Duke Research Blog

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

Category: Science Communication & Education (Page 1 of 16)

The Importance of Evidence in Environmental Conservation

What counts as good evidence?

In medical research, a professional might answer this question as you would expect: evidence can be trusted if it is the result of a randomized, controlled, double-blind experiment, meaning the evidence is only as strong as the experiment design. And in medicine, it’s possible (and important) to procure this kind of strong evidence.

But when it comes to conservation, it’s a whole different story.

Dr. David Gill (photo from The Nicholas School)

The natural world is complicated, and far beyond our control. When studying the implications of conservation, it’s not so easy to design the kind of experiment that will produce “good” evidence.

David Gill, a professor in Duke’s Nicholas School for the Environment, recently led a study featured in the journal Nature that needed to  define what constitutes good evidence in the realm of marine conservation. Last Wednesday, he made a guest appearance in my Bass Connections meeting to share his work and a perspective on the importance of quality evidence.

Gill’s research has been centered around evaluating the effectiveness of Marine Protected Areas (or MPAs) as a way of protecting marine life. Seven percent of the world’s oceans are currently designated as MPAs, and by 2020, the goal is to increase this number to 10 percent. MPAs arguably have massive effects on ecosystem health and coastal community functioning, but where is the evidence for this claim?

Although past investigations have provided support for creating MPAs,  Gill and his team were concerned with the quality of this evidence, and the link between how MPAs are managed and how well they work. There have historically been acute gaps in study design when researching the effects of MPAs. Few experiments have included pre-MPA conditions or an attempt to control for other factors. Most of these studies have been done in hindsight, and have looked only at the ecological effects within the boundaries of MPAs, without any useful baseline data or control sites to compare them to.

As a result of these limitations, the evidence base is weak. Generating good evidence is a massive undertaking when you are attempting to validate a claim by counting several thousand moving fish.

Gill’s measure of ecosystem health includes counting fish. (Photo from Avoini)

So is there no way to understand the impacts of MPAs? Should conservation scientists just give up? The answer is no, absolutely not.

To produce better evidence, Gill and his team needed to design a study that would isolate the effects of MPAs. To do this, they needed to account for location biases and other confounding variables such as the biophysical conditions of the environment, the population density of nearby human communities, and the national regulations in each place.

The solution they came up with was to compare observations of current conditions within MPAs to “counterfactual” evidence, which is defined as what would have happened had the MPA not been there. Using statistical matching of MPAs to nearby non-MPA and pre-MPA sites, they were able to obtain high-quality results.

A happy sea turtle pictured in a marine protected area (photo from English Foreign and Commonwealth Office.)

The research showed that across 16,000 sampled sites, MPAs had positive ecological impacts on fish biomass in 71 percent of sites. They also discovered that MPAs with adequate staffing had far greater ecological impacts than those without, which is a pretty interesting piece of feedback when it comes to future development. It’s probably not worth it to create MPAs before there is sufficient funding in place to maintain them.

Gill doesn’t claim that his evidence is flawless; he fully admits to the shortcomings in this study, such as the fact that there is very little data on temperate, coldwater regions — mostly because there are few MPAs in these regions.

The field is ripe for improvement, and he suggests that future research look into the social impacts of MPAs and the implications of these interventions for different species. As the evidence continues to improve, it will be increasingly possible to maximize the win-wins when designing MPAs.

Conservation science isn’t perfect, but neither is medicine. We’ll get there.

Sean Carroll on the Evolution of Snake Venom

What’s in a snake bite?

According to University of Wisconsin-Madison evolutionary biologist Sean Carroll who visited Duke and Durham last week, a snake bite contains a full index of clues.

In his recent research, Carroll has been studying the adaptations of novelties in animal form, such as snake venom. Rattlesnakes, he explains, are the picture of novelty. With traits such as a limbless body, fangs, infrared pits, patterned skin, venom, and the iconic rattle, they represent an amazing incarnation of evolution at work.

Rattlesnakes: the picture of novelty (Photo from USGS)

Snake venoms contain a complex mixture of proteins. This mixture can differ in several ways, but the most interesting difference to Carroll is the presence or absence of neurotoxins. Neurotoxic venom has proven to be a very useful trait, because neurotoxins destroy the nervous tissue of prey, effectively paralyzing the animal’s respiratory system.

Some of today’s rattlesnake species have neurotoxic venom, but some don’t. So how did this happen? That’s what Carroll was wondering too.

Some genes within genomes, such as HOX genes, evolve very slowly from their original position among the chromosomes, and see very few changes in the sequence in millions of years.

But snake venom Pla2 genes are quite the opposite. In recent history, there has been a massive expansion of these genes in the snake genome, Carroll said. When animals evolve new functions or forms, the question always arises: are these changes the result of brand new genes or old genes taking on new functions?

Another important consideration is the concept of regulatory versus structural genes. Regulatory genes control the activity of other genes, such as structural genes, and because of this, duplicates of regulatory genes are generally not going to be a favorable adaptation. In contrast, structural gene activity doesn’t affect other genes, and duplicates are often a positive change. This means it is easier for a new structural gene to evolve than a regulatory one. Carroll explained.

Evolutionary Biologist Sean Carroll (Photo from seanbcarroll.com)

Carroll examined neurotoxic and non-neurotoxic snakes living in overlapping environments. His research showed that the most recent common ancestor of these species was a snake with neurotoxic venom. When comparing the genetic code of neurotoxic snakes to non-neurotoxic ones, he found that the two differed by the presence or absence of 16 genes in the metalloproteinase gene complex. He said this meant that non-neurotoxic venom could not evolve from neurotoxic venom.

So what is the mechanism behind this change? What could be the evolutionary explanation?

When Carroll’s lab compared another pair of neurotoxic and non-neurotoxic species in a different region of the US, they found that the two species differed in exactly the same way, with the same set of genes deleted as had been observed in the first discovery. With this new information, Carroll realized that the differences must have occurred through the mechanism of hybridization, or the interbreeding of neurotoxic and non-neurotoxic species.

Carroll’s lab is now doing the structural work to study if the genes that result in neurotoxic and  non-neurotoxic protein complexes are old genes carrying out new functions or entirely new genes. They are using venom gland organoids to look into the regulatory processes of these genes.

In addition to his research studying the evolution of novelties, Carroll teaches molecular biology and genetics at Madison and has devoted a large portion of his career to  storytelling and science education.

Meet New Blogger Anne Littlewood – Working on Biology and Puppies

My name is Anne Littlewood and I am a sophomore here at Duke. I grew up in San Francisco, spent a brief moment living on the island of Kauai, and finished high school in Pebble Beach, California. I am studying the intersection of biology and psychology here at Duke, in an effort to understand how biological mechanisms inform our interactions with the environment.

Snuggles in Puppy Kindergarten!

Outside the classroom, I can be found frequenting Duke’s beloved Puppy Kindergarten, where I work as a volunteer. Recently, I’ve become an Associate Editor for Duke’s literary magazine, The Archive. I love writing creatively, and it’s been so great to find a community of my literature- loving peers. I’m also participating in a Bass Connections project this year, and working on a team to evaluate the outcomes of different conservation interventions through the synthesis of an evidence gap map for World Wildlife fund.

Me and Cricket on Carmel Beach

Most of all I love to spend time outdoors, whether it’s exploring the mountains of North Carolina on a backpacking trip, lying in my hammock at Eno Quarry, or walking through the gardens each day on my way to class. I’m a huge animal lover, and I’m way too obsessed with my dog, a 12-pound cavalier King Charles spaniel named Cricket.

I’ve always been into science, but I think I really fell in love with Biology my freshman year of high school, when my all time favorite teacher, Mr. Cinti helped me extract my DNA one afternoon, just for fun. Writing is my passion, and I’m excited to explore my skills in a variety of genres this year. This blog is my first ever attempt at journalism/ science writing, and I’m excited to give it a try!

Considerations about AIDS from Brazilian literature

To know what illness is, you have to be ill first.

This was one of the points that post-doctoral student and essayist  Milena Mulatti Magri emphasized in her talk on Oct. 15. She was discussing Brazilian writer Caio Fernando Abreu’s writings about AIDS and its effect on groups who already faced societal prejudice before the breakout of AIDS in the 1980’s and 90’s, when patients were identified mainly as homosexual.

By studying research done by Professor Vladimir Safatle and physician and philosopher Georges Canguilhem, Magri has pieced together that health is seen as a form of normativity and disease as a deviation. Thus, ostracizing and excluding those who contract disease is seen as justifiable because they have deviated from what is seen as normal, even when the disease is not the fault of the patient.

Magri has also analyzed essays about the relationship between disease, metaphor and patient stigma, such as cancer patients who, in addition to combating the illness growing unwelcome inside their own bodies, also have to deal with social stigmas that come with disease, such as cancer as a representation for evil.

Brazilian author and columnist Caio Fernando Abreu. (Image from KD Frases.)

However, while Magri emphasized that social metaphors of different diseases should be deconstructed, she has also found that literature and personal writing can be a way to discuss and otherwise “incommunicable experience.”

During a time when it was seen as shameful to have AIDS, Caio Fernando Abreu began a biweekly publication of his health chronicles in the newspaper O Estado de São Paulo, which was one of the first instances of someone publicly discussing their experience with AIDS from the perspective of the ill person, as opposed to from the perspective of doctors or health experts.

Abreu’s columns confronted the difficulty of living with disease and living in proximity to death, and discuss the increased social prejudice as a result of the disease. Abreu also wrote a play called “O homem e amancha” (in English, “The Man and the Stain”), which is an intertextual reading of the famous Spanish novel Don Quijote de la Mancha. In her talk, Magri explained that “Mancha,” which in English means “stain,” can refer to both the home of Don Quijote before he sets off of on his adventures and the rare skin cancer that often accompanies AIDS called Kaposi Sarcoma, which forms lesions on the skin that resemble stains.

Abreu intended to use his own experiences to question the social prejudice against AIDS, and there Magri highlighted a marked change, even between his own writings at the beginning of his diagnosis compared to those at the end of his life, when he spoke openly and without metaphor about suffering that is amplified by social exclusion. 

Magri believes that Abreu’s writings were pioneering acts of courage, and that from his writing we learn to empathize rather than to judge and stigmatize.

Post by Victoria Priester

Victoria Priester

Coding: A Piece of Cake

Image result for cake

Imagine a cake, your favorite cake. Has your interest been piqued?

“Start with Cake” has proved an effective teaching strategy for Mine Cetinkaya-Rundel in her introduction-level statistics classes. In her talk “Teaching Computing via Visualization,” she lays out her classroom approaches to helping students maintain an interest in coding despite its difficulty. Just like a cooking class, a taste of the final product can motivate students to master the process. Cetinkaya-Rundel, therefore, believes that instead of having students begin with the flour and sugar and milk, they should dive right into the sweet frosting. While bringing cake to the first day of class has a great success rate for increasing a class’s attention span (they’ll sugar crash in their next classes, no worries), what this statistics professor actually refers to is showing the final visualizations. By giving students large amounts of pre-written code and only one or two steps to complete during the first few class periods, they can immediately recognize coding’s potential. The possibilities become exciting and capture their attention so that fewer students attempt to vanish with the magic of drop/add period. For the student unsure about coding, immediately writing their own code can seem overwhelming and steal the joy of creating.

Example of a visualization Cetinkaya-Rundel uses in her classes

To accommodate students with less background in coding, Cetinkaya-Rundel believes that skipping the baby steps proves a better approach than slowing the pace. By jumping straight into larger projects, students can spend more time wrestling their code and discovering the best strategies rather than memorizing the definition of a histogram. The idea is to give the students everything on day one, and then slowly remove the pre-written coding until they are writing on their own. The traditional classroom approach involves teaching students line-by-line until they have enough to create the desired visualizations. While Cetinkaya-Rundel admits that her style may not suit every individual and creating the assignments does require more time, she stands by her eat-dessert-first perspective on teaching. Another way she helps students maintain their original curiosity is by cherishing day one through pre-installed packages which allow students to start playing with visualizations and altering code right away.

Not only does Cetinkaya-Rundel give mouth-watering cakes as the end results for her students but she also sometimes shows them burnt and crumbling desserts. “People like to critique,” she explains as she lays out how to motivate students to begin writing original code. When she gives her students a sloppy graph and tells them to fix it, they are more likely to find creative solutions and explore how to make the graph most appealing to them. As the scaffolding falls away and students begin diverging from the style guides, Cetinkaya-Rundel has found that they have a greater understanding of and passion for coding. A spoonful of sugar really does help the medicine go down.  

    Post by Lydia Goff

Meet New Blogger Brian Du

Brian survives his week in the desert.

Hi! My name is Brian Du, and I’m a sophomore from Texas. I’m a pre-med majoring in computer science. I like vacations, hiking, and hiking on vacation. Besides these hobbies, I also love learning about science and hearing a good story. These latter two are exactly why I’m excited to be writing for the Duke Research Blog.

My first exposure to science happened in third grade because my goldfish kept getting sick and dying. This made me sad and I became invested in making them well again. I would measure pH levels regularly with my dad and keep notes on the fishes’ health. Eventually the process turned into a science fair project. I remember I loved presenting because I got to point out to the judges the ‘after’ pictures of my fish, which showed them alive, healthy, and happy (I think? it’s hard to tell with fish).

One happy fish!
Source: Reddit

My fish and I go way back.

After that third-grade experiment, I kept doing science projects — almost year after year actually — since I love the research process. From framing the right questions and setting up the experiment, to running the trials and writing up and sharing my work, my enthusiasm grew with each step. Come competition day, I noticed that in interviews that went well, my excitement was contagious, so that judges grew more eager too as they listened. And so I understood: a huge part to science is communication. Science, like food or a good story, is meant to be shared with others. The scientist is a storyteller, adjusting his presentation to captivate different audiences. With judges, I spoke jargon, but during public exhibition, where I chatted with anyone who came up to me, I got creative when asked about my research. Analogies helped me link strange concepts to everyday objects and experiences. An important protein channel became a pipe, and its inhibitor molecule a rock which would clog the pipe to make it unusable.

protein channel “pipe”
edited from CThompson02

Now that I’m at Duke, there’s so many stories to tell of the rich variety of research being done right on campus! I’ve written a few articles for the Chronicle covering some of the new medicine or proteins Duke professors have been involved in developing. As I keep an ear out for more stories, I hope to share a few of them in my upcoming posts, because I know they’ll be exciting!

Falling Out of Love With Science and Our Civic Duties

Last Friday, I attended Falling Out of Love with Science, a lunch function during which Milan Yager,executive director of the American Institute for Medical and Biological Engineering, discussed why those of us interested in scientific research should care about the actions of prominent politicians, especially those that relate to the underfunding of scientific research.

Milan Yager of AIMBE

Milan Yager is the executive director of the American Institute for Medical and Biological Engineering.

Before attending Yager’s talk, I guess I didn’t quite realize how much of innovation was enabled by government funding. Many revolutionary discoveries are made possible through the NIH (https://www.nih.gov) that we don’t even realize we use on a daily basis.

However, as I came to realize, public support for research funding is jeopardized by the propagation of fake news defeating the need for concrete scientific research, hence propelling research under-funding. Over time, funding for the NIH and other government research funding has declined, which has slowed American innovation.

What I enjoyed most about his talk however, was the unexpected motivational turn that it took at the end. He discussed how we, as young researchers invested in finding our personal truths through science, needed to use our voices to stand up against the proliferation of myths in politics in favor of concrete facts.

NIH funding trends

Here’s a curve we definitely want to bend: NIH research funding has flattened and fallen.

Though this can be done in different ways, Yager made sure to point out how essential it is for Americans to vote, citing a statistic that points out that 20 percent of Americans don’t vote because they are “simply too lazy.” (Learn how to register to vote in North Carolina.)

He also encouraged us to send letters to our senators, rally for what we believed in, and not give up on our goals in the face of adversity — something that he called “sitting at the table.” Yager points out that if you don’t “sit at the table,” then your issue won’t get the necessary exposure needed for it to be fixed.

What can we, as Duke students, take away from what Yager had to say? Mainly this: Duke is a research institution that is partially made capable by government funding; for our capacity for research to be continued to be fully realized, we must use our voices to make sure that the propagation of ‘fake news’ does not cut funding for factual research.

This is mainly achieved by voting– those who perpetuate false “facts” in order to remain in power must be replaced with those who realize the importance of scientific research.

Perhaps, for society to fall back in love with science, we need to fall out of love with the myths propagated by tribal politics.

Post by Rebecca Williamson

New Blogger Rebecca Williamson: The Moon and Some Stars

Hello! My name is Rebecca Williamson, and I am a freshman here at Duke University. Coming into college, I plan to major in economics, but that could very well change. As for my interests outside of the classroom, I enjoy singing and theater and am a member of Out of the Blue, one of the all-female a cappella groups here at Duke!

Rebecca Williamson, Duke 2022

Rebecca Williamson, Duke 2022

I fell in love with Duke the second I stepped on campus. I am excited to see what Duke has to offer me, but more importantly, what I can offer to Duke.

My interest in science, specifically astronomy, was piqued at a very young age. By age six, I had not one, but three,  Moon in my Room light up toys (remote controlled models of the Moon that scrolled through the waxing and waning phases of the Moon at the touch of a button) mounted in my bedroom. By nine, I had the entire planetary system (yes, including Pluto) hanging from my ceiling. Though I cannot say that my interests remain with astronomy, it is what first got me invested in science. I have since gained interest in the natural sciences and animal sciences, though every so often I do press some of the buttons on my Moon in my Room remote.

Some random boy imagines he's as cool as six-year-old Rebecca.

Some random boy imagines he’s as cool as six-year-old Rebecca.

My love of writing, however, was spawned by my love of theater. As an active member of my high school’s theater community, I was roped into being a part of, and eventually became the president, of my school’s Cappies Critics team. As a Cappie, I was expected to watch local high school plays and musicals and write critical, holistic reviews of them. This program jump-started my love for writing and helped me to develop my own unique journalistic voice.

solar system mobile. www.luxrysale.comI hope to combine my interest in the natural and animal sciences with my love for writing and chronicle some of the amazing research going on in these fields both on campus and around Durham! I also hope to incorporate my interests in music and theater into my inquiries and document scientific research surrounding music and the arts in the Duke community.

Duke University Research Blog, look out, because here I come!

Post by Rebecca Williamson

New Blogger: Victoria Priester Loves Animals and Books

Hi! My name is Victoria Priester, and I’m a sophomore at Duke and one of this year’s new Duke Research bloggers.

Victoria meeting a very intelligent mammal.

I’m pre-vet, but I’ve always been a bookworm and have a love for expressing myself through writing that has given me a strained relationship with word counts. I’ll try to keep this intro post brief!

I’m majoring in English in addition to taking pre-veterinary classes, so my time in the library so far this year has been spent alternating between drawing resonance structures for organic chemistry and reading Jane Eyre in the Gothic Reading Room, which is my favorite study spot on campus.

Effective puppy medicine includes hugging and kissing.

I grew up in the suburbs of Washington, D.C. and now I work in the veterinary department at Duke Lemur Center. I’m also an editor and opinion columnist for The Chronicle. My favorite part of the academic scene at Duke is that pursuing such different interests at the same time is encouraged.

This year, I’m a part of the Bass Connections team that is studying how using expressive writing for resilience can help cancer patients process their experiences during treatment. I love finding new ways to connect my passion for writing with my interest in science, conservation and zoology.

One of the reasons I want to be a veterinarian is because I think veterinarians can and do play a crucial role in species conservation in zoos and animal sanctuaries. However, there is still a lot left to be learned about the animal species they care for.

For example, there is a species of lemur that consistently develops dental problems in captivity that lead to tooth loss, so there must be something about its diet in captivity compared to its diet in Madagascar that affects the health of its teeth. I care a lot about research concerning animals, conservation and pets, in addition to the health benefits of cathartic writing.

Victoria REALLY likes books.

I follow National Geographic on Twitter and read their articles as often as I can, but I usually end up just telling all of the cool facts I just learned to my parents, close friends or anyone else who is close enough to me to feel a slight obligation to listen and feign interest.

Through blogging, I hope to find a platform to synthesize new scientific findings surrounding animals, marine life or cathartic writing and post them to a place where people who care about and want to read about these topics can find them.

Post by Victoria Priester

Looking at Cooking as a Science Experiment

From five-star restaurants to Grandma’s homemade cookies, cooking is an art that has transformed the way we taste food. But haven’t you ever wondered how cooking works? How in the world did people discover how to make Dipping Dots or Jell-O?

Patrick Charbonneau is an Associate Professor of Chemistry here at Duke and last Friday he gave a delicious talk about the science of cooking (with samples!).

Patrick Charbonneau, Duke Chemist and Foodie

Around 10,000 years ago humans discovered that by fermenting milk you could turn it into yogurt, something that is more transportable, lasts longer, and digests easier. In the 1600s a new cooking apparatus called the “bone digester” (pressure cooker) allowed you to cook things faster while enhancing the flavor. When the 1800s came around, a scientist named Eben Horsford discovered that adding an acid with sodium bicarbonate creates baking powder. Soon enough scientific and kitchen minds started to collaborate, and new creations were made in the culinary world. As you can see, a lot of fundamental cooking techniques and ingredients we use today are a product of scientific discoveries.

Old-school pressure cookers. Forerunners of the Instant Pot.

Whisked Toffee

Freezer toffee, AKA caramel

A huge part of cooking is controlling the transformation of matter, or “a change in phase.” Professor Charbonneau presented a very cool example demonstrating how controlling this phase shift can affect your experience eating something. He made the same toffee recipe twice, but he changed it slightly as the melted toffee mixture was cooling. One version you stick straight in the freezer; the other you whisk as it cools. The whisked version turns out crumbly and sweeter; the other one turns into a chewy, shiny caramel. The audience got samples, and I could easily tell how different each version looked and tasted.

Charbonneau explained that while both toffees have the same ingredients, most people prefer the crumbly one because it seems sweeter (I agreed). This is because the chewier one takes longer to dissolve onto your taste buds, so your brain registers it as less sweet.

I was fascinated to learn that a lot of food is mostly just water. It’s weird to think a solid thing could be made of water, yet some foods are up to 99% water and still elastic! We have polymers — long repeating patterns of atoms in a chain — to thank for that. In fact, you can turn almost any liquid into a gel. Polymers take up little space but play a vital role in not only foods but other everyday objects, like contact lenses.

Charbonneau also showed us a seemingly magical way to make cake. He took about half a Dixie cup of cake batter, stuck a whipping siphon charged with nitrous oxide inside it for a second, then threw it in the microwave for thirty seconds. Boom, easy as cake. Out came a cup full of some pretty darn good fluffy chocolate cake. The gas bubbles in the butter and egg batter expand when they are heated up, causing the batter to gel and form a solid network.

Professor Charbonneau is doing stuff like this in his class here at Duke, “The Chemistry and Physics of Cooking,” all the time.

In the past ten years a surge in science-cooking related classes has emerged. The experiments you could do in a kitchen-lab are so cool and can make science appealing to those who might normally shy away from it.

Another cool thing I learned at the stations outside of Charbonneau’s talk was that Dipping Dots are made by dripping melted ice cream into a bowl of liquid nitrogen. The nitrogen is so cold that it flash-freezes the ice cream droplet into a ball-like shape!

Post by Will Sheehan

Will Sheehan

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