, being out in remote wilderness has its own soothing charm, and chance also often allows us to spot cool animals, like the frilled lizard and wallaby we saw on this trip.

Funding for this type of fieldwork is becoming increasingly rare, so I am grateful to the National Geographic Society for seeing the value in this work and funding my three-week expedition. I was able to cover about 400 miles of Australia from north to south, visiting twenty-four different sites, including eight parks, and ranging from lush rainforest to dry, rocky scrub. We collected fifty-five samples, including some that may be new species, and took careful notes and photographs of how these plants grow in the wild, something you can’t tell from dried-up specimens.

Knowing what species are out there and how they exist within the environment is important not only because it may provide solutions to human problems, but also because understanding what biodiversity we have can help us take better care of it in the future.

Guest Post by graduate student Karla Sosa

Chronicling Migrant Deaths Along the US-Mexico Border

By Guest Post

On April 17, 2019

In Art, Climate/Global Change, Field Research, Guest Post

Science, especially social science, is rarely apolitical. Nonetheless, researchers are often hesitant to engage with the political implications of their work. Striving to protect their objective, scientific stance, they leave the discussing and at times the fighting to the politicians and legislators.

University of Michigan anthropologist Jason de León is not one of those researchers. Politics is not merely implicated in his work, but rather drives it. De León studies undocumented migration between Mexico and the United States.

University of Michigan anthropologist Jason De León directs the Undocumented Migration Project.

As director of the Undocumented Migration Project, De León studies what happens to the bodies of migrants crossing the desert to reach the U.S. using “any genre I can steal from,” he told an audience at Duke University on April 5. Using tools from archeology, forensics, photography, and ethnography, de León and his team have been providing novel insights into one of the most urgent political challenges currently facing the nation.

De León acknowledged the political reality of his work immediately by opening his talk with a quote from President Trump about building a “great wall.” However, he was quick to clarify that the problem of missing migrants is not partisan. Rather, it has a long history that he argues started with the 1993 immigration enforcement policy, “Prevention through Deterrence.” This policy’s aim was to redirect illegal immigration to the desert rather than to stop it. Politicians hoped that in the desert, where security is weak and the terrain treacherous, the natural terrain would serve as a border wall. Inherent in this policy is the assumption that migrant life is expandable.

In the wake of this policy, the human smuggling industry in northern Mexico experienced a swift influx and the number of known migrant deaths began to rise. Since the 1990s, over 600 migrant bodies have been recovered from the Sonoran Desert of Arizona where de León conducts his research. Until his team conducted the first forensic experiments on the site, people could only speculate as to what was happening to the bodies of missing loved ones hoping to make it across the border. Now, de León can offer some helpful if heartbreaking data.

De León examines the human consequences of U.S. immigration policy in his book, “The Land of Open Graves”

De León’s archeological method, “desert taphonomy,” examines both the natural and cultural processes that determine what happens to a dead body. Anthropologists studying the body’s decomposition were initially interested only in natural factors like the climate and scavenging animals. Recently, they have realized that the decomposition process is as social as it is natural, and that the beliefs and attitudes of the agents involved affect what happens to human remains. According to this definition, a federal policy that leaves dead bodies to decompose in the Arizona desert is taphonomy, and so is the constellation of social, economic, and political factors that drive people to risk their lives crossing a treacherous, scorching desert on foot.

Guided by this new approach, de León studies social indicators to trace the roots of missing bodies, such as “migrant stations” made up of personal belongings left behind by migrant groups, which he says can at times be too big to analyze. De León and his team document these remnants with the same respect they pay to any traditional archeological trail. Items that many would dismiss as trash, such as gendered items including clothes and hygiene products, can reveal much needed information about the makeup of the migrant groups crossing the desert.

De León argues that human decomposition is a form of political violence, caused by federal policies like Prevention through Deterrence. His passion for his research is clearly not driven by mere intellectual curiosity; he is driven by the immense human tragedy of migrant deaths. He regularly conducts searches for missing migrants that families reach out to him about as a desperate last measure. Even though the missing individuals are often unlikely to be found alive, de León hopes to assuage the trauma of “ambiguous loss,” wherein the lack of verification of death freezes the grief process and makes closure impossible for loved ones.

The multifaceted nature of de León’s work has allowed him to inspire change across diverse realms. He has been impactful not only in academia but also in the policy and public worlds. His book, “The Land of Open Graves,” is accessible and poetic. He has organized multiple art exhibitions that translate his research to educate and empower the public. Through the success of these installations, he has come to realize that exhibition work is “just as valuable as a journal article.”

Backpacks left behind by undocumented immigrants in the exhibition,
“State of Exception.”

Hearing about the lives that de León has touched suggests that perhaps, all researchers should be unafraid to step outside of their labs to not only acknowledge but embrace the complex and critical political implications of their work.

‘Death is a Social Construct’

By Guest Post

On April 1, 2019

In Behavior/Psychology, Biology, Guest Post, Medicine, Policy

Of the few universal human experiences, death remains the least understood. Whether we avoid its mention or can’t stop thinking about it, whether we are terrified or mystified by it, none of us know what death is really like. Turns out, neither do the experts who spend every day around it.

Nobody who sees this guy reports back, so we can only guess.

This was the overarching lesson of Dr. Robert Truog’s McGovern Lecture at Trent Semans Center for Health Education, titled “Defining Death: Persistent Problems and Possible Solutions.”

Dr. Truog is this year’s recipient of the McGovern Prize, an award honoring individuals who have made outstanding contributions to the art and science of medicine. Truog is a professor of medical ethics, anesthesiology and pediatrics and director of the center for bioethics at Harvard Medical School. He is intimately familiar with death, not only through his research and writings, but through his work as a pediatric intensive care doctor at Boston Children’s Hospital. Truog is also the author of the current national guidelines for end-of-life care in the intensive care unit.

In short, Truog knows a lot about death. Yet certain questions about the end of life remain elusive even to him. In his talk, he spoke about the biological, sociological, and ethical challenges involved in drawing the boundary between life and death. While some of these challenges have been around for as long as humans have, certain ones are novel, brought on by technological advancements in medicine that allow us to prolong the functioning of vital organs, mainly the brain and the heart.

The “irreversible cessation of function” of these organs results in brain and cardiac death, respectively. When both occur together, the patient is declared biologically dead. When they don’t, such as when all brain function except for those that support the patient’s digestive system is lost, for instance, the patient can be legally alive without any hope of recovery of consciousness.

According to Truog, it is in these moments of life after the loss of almost every brain function that we realize “death is a social construct.” This claim likely sounds counterintuitive, if not entirely nonsensical, as dying is the moment we have the least control over our biology. What Dr. Truog means, however, is that as technology continues to mend failures of biology that would have once been fatal, our social and philosophical understanding of dying, what he calls “person death” will increasingly separate from the end of the body’s biological function.

Biologically, death is the moment when homeostasis, the body’s internal state of equilibrium including body temperature, pH levels and fluid balance, fails and entropy prevails.

Personhood, however, is not mere homeostasis. Dr. Truog cited Robert Veatch, ethicist at Georgetown University, in defining person death as the “irreversible loss of that which is essentially significant to the nature of man.” For those patients who are kept alive by ventilators and who have no hope of regaining consciousness, that essentially significant nature appears to have been lost.

Nonetheless, for loved ones, signs like spontaneous breathing, which can occur in patients in persistent vegetative state, intuitively feel like signs of life. This intuitive sign of life is what made Jahi McMath’s parents refuse an Oakland California hospital’s declaration that their daughter was dead. A ventilator kept the 13-year-old breathing, even though she had been declared brain-dead. After much conflict, McMath’s parents moved her to a hospital in New Jersey, one of just two states where families can reject brain death if it does not align with their religious beliefs. In the end, McMath had two death certificates that were five years apart.

Muslim cemetery at sunset in Marrakech Morocco.
(Mohamed Boualam via Wikimedia commons)

The emotional toll of such an ordeal is immense, as the media outcry around McMath made more than clear. There are more concrete, quantifiable costs to extending biological function beyond the end of personhood: the U.S. is facing an organ shortage. As people are kept on life support for longer periods, it is going to become increasingly difficult for patients who desperately need organs to find donors.

In closing, Dr. Truog reminded us that “in the spectrum between alive and dead, we set the threshold… Death is not a binary state, but a complex social choice.” People will likely continue to disagree about where we should set the threshold, especially as technology develops.

However, if we want to have a thoughtful discussion that respects the rights, wishes, and values of patients, loved ones, and everybody else who will one day face death, we need to first agree that there is a choice to be made.

Guest Post by Deniz Ariturk, Science & Society graduate student

Science Gets By With a Little Help From Its Friends

By Guest Post

On March 29, 2019

In Biology, Environment/Sustainability, Guest Post, Science Communication & Education, Students

There are many things in life that are a little easier if one recruits the help of friends. As it turns out, this is also the case with scientific research.

Lilly Chiou, a senior majoring in biology, and Daniele Armaleo, a professor in the Biology Department had a problem. Lilly needed more funding before graduation to initiate a new direction for her project, but traditional funding can sometimes take a year or more.

So they turned to their friends and sought crowdfunding.

Chiou and Armaleo are interested in lichens, low-profile organisms that you may have seen but not really noticed. Often looking like crusty leaves stuck to rocks or to the bark of trees, they — like most other living beings — need water to grow. But, while a rock and its resident lichens might get wet after it rains, it’s bound to dry up.

If you’re likin’ these lichens, perhaps you’d like to support some research…

This is where the power of lichens comes in: they are able to dry to a crisp but still remain in a suspended state of living, so that when water becomes available again, they resume life as usual. Few organisms are able to accomplish such a feat, termed desiccation tolerance.

Chiou and Armaleo are trying to understand how lichens manage to survive getting dried and come out the other end with minimal scars. Knowing this could have important implications for our food crops, which cannot survive becoming completely parched. This knowledge is ever more important as climate becomes warmer and more unpredictable in the future. Some farmers may no longer be able to rely on regular seasonal rainfall.

They are using genetic tools to figure out the mechanisms behind the lichen’s desiccation tolerance [. Their first breakthrough came when they discovered that extra DNA sequences present in lichen ribosomal DNA may allow cells to survive extreme desiccation. Now they want to know how this works. They hope that by comparing RNA expression between desiccation tolerant and non-tolerant cells they can identify genes that protect against desiccation damage.

As with most things, you need money to carry out your plans. Traditionally, scientists obtain money from federal agencies such as the National Science Foundation or the National Institutes of Health, or sometimes from large organizations such as the National Geographic Society, to fund their work. But applying for money involves a heavy layer of bureaucracy and long wait times while the grant is being reviewed (often, grants are only reviewed once a year). But Chiou is in her last semester, so they resorted to crowdfunding their experiment.

This is not the first instance of crowdfunded science in the Biology Department at Duke. In 2014, Fay-Wei Li and Kathleen Pryer crowdfunded the sequencing of the first fern genome, that of tiny Azolla. In fact, it was Pryer who suggested crowdfunding to Armaleo.

Chiou was skeptical that this approach would work. Why would somebody spend their hard-earned money on research entirely unrelated to them? To make their sales pitch, Chiou and Armaleo had to consider the wider impact of the project, rather than the approach taken in traditional grants where the focus is on the ways in which a narrow field is being advanced.

What they were not expecting was that fostering relationships would be important too; they were surprised to find that the biggest source of funding was their friends. Armaleo commented on how “having a long life of relationships with people” really shone through in this time of need — contributions to the fund, however small, “highlight people’s connection with you.” That network of connections paid off: with 18 days left in the allotted time, they had reached their goal.

After their experience, they would recommend crowdfunding as an option for other scientists. Having to create widely understood, engaging explanations of their work, and earning the support and encouragement of friends was a very positive experience.

“It beats writing a grant!” Armaleo said.

Guest Post by Karla Sosa, Biology graduate student