Duke Research Blog

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

Category: Biology Page 1 of 22

These Microbes ‘Eat’ Electrons for Energy

The human body is populated by a greater number of microbes than its own cells. These microbes survive using metabolic pathways that vary drastically from humans’.

Arpita Bose’s research explores the metabolism of microorganisms.

Arpita Bose, PhD, of Washington University in St. Louis, is interested in understanding the metabolism of these ubiquitous microorganisms, and putting that knowledge to use to address the energy crisis and other applications.

Photoferrotrophic organisms use light and electrons from the environment as an energy source

One of the biggest research questions for her lab involves understanding photoferrotrophy, or using light and electrons from an external source for carbon fixation. Much of the source of energy humans consume comes from carbon fixation in phototrophic organisms like plants. Carbon fixation involves using energy from light to fuel the production of sugars that we then consume for energy.

Before Bose began her research, scientists had found that some microbes interact with electricity in their environments, even donating electrons to the environment. Bose hypothesized that the reverse could also be true and sought to show that some organisms can also accept electrons from metal oxides in their environments. Using a bacterial strain called Rhodopseudomonas palustris TIE-1 (TIE-1), Bose identified this process called extracellular electron uptake (EEU).

After showing that some microorganisms can take in electrons from their surroundings and identifying a collection of genes that code for this ability, Bose found that this ability was dependent on whether a light source was also present. Without the presence of light, these organisms lost 70% of their ability to take in electrons.   

Because the organisms Bose was studying can rely on light as a source of energy, Bose hypothesized that this dependence on light for electron uptake could signify a function of the electrons in photosynthesis.  With subsequent studies, Bose’s team found that these electrons the microorganisms were taking were entering their photosystem.

To show that the electrons were playing a role in carbon fixation, Bose and her team looked at the activity of an enzyme called RuBisCo, which plays an integral role in converting carbon dioxide into sugars that can be broken down for energy. They found that RuBisCo was most strongly expressed and active when EEU was occurring, and that, without RuBisCo present, these organisms lost their ability to take in electrons. This finding suggests that organisms like TIE-1 are able to take in electrons from their environment and use them in conjunction with light energy to synthesize molecules for energy sources.  

In addition to broadening our understanding of the great diversity in metabolisms, Bose’s research has profound implications in sustainability. These microbes have the potential to play an integral role in clean energy generation.

Post by undergraduate blogger Sarah Haurin
Post by undergraduate blogger Sarah Haurin

Combining Up-Close Views of Science, Nature With the Magic of Light

Zinnia stamen by Thomas Barlow, Duke University

Thomas Barlow ’21 finds inspiration in small everyday things most people overlook: a craggy lichen growing on a tree, a dead insect, the light reflected by a pane of glass. Where we might see a flower, Barlow looks past the showy pink petals to the intricate parts tucked within.

The 20-year-old is a Duke student majoring in biology. By day, he takes classes and does research in a lab. But in his spare time, he likes to take up-close photographs using objects he finds outside or around the lab: peach pits, fireflies. But also pipettes, pencils.

A handheld laser pointer and flitting fireflies become streaks of light in this long-exposure image in Duke Forest. By Thomas Barlow.

Barlow got interested in photography in middle school, while playing around with his dad’s camera. His dad, a landscape architect, encouraged the hobby by enlisting him to take photos of public parks, gardens and playgrounds, which have been featured on various architects’ websites and in national publications such as Architecture Magazine. But “I always wanted to get closer, to see more,” Barlow said.

In high school he started taking pictures of still lifes. But he didn’t just throw flowers and fruit onto a backdrop and call it art. His compositions were a mishmash of insects and plants arranged with research gadgets: glass tubes, plastic rulers, syringes, or silicon wafers like those used for computer chips.

“I like pairing objects you would never find together normally,” Barlow said. “Removing them from their context and generating images with interesting textures and light.”

Sometimes his mother sends him treasures from her garden in Connecticut to photograph, like the pale green wings of a luna moth. But mostly he finds his subjects just steps from his dorm room door. It might be as easy as taking a walk through Duke Gardens or going for one of his regular runs in Duke Forest.

Having found, say, a flower bud or bumblebee, he then uses bits of glass, metal, mirrors and other shiny surfaces — “all objects that interact with light in some interesting way” – to highlight the interaction of light and color.

“I used to be really obsessed with dichroic mirrors,” pieces of glass that appear to change colors when viewed from different angles, Barlow said. “I thought they were beautiful objects. You can get so many colors and reflections out of it, just by looking at it in different ways.”

In one pair of images, the white, five-petaled flowers of a meadow anemone are juxtaposed against panels of frosted glass, a pipette, a mechanical pencil.

Another image pair shows moth wings. One is zoomed in to capture the fine details of the wing scales. The other zooms out to show them scattered willy-nilly around a shimmering pink circle of glass, like the remnants of a bat’s dinner plate.

Luna moth wings and wing scales with dichroic mirror, Thomas Barlow

For extreme close-ups, Barlow uses his Canon DSLR with a microscope objective mounted onto the front of a tube lens. Shooting this close to something so small isn’t just a matter of putting a bug or flower in front of the camera and taking a shot. To get every detail in focus, he takes multiple images of the same subject, moving the focal point each time. When he’s done he’s taken hundreds of pictures, each with a different part of the object in focus. Then he merges them all together.

At high magnification, Barlow’s flower close-ups reveal the curly yellow stamens of a zinnia flower, and the deep red pollen-producing parts of a tiger lily.

“I love that you can see the spikey pollen globules,” Barlow said.

Stomata and pollen on the underside of a tiger lily stamen, by Thomas Barlow

When he first got to Duke he was taking photos using a DIY setup in his dorm room. Then he asked some of the researchers and faculty he knew if there was anything photography-related he could do for their labs.

“I knew I was interested in nature photography and I wanted to practice it,” Barlow said.

One thing led to another, and before long he moved his setup to the Biological Sciences building on Science Drive, where he’s been photographing lichens for Daniele Armaleo and Jolanta Miadlikowska, both lichenologists.

“A lichen photo might not seem like anything special to an average person,” Barlow said. “But I think they’re really stunning.”

Love at First Whiff

Many people turn to the Internet to find a Mr. or Ms. Right. But lemurs don’t have to cyberstalk potential love interests to find a good match — they just give them a sniff.

A study of lemur scents finds that an individual’s distinctive body odor reflects genetic differences in their immune system, and that other lemurs can detect these differences by smell.

Smell check: Fritz the ring-tailed lemur sniffs a tree for traces of other lemurs’ scents at the Duke Lemur Center.
Smell check: Fritz the ring-tailed lemur sniffs a tree for traces of other lemurs’ scents. Photo by David Haring, Duke Lemur Center.

From just one whiff, these primates are able to tell which prospective partners have immune genes different from their own. The ability to sniff out mates with different immune genes could make their offspring’s immune systems more diverse and able to fight more pathogens, said first author Kathleen Grogan, who did the research while working on her Ph.D. with professor Christine Drea at Duke University.

The results appeared online August 22 in the journal BMC Evolutionary Biology.

Lemurs advertise their presence by scent marking — rubbing stinky glands against trees to broadcast information about their sex, kin, and whether they are ready to mate.

Lemurs can tell whether a mate’s immune genes are a good genetic match by the scents they leave behind.
Lemurs can tell whether a mate’s immune genes are a good genetic match by the scents they leave behind. Photo by David Haring, Duke Lemur Center

For the study, Grogan, Drea and colleagues collected scent secretions from roughly 60 lemurs at the Duke Lemur Center, the Indianapolis Zoo, and the Cincinnati Zoo. The team used a technique called gas chromatography-mass spectrometry to tease out the hundreds of compounds that make up each animal’s signature scent.

They also analyzed the lemurs’ DNA, looking for differences within a cluster of genes called MHC that help trigger the body’s defenses against foreign invaders such as bacteria and viruses.

Their tests reveal that the chemical cocktail lemurs emit varies depending on which MHC types they carry.

To see if potential mates can smell the difference, the researchers presented lemurs with pairs of wooden rods smeared with the bodily secretions of two unfamiliar mates and observed their responses. Within seconds, the animals were drawn to the smells wafting from the rods, engaging in a frenzy of licking, sniffing, or rubbing their own scents on top.

In 300 trials, the team found that females paid more attention to the scents of males whose immune genes differed from their own.

MHC genes code for proteins that help the immune system recognize foreign invaders and distinguish “friend” from “foe.” Since different genetic versions respond to different sets of foreign substances, Grogan said, sniffing out genetically dissimilar mates produces offspring more capable of fighting a broad range of pathogens.

Just because females spent more time checking out the scents of dissimilar males doesn’t necessarily make them more likely to have kids together, Grogan said. Moving forward, she and her colleagues plan to use maternity and paternity DNA test results from wild lemurs living in Beza Mahafaly Reserve in Madagascar to see if lemur couples are more different in their MHC type than would be expected by chance.

Similar results have been found in humans, but this is the first time the ability to sniff out partners based on their immune genes has been shown in such distant primate kin, said Grogan, who is currently a postdoctoral fellow at Pennsylvania State University.

“Growing evidence suggests that primates rely on olfactory cues way more than we thought they did,” Grogan said. “It’s possible that all primates can do this.”

This research was supported by the National Science Foundation (BCS #0409367, IOS #0719003), the National Institutes of Health (F32 GM123634–01), and the Duke University Center for Science Education.

CITATION: “Genetic Variation at MHC class II Loci Influences Both Olfactory Signals and Scent Discrimination in Ring-Tailed Lemurs,” Kathleen E. Grogan, Rachel L. Harris, Marylène Boulet, and Christine M. Drea. BMC Evolutionary Biology, August 22, 2019. DOI: 10.1186/s12862-019-1486-0

Post by Robin A. Smith

Do DNA Tests Sell Rosy Ideas About Race for Profit?

Earlier this year,  the online DNA testing company Ancestry.com faced a media firestorm and social media backlash after posting a controversial ad on its YouTube page.

The DNA testing company Ancestry.com took down its ad, “Inseparable,” in April 2019 in response to criticism that it romanticized slavery.

Titled “Inseparable,” the 30-second ad depicted a white man in the antebellum South asking an African-American woman to flee to the North with him. Before the woman can answer, the piece cuts to a tagline: “Only you can keep the story going. Uncover the lost chapters of your family history with Ancestry.” Many criticized the ad’s historical inaccuracy, showcasing a rosier portrayal of a complicated past. To extinguish flames, Ancestry completely pulled the ad from its platforms.

A recent Duke study of dozens of other ads across multiple DNA testing companies shows that this isn’t the only example of mixed messaging about race and identity from the world of genetic ancestry tests.

The tests are quite simple: order a kit, send off a saliva sample and receive an ethnicity estimate within weeks. A test taker’s ethnicity is broken down into percentages based off their DNA matches compared to a globally referenced DNA database. Kits can range in price from $79 to$400. Sales of DNA testing kits had reached 12 million people by 2017, as reported by ScienceLine.

As part of the six-week summer research program Story+, Duke students Dakota Douglas, Mona Tong and Madelyn Winchester analyzed the messaging in 90 video ads from the companies 23andMe, AncestryDNA and MyHeritageDNA to see what they promise consumers.

Many of the ads lured customers with promises of a newfound identity and possible family members, the team found. One Ancestry.com ad, entitled “Kyle,” depicts a customer whose childhood was steeped in German culture, but discovers as an adult that he is also part Scottish and Irish. He happily “traded in his lederhosen for a kilt,” completely forgoing his previous heritage and reducing a newly discovered culture to stereotypes.

“There were a lot of advertisements similar to that one,” said team member Mona Tong. “Many found a new identity embracing it fully despite a lack of any cultural connections.”

“Kyle” illustrates a phenomenon described in a 2018 study from the University of British Columbia, which found that people tended to “cherry-pick” the results, identifying more with certain ethnicities and cultures to appear different. Whites were more likely to see their results as “transformational” than their nonwhite counterparts.

“It’s not a bad idea to test your genes for medical reasons,” said Patricia Bass, the team’s project mentor. “However, these ads can be misleading by assuming that someone’s cultural and racial heritage are determined by genes.”

While the majority of subjects featured within the ads were white, the few ads that featured people of color often glossed over the complicated history of someone’s lineage or conveniently left out difficult topics. Ancestry’s “Anthem” ad detailed historical reenactments of an African tribal women, prohibition gangsters, a man fleeing England for America and Native Americans somberly heading to a new land. A voiceover speaks with inspiration ending with a shot of a biracial woman.

In marketing the idea that we are all one, the ads fetishized mixed-race subjects, while ignoring the genocide and displacement of people, the team found.

The team hopes future research will further examine the impact of these ads on people’s view of identity. Importantly, one could note if there were any focus groups to test these ads before release.

“It furthers the idea of colorblindness,” Tong said. “It assumes that relationships are contingent upon common ancestry and genes.”

“In a way, companies are trying to help by focusing on the interconnectivity and commonalities between people,” Tong said. “But it hurts more than it helps.”

Story+ is a six-week undergraduate research program offered through the John Hope Franklin Humanities Institute and Bass Connections, with support from the Duke University Libraries and Versatile Humanists at Duke.

By Deja Finch

Overdiagnosis and the Future of Cancer Medicine

For many years, the standard strategy for fighting against cancer has been to find it early with screening when the person is still healthy, then hit it with a merciless treatment regimen to make it go away.

But not all tumors will become life-threatening cancers. Many, in fact, would have caused no issues for the rest of the patients’ lives had they not been found by screening. These cases belong to the category of overdiagnosis, one of the chief complaints against population-level screening programs.

Scientists are reconsidering the way to treat tumors because the traditional hit-it-hard approach has often caused the cancer to seemingly go away, only to have a few cells survive and the entire tumor roar back later with resistance to previously effective medicine.

Dr. Marc Ryser, the professor who gave this meaty talk

In his May 23 talk to Duke Population Health, “Cancer Overdiagnosis: A Discourse on Population Health, Biologic Mechanism and Statistics,” Marc Ryser, an assistant professor at Duke’s Departments of Population Health Sciences and Mathematics, walked us through how parallel developments across different disciplines have been reshaping our cancer battle plan. He said the effort to understand the true prevalence of overdiagnosis is a point of focus in this shift.

Past to Future: the changing cancer battle plan
Credit: Marc Ryser, edit: Brian Du

Ryser started with the longstanding biological theory behind how tumors develop. Under the theory of clonal sweeps, a relatively linear progression of successive key mutations sweeps through the tumor, giving it increasing versatility until it is clinically diagnosed by a doctor as cancer.

Clonal sweeps model, each shade is a new clone that introduces a mutation credit: Sievers et al. 2016

With this as the underpinning model, the battle plan of screen early, treat hard (point A) makes sense because it would be better to break the chain of progression early rather than later when the disease is more developed and much more aggressive. So employing screening extensively across the population for the various types of cancer is the sure choice, right?

But the data at the population level for many different categories of cancers doesn’t support this view (point B). Excluding the cases of cervical cancer and colorectal cancer, which have benefited greatly from screening interventions, the incidence of advanced cases of breast cancer and other cancers have stayed at similar levels or actually continued to increase during the years of screening interventions. This has raised the question of when screening is truly the best option.

Scientists are thinking now in terms of a “benefit-harm balance” when mass-screening public health interventions are carried out. Overdiagnosis would pile up on the harms side, because it introduces unnecessary procedures that are associated with adverse effects.

Thinking this way would be a major adjustment, and it has brought with it major confusion.

Paralleling this recent development on the population level, new biological understanding of how tumors develop has also introduced confusion. Scientists have discovered that tumors are more heterogeneous than the clonal sweeps model would make it appear. Within one tumor, there may be many different subpopulations of cancer cells, of varying characteristics and dangerousness, competing and coexisting.

Additional research has since suggested a more complex, evolutionary and ecological based model known as the Big Bang-mutual evolution model. Instead of the “stepwise progression from normal to increasingly malignant cells with the acquisition of successive driver mutations, some cancers appear to evolve more like a Big Bang, where the malignant ability is already concentrated in the founder cell,” Ryser said.

As the first cell starts to replicate, its descendants evolve in parallel into different subpopulations expressing different characteristics. While more research has been published in favor of this model, some scientists remain skeptical.

Ryser’s research contributes to this ongoing discussion. In comparing the patterns by which mutations are present or absent in cancerous and benign tumors, he obtained results favoring the Big Bang-mutual evolution model. Rather than seeing a neat region of mutation within the tumor, which would align with the clonal sweeps model, he saw mutations dispersed throughout the tumor, like the spreading of newborn stars in the wake of the Big Bang.

How to think about mutations within a tumor
credit: NASA

The more-complicated Big Bang-mutual evolution model justifies an increasingly nuanced approach to cancer treatment that has been developing in the past few years. Known as precision medicine (point C), its goal is to provide the best treatment available to a person based on their unique set of characteristics: genetics, lifestyle, and environment. As cancer medicine evolves with this new paradigm, when to screen will remain a key question, as will the benefit-harm balance.

There’s another problem, though: Overdiagnosis is incredibly hard to quantify. In fact, it’s by nature not possible to directly measure it. That’s where another area of Ryser’s research seeks to find the answers. He is working to accurately model overdiagnosis to estimate its extent and impact.

Going forward, his research goal is to try to understand how to bring together different scales to best understand overdiagnosis. Considering it in the context of the multiscale developments he mentioned in his talk may be the key to better understand it.

Post by Brian Du

Pot Not So Harmless for Teens

Marijuana is becoming legalized and decriminalized to the point that more than 63 percent of Americans have access to medical and recreational cannabis. But researchers and policy experts still don’t know very much about the long-term health effects.

The 2019 annual symposium by Duke’s Center on Addiction & Behavior Change,  “Altered States of Cannabis Regulation: Informing Policy with Science,” provided some scientific answers. Madeline Meier, assistant professor of Psychology at Arizona State University and a former Duke post-doc, spoke about her longitudinal research projects that offer critical insights about the long-term effects of cannabis use.

Meier investigates the relationship between cannabis use and IQ in a 38-year-long study that has been collecting data on a group of 1,000 people born in New Zealand since birth. Longitudinal studies like this that follow the same group of individuals across their lifespan are vital to understanding the effects of extended cannabis use on the human body, but they are difficult to conduct and keep funded. The 95 percent retention rate of this study is quite impressive and provides much-needed data.


Madeline Meier of Arizona State University

The researchers had tested the babies’ IQ at early childhood, then conducted regular IQ and cannabis use assessments between the ages of 18 and 38. They found that participants who heavily used weed for extended periods of time experienced a significant IQ drop, as well as other impairments in learning and memory skills. Specifically, users who had three or more clinical diagnoses of cannabis dependency, defined as compulsive use despite physical, legal, or social problems caused by the drug, showed an average 6-point IQ drop over the years. Those who only tried the drug a few times showed no decline, and those who never used weed showed a 1-point IQ increase.

Notably, however, the results depended on age of onset and level of use. Meier emphasized that her results do not support the common misconception that any amount of weed use can immediately lead to IQ decline. To the contrary, Meier’s team found that short-term, low-level use did not have any effect on IQ; only heavy users suffered the negative effects. The age of onset of cannabis use was critical, too: Adolescents were more vulnerable to the drug’s harms, with study participants who started using as adolescents showing an 8-point drop in IQ points. Given what we know about adolescents’ affinity for risky behavior, specifically around experimentation with drugs, this finding is particularly worrisome.

In addition to causing cognitive impairment, persistent cannabis use jeopardizes people’s psychosocial functioning as well. The Dunedin longitudinal study has also revealed that people who continued to use weed despite multiple dependency diagnoses experienced downward social mobility, relationship problems, antisocial workplace behavior, financial difficulties, and even higher numbers of traffic convictions. In short, social life is likely to be perilous for heavy weed users.

While some have suggested that the harmful effects of weed might be caused not by the drug itself but by the reduced years of education, low socioeconomic status, mental health problems, or simultaneous use of tobacco, alcohol or other drugs among weed users, Meier and her team found that the impairments persisted even when these factors were accounted for. Cannabis alone was responsible for the effects reflected in Meier’s research. In fact, there is limited evidence for the opposite causational link: weed use may be the cause of mental health problems rather than being caused by them. One study found a weak correlation between years of marijuana use and depression, but Meier was careful to point out that it would take “a lot of cannabis use to lead to clinically diagnosed depression.”

Given this data, Meier called on the policy-makers in the room to focus their efforts on delaying the onset of cannabis use in youth and encouraging cessation (especially among adolescents). In appealing to the researchers, she underlined the need for additional longitudinal studies into the mechanisms and parameters of cannabis use that produce long-term impairments.

As public and political support of marijuana legalization grows, we must be careful not to underestimate the dangers of the drug. Without knowing the full extent of the risks and benefits of weed, policy-makers cannot effectively promote public health, safety, and social equity.

Guest Post by Deniz Ariturk

How the Flu Vaccine Fails

Influenza is ubiquitous. Every fall, we line up to get our flu shots with the hope that we will be protected from the virus that infects 10 to 20 percent of people worldwide each year. But some years, the vaccine is less effective than others.

Every year, CDC scientists engineer a new flu virus. By examining phylogenetic relationships, which are based on shared common ancestry and relatedness, researchers identify virus strains to target with a vaccine for the following flu season.

Sometimes, they do a good job predicting which strains will flourish in the upcoming flu season; other times, they pick wrong.

Pekosz’s work has identified why certain flu seasons saw less effective vaccines.

Andrew Pekosz, PhD, is a researcher at Johns Hopkins who examines why we fail to predict strains to target with vaccines. In particular, he examines years when the vaccine was ineffective and the viruses that were most prevalent to identify properties of these strains.

A virus consists of RNA enclosed in a membrane. Vaccines function by targeting membrane proteins that facilitate movement of the viral genome into host cells that it is infecting. For the flu virus, this protein is hemagglutinin (HA). An additional membrane protein called neuraminidase (NA) allows the virus to release itself from a cell it has infected and prevents it from returning to infected cells.  

The flu vaccine targets proteins on the membrane of the RNA virus. Image courtesy of scienceanimations.com.

Studying the viruses that flourished in the 2014-2015 and 2016-2017 flu seasons, Pekosz and his team have identified mutations to these surface proteins that allowed certain strains to evade the vaccine.

In the 2014-2015 season, a mutation in the HA receptor conferred an advantage to the virus, but only in the presence of the antibodies present in the vaccine. In the absence of these antibodies, this mutation was actually detrimental to the virus’s fitness. The strain was present in low numbers in the beginning of the flu season, but the selective pressure of the vaccine pushed it to become the dominant strain by the end.

The 2016-2017 flu season saw a similar pattern of mutation, but in the NA protein. The part of the virus membrane where the antibody binds, or the epitope, was covered in the mutated viral strain. Since the antibodies produced in response to the vaccine could not effectively identify the virus, the vaccine was ineffective for these mutated strains.

With the speed at which the flu virus evolves, and the fact that numerous strains can be active in any given flu season, engineering an effective vaccine is daunting. Pekosz’s findings on how these vaccines have previously failed will likely prove invaluable at combating such a persistent and common public health concern.

Post by undergraduate blogger Sarah Haurin
Post by undergraduate blogger Sarah Haurin


Building a Mangrove Map

“Gap maps” are the latest technology when it comes to organizing data. Although they aren’t like traditional maps, they can help people navigate through dense resources of information and show scientists the unexplored areas of research.

A ‘gap map’ comparing conservation interventions and outcomes in tropical mangrove habitats around the world turns out to be a beautiful thing.

At Duke’s 2019 Master’s Projects Spring Symposium, Willa Brooks, Amy Manz, and Colyer Woolston presented the results of their year-long Masters Project to create this map.

You’d never know by looking at the simple, polished grid of information that it took 29 Ph.D. students, master’s students and undergraduates nearly a full year to create it. As a member of the Bass Connections team that has been helping to support this research, I can testify that gap maps take a lot of time and effort — but they’re worth it.

Amy Manz, Willa Brooks, and Colyer Woolston present their evidence map (or gap map) at the 2019 Master’s Projects Spring Symposium

When designing a research question, it’s important to recognize what is already known, so that you can clearly visualize and target the gaps in the knowledge.

But sifting through thousands of papers on tropical mangroves to find the one study you are looking for can be incredible overwhelming and time-intensive. This is purpose of a gap map: to neatly organize existing research into a comprehensive grid, effectively shining a light on the areas where research is lacking, and highlighting patterns in areas where the research exists.

In partnership with World Wildlife Fund, Willa, Amy, and Colyer’s team has been working under the direction of Nicholas School of the Environment professors Lisa Campbell and Brian Silliman to screen the abstracts of over 10,000 articles, 779 of which ended up being singled out for a second round of full-text screening. In the first round, we were looking for very specific inclusion criteria, and in the second, we were extracting data from each study to identify the outcomes of conservation interventions in tropical mangrove, seagrass, and coral reef habitats around the world.

Coastal Mangroves (Photo from WikiCommons: US National Oceanic and Atmospheric Administration)

While the overall project looked at all three habitats, Willa, Amy, and Colyer’s Master’s Project focused specifically on mangroves, which are salt-tolerant shrubs that grow along the coast in tropical and subtropical regions. These shrubs provide a rich nursery habitat to a diverse group of birds and aquatic species, and promote the stability of coastlines by trapping sediment runoff in their roots. However, mangrove forests are in dramatic decline.

According to World Wildlife Fund, 35 percent of mangrove ecosystems in the world are already gone. Those that remain are facing intense pressure from threats like forest clearing, overharvesting, overfishing, pollution, climate change, and human destruction of coral reefs. Now more than ever, it is so important to study the conservation of these habitats, and implement solutions that will save these coastal forests and all the life they support. The hope is that our gap map will help point future researchers towards these solutions, and aid in the fight to save the mangroves.

This year’s team built a gap map that successfully mapped linkages between interventions and outcomes, indicating which areas are lacking in research. However, the gap map is limited because it does not show the strength or nature of these relationships. Next year, another Bass Connections team will tackle this challenge of analyzing the results, and further explore the realm of tropical conservation research.

Post by Anne Littlewood, Trinity ’21

‘Death is a Social Construct’

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.

Robert Truog teaching (Harvard photo)

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

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 (left) and Armaleo in a video.

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


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