Environment/Sustainability | Duke Research Blog

Visible Thinking 2013!

April 24th, 2013

By Pranali Dalvi

Students explain their research to peers and faculty at Visible Thinking 2013 in the French Family Science Center. Photo credit: Pranali Dalvi

On April 19, Duke undergrads gathered in the French Family Science Center for Visible Thinking 2013.

The event showcases the exciting research undergraduates are doing in every discipline from the biological sciences to the humanities. For many students, it was also a celebration of several semesters and summers of hard work. Like seasoned scientists, students explained their research to their mentors, peers and prospective Dukies during the annual poster session.

Renata Dinamarco, a Trinity senior, studied the entrepreneurial preparedness of small businesses in Pembroke Pines, Florida.

Renata Dinamarco, Trinity’13. Photo credit: Pranali Dalvi

People are moving to the newer, western front of the city, so the eastern portion of Pembroke Pines is being redeveloped. Many people believed business owners in the east were underprepared as compared to the west when it came to opening small businesses.

When Renata interviewed 55 small business owners, she found that there was no statistical difference between entrepreneurs in the east versus the west. But, she did find that business owners in the east were more likely to view the city government negatively. Renata’s study of the demographics of small business populations is important for making informed policy decisions.

Christine Tsai, Trinity’14. Photo credit: Pranali Dalvi

Junior Christine Tsai studied the expression of gut-specific genes three days after fertilization in zebrafish. In a healthy developing embryo, epithelial cells line the internal organs.

To explore what genes are turned on and off during the development of the cells, Tsai compared gene expression from the gut cells to gene expression of cells from the entire body. Zebrafish have clear embryos that develop quickly, making them easy to study and use as a system to study genetics.

“I plan to continue conducting undergraduate research and know that the techniques and skills I have acquired and continue to develop through my research will further my understanding of processes in cell and molecular biology,” she said.

Ben Finkel, Trinity’13. Photo credit: Pranali Dalvi

For his honors thesis in evolutionary anthropology, Ben Finkel worked in Dr. Brian Hare’s lab combining his interest in education outreach with his passion for conservation. Finkel’s project examines how portrayals of chimpanzees as either aggressive or affiliative can affect our conservation perception. Through his research, Finkel wanted to understand how media steers conservation beliefs. He found that people were less likely to promote conservation of chimanzees if they showed aggressive behaviors rather than affiliative behaviors.

For more from Visible Thinking, check out my video about senior Emily Ngan who studies the brain’s immune system cells and their role in addiction.

Students Create Multimedia Ocean Conservation Text

April 16th, 2013

By Ashley Yeager

This screenshot shows one of the opening page of of Johnston's new iBook. Image courtesy of Dave Johnston, Duke.

This screenshot shows one of the opening pages of a chapter in Johnston’s new iBook. Image courtesy of Dave Johnston, Duke.

Duke marine biologist Dave Johnston and his students are back in business on iTunes.

They’ve just released The View From Below, a free iBook for middle school students and teachers that uses multimedia and classroom exercises to discuss overfishing, marine debris, climate change, invasive species and other issues related to marine conservation.

This is Johnston’s second digital textbook. His first was Cachalot, an iPad textbook covering the latest science of marine mammals like whales, dolphins and seals. Experts contributed the text, images and open-access papers.

The View From Below, however, is a bit different.

Undergraduate students in Johnston’s Marine Conservation Service Learning class wrote the book using Apple’s iBooks authoring tool. Johnston and Tom Schultz, Director of the Marine Conservation Molecular Facility at Duke’s Marine Lab, edited it.

“There are a lot of people exploring the use of the iBooks platform for student-generated content, among other development platforms,” Johnston says. “I don’t think we’ve seen many that focus on marine science yet though, and I’m pretty sure it’s the first marine conservation textbook written by students on the iTunes store.”

Johnston says the class chose to use the iBooks software because the technology is free, easy to use and provides “great templates to get things going quickly.” The software also works well because Duke’s Marine Lab has an iPad loaner program, making the tablet the platform of choice for developing and testing the textbook.

The middle school that the service learning class works with also has access to iPads for students and instructors, so the audience was there for the iPad format, Johnston adds.

His students chose to write the book as the class project to spur learning and discussion about some of the most serious problems facing Earth’s oceans.

“As the text indicates, all life on earth is ultimately supported by the ocean, so we need to take care of it,” he says.

Sharing food beyond the table

April 7th, 2013

By Nonie Arora

Duke Senior Emily McGinty is pioneering an effort to connect campus farms across the country. McGinty, a senior Baldwin Scholar and public policy major from Pittsburgh, Pennsylvania, has been passionate about food issues since high school. On campus, she is also actively engaged in Round Table Selective Living Group and Team Kenan, and is the managing editor for Rival magazine.

Emily braids and hangs garlic after harvest to cure it for longer-term use at the Duke Campus Farm. Credit: Emily McGinty

When she was organizing food-related discussions with Nicole Tocco, a former Duke masters student at the Nicholas School of the Environment and current employee of Bon Appetit Management Company, McGinty had a breakthrough about one of the fundamental problems in campus growing communities. “There was no platform for connecting, no hub for sharing best practices and ideas,” McGinty said. She wanted to create a centralized resource that would enable campus growers to communicate best practices in their investigative agricultural work.

McGinty’s underlying inspiration to create this centralized hub for campus farmers and growers comes from her experience helping develop the Duke Campus Farm. While Duke’s campus farm is only two and half years old, it is well established and strongly documents its own agricultural practices and research. Students work with professors and practitioners around the Triangle to investigate problems from crop science to building construction. The Duke Campus Farm community is also committed to intentional community building. McGinty explained, “It’s about developing reciprocal relationships. It’s very much a process – not just ‘making friends.’ But you can call it a professional site visit or hopping over to say hey to a neighbor. We’re all about building a strong community and learning from each other.”

She said she feels privileged to work in an area where sharing ideas has no drawbacks. “A fundamental piece of our desire to create a central hub is that we [campus farmers and gardeners] are in a remarkable situation where we have nothing to lose by sharing business plans. Your average corporation cannot share all their business plans and how they function the way they are, but we only benefit from ideas spreading,” McGinty said. “We can share everything from the structure of our board of advisors to parameters used for growing 500 feet of potatoes.”

Popular sungold tomatoes are packed for the Duke Campus Farm’s trip to market. Credit: Emily McGinty

Her team started by building an online platform where people across several college campuses could become members. They began with an online document, where members could upload their research practices in sustainable agriculture. Since then, they have gone through multiple iterations to find the best online home for the hub, which is still under development.

Over the last 6 months, she has conducted many site visits in North and South Carolina to pitch the idea and ask questions about how the hub would benefit others. One of McGinty’s major goals is to get students outside of the immediately interested food community to plug in. McGinty said she strongly believes that food work is interdisciplinary and undergraduate and graduate student research isn’t shared enough. She hopes that this website will reenergize original work produced by undergraduates relating to food issues.

Ultimately, McGinty hopes this open source philosophy will help campus farms across the country thrive by building communication networks and promoting evidence-based agriculture.

Activist targets inner child not ‘target audience’

March 4th, 2013

By Ashley Yeager

A baby albatross carcass full of plastic “food.” Credit: Chris Jordan.

When artist Chris Jordan works on a photograph or film, he doesn’t think about his audience. He said he thinks the phrase “target audience” is a disrespectful, manipulative business concept.

“I want to be as authentic as possible with my work,” Jordan said, explaining that each of his pieces instead taps into that “universality in us that we all carry, a deep appreciation for the abiding beauty of our world and the miracle of our own lives.”

An environmental activist as well as an artist, Jordan is challenging others to target that universality too as they convey messages about the issues that affect the planet.

Jordan spoke March 1 as part of a working group to discuss questions about how environmentalists, neuroscientists and artists can work together to better communicate about issues affecting the planet. The Nicholas School of the Environment and the Duke Institute for Brain Sciences sponsored the discussion.

Duke ecologist Nicole Heller moderated the discussion, opening it with the idea that scientists are frustrated with their inability to communicate with politicians and the public about the environment.

“In the ’70s, yucky or scary images might have worked, but now they don’t. That’s no longer appealing. We need different kinds of imagery to reach across people’s biases,” Heller said. She invited Jordan to speak because of his reputation for being able to move audiences from diverse backgrounds and education levels.

“Second graders are some of the most passionate and responsive to these issues,” Jordan said, adding that perhaps the best thing we can do is to appeal to an individual’s inner child – that curious spirit we have to understand how the world works.

One example of this approach is the film Jordan is working on to explore the mating dance of albatrosses on Midway Atoll in the Pacific Ocean. He’s photographed dead baby albatrosses, whose stomachs are full of plastic trash their parents fed to them because they mistake the plastic for food. The work was to make people aware of the plastic vortex, or Great Pacific Garbage Patch, swirling beyond the horizon and therefore beyond our conscious concern.

Jordan decided to capture the wonder of the albatrosses as they mate, rather than just their rotting carcasses, hoping to feed his audiences — no matter their background — with life, rather than depress them with death.

“Like the albatross, we first-world humans find ourselves lacking the ability to discern anymore what is nourishing from what is toxic to our lives and our spirits. Choked to death on our waste, the mythical albatross calls upon us to recognize that our greatest challenge lies not out there, but in here,” Jordan writes on his Web site.

Designing Microbial “Factories” Rationally

January 29th, 2013

By Pranali Dalvi

Using microbes to manufacture chemicals is starting to be cheaper and greener than traditional chemistry. And their feedstock is sugar, not oil.

Source: 2010 Agricultural Biotechnology International Conference

On Friday, Dr. Michael Lynch spoke to an engaged audience about how microbes have ushered in a new era in metabolic and genetic engineering. Lynch is the co-founder and CSO of OPX Biotechnologies, a Colorado-based company that makes bio-based chemicals and fuels from microbes. OPXBIO microbes produce fatty acids from hydrogen and carbon dioxide. In turn, the fatty acids are used to make cleaners, detergents, jet fuel, and diesel.

Lynch said it’s easier to understand the genetic circuits and enzymatic pathways of microbes, thanks to much cheaper DNA sequencing. What we still lack though, is an understanding of how to rationally design complex biological systems – likely because we fail to recognize the interplay among an organism’s genotype, phenotype, and environment.

It’s a complex set of factors that go into making phenotypic traits such as color, size, or shape.

“In an industrial setting [phenotypes] are equivalent to metabolism or higher production of the product of interest,” Lynch said. “In a clinical setting, [phenotypes] could be virulence or pathogenesis.”

One approach to understanding how phenotypes are controlled has been through functional genomics.

Let’s say we take a population of wildtype microorganisms and introduce genetic modifications in a controlled way. Next, we selectively screen for the phenotype of interest and compare the sequence of this phenotype to the wildtype to pinpoint the genetic mutations that made the difference.

Comparing phenotypes one at a time is inefficient, though. Lynch wanted to find a way to speed up this process.

“We wanted a process or technology or toolkit that evaluates all of your genes in parallel in a single experiment for the phenotype of interest,” Lynch explained.

Lynch found his inspiration in microbial biofilms, extracellular polysaccharide matrices that grow quickly.

OPXBIO’s Efficiency Directed Genome Engineering (EDGE) technology platform, Source: opxbio.com

Lynch’s studies revealed that microbial cultures grown in enriched media made biofilms, while those in minimal media did not. In a process known as destructional mutagenesis, Lynch and his colleagues then knocked out biofilm-making genes to identify what genes cause the biofilm phenotype in enriched medium but prevent it in minimal medium.

Lynch saw the individual microbial systems as factories that he can genetically modify to produce chemical compounds in biofilms – specifically, 3-hydroxypropionic acid – that can be chemically converted to commercially relevant compounds such as acrylic.

Scientists at OPXBIO have cracked the code for making acrylic from sugar. They give sugar feedstocks to genetically modified bacteria, whose enzymes convert the sugar into acrylic molecules. Acrylic has broad commercial applications in paints, adhesives, diapers, detergents, and even fuel – a $10 billion global market.

Not Swimming with Spinners

December 17th, 2012

By Ashley Yeager

Spinner dolphins swimming just off the bow of a boat. Image courtesy of Dave Johnston, Duke.

Waianae, HI – Pet a dolphin for me, my sister texted as I stepped onto a catamaran in West Oahu. I didn’t have the heart to tell her that is exactly what I would NOT be doing, under any circumstances.

I have to admit that a little later, as a pod of wild spinner dolphins undulated just ahead of the bow of our boat, it was really hard not to reach out and try to touch one of them.

It was almost as if getting closer to the creatures as they slid through the water would free us, if only for a moment, from our artificial world of buildings, cars, computers and cell phones. But, in reality, interacting with spinners can’t take us away from our hyper-connected world, and chasing and touching the dolphins is not good for them either.

“If you try to play with spinners during the day, it’s like a stranger coming into your bedroom in the middle of the night and trying to wake you up,” says Nicholas School marine biologist Dave Johnston. He comes to Hawaii a few times each year to take photographs and other data on the islands’ spinner dolphins to learn more about their behaviors, population size and the bays they are swimming in during the day.

Spinner dolphins — Stenella longirostris – swim into shallow bays off Hawaii’s coast during the day to rest, turning off half of their brain at a time as they sleep. With one half on and one half off, they can still swim to the surface to breathe and ultimately recharge for the next night’s hunt.

But lots of vacationing people swimming and sailing in the bays aren’t thinking of the dolphins’ schedule and rest, they are only wanting to get closer to the wild animals. And the dolphins, much like humans, are curious. They’re going to check you out if you’re in their space, just like you would if you hear a strange noise in your room while your trying to sleep, our guides from Hawaii Nautical tell us as we cruise out of Waianae Harbor on West Oahu.

We sail for a bit and then come upon a pod of spinner dolphins resting off our port side. Everybody bunches to the front of the boat to get as close as they can to the animals. Our guides remind us of the dolphins’ sleep cycle and explain that the tour company follows the NOAA-sponsored Dolphin SMART program.

SMART stands for: Staying back from the dolphins; Moving away if they seem disturbed; Always keep a boat engine in neutral if you are near a pod; Refraining from feeding or touching them; and Teaching others to be dolphin SMART. Needless to say, we didn’t swim with or touch the dolphins. Sorry sis. Instead, we sailed a bit more, snorkeled with some sea turtles, not touching them of course, and then sailed back toward the harbor.

On the way back, we spotted another pod of spinners, and even more inspiring, we simply watched the animals. They were enjoying their rest, undisturbed in their home — something we all crave and appreciate when we can get it.

The new blood diamond is your cell phone

December 13th, 2012

by Ashley Mooney

There is an African proverb that says “when the elephants fight, the grass suffers.”

In the Democratic Republic of the Congo, the elephants are militias and the grass is the women, said John Prendergast, co-founder of Enough Project, an organization that fights to end genocide.

Congolese rape victims assemble outside of a peace hut. Courtesy of Wikimedia Commons.

Prendergast, who spoke at Duke Nov. 29, said the DRC is now the home of the deadliest war since World War II. The conflict has been created in part by large corporations seeking a variety of natural resources within the region throughout the past 150 years. Currently, the Congo is the main source of gold, tantalum, tin and tungsten, which are used to power electronics such as cell phones, laptops and digital cameras.

“Congo is now the most dangerous war because powerful corporations have come to [the country] for the last few centuries to take whatever they want, and structured the state to facilitate that,” he said. His talk was part of the Ferguson Family Distinguished Lectureship series on the Environment and Society.

The nation is currently riddled by struggles between the Congolese armies, militias and other groups from bordering nations Rwanda and Uganda. Many of the groups utilize brutal tactics throughout mineral-smuggling networks, and, Prendergast said, use sexual violence at the center of their methodology.

“[There has been] no other war in the world where the link between our consumer appetites and sexual violence is so direct,” he said. “All of these groups use rape as a means of social control… They target women to humiliate and destroy the will of the community.”

Prendergast has dedicated himself to the pursuit of peace in the region for over 30 years and has lobbied several companies – including Apple – to use free-trade models of mineral trade.

“Unless international capital or profit-seeking capital is regulated in some way, it will trample all over human rights,” he said.

Prendergast credited Duke’s student body for leading the nation in the Conflict-Free Campus Initiative, which 115 schools are involved in.

The way to create peace, he said, is to pressure the United States government to encourage the United Nations and other countries to support “an African-led peace process in Congo,” which deals with the root causes of the issue.

“We aren’t going to solve all of the Congo’s problems sitting here – we aren’t going to solve them in the United States or Europe,” he said. “But we can play a major role in supporting the Congolese to find those solutions.”

He added that until everyone is more aware of the root cause – the demand for phones, laptops and other electronics – the conflict will not end.

“When you log onto your laptops tonight, remember they wouldn’t be so cheap without minerals from the Congo,” he said. “When you answer your cell phone or make a call, remember… all of the women of the Congo who have survived sexual attacks.

Lemurs Most Threatened Mammals on the Planet

July 24th, 2012

By Karl Leif Bates

Things seem to be going from bad to worse for the lemurs of Madagascar.

A report issued two weeks ago by a working group in Antananarivo, Madagascar’s capital, concludes that these prosimian primate cousins of ours are THE most endangered mammals on the planet with 91 percent of all lemurs on the Red List of threatened status.

The 5,000-acre Betampona Nature Reserve in the eastern rainforest region is the smallest and oldest of Madagascar's officially protected areas. It looks like a green island surrounded by damaged forests and subsistence farming. The reserve is jointly managed by the Madagascar Fauna Group, of which the Duke Lemur Center is a founding partner, and was the site of first reintroduction of lemurs which had been bred in captivity at DLC.

In a poor and poorly governed country, humans are steadily chewing away at lemur habitat and at the lemurs themselves.

One species, the northern sportive lemur, is down to just 18 individuals on a tiny speck of habitat at the extreme northern end of the island. There are none in captivity.

“When these species disappear from Madagascar, they are lost forever,” Lemur Center Director Anne Yoder said. Captive breeding programs, like the one at the Duke Lemur Center, are a poor substitute for the protection lemurs really need.

The warning is unfortunately all too familiar to the faculty, staff and volunteers of the DLC, and it casts their work in conservation, education and research as even more critical.

In addition to its crucial work in Durham, DLC has been working on the ground in Madagascar for more than 20 years to preserve habitat and build a corps of conservation-minded citizens. Post-doctoral researcher Erik Patel participated in the Antananarivo workshop and reported on the meeting last week.

Learn More:

Anne Yoder and Charlie Welch on Duke Lemur Center blog.

Russ Mittermeier, chairman of the Madagascar Primate Specialist Group and President of Conservation International in the Huffington Post.

The Duke Lemur Center's breeding population becomes ever more important as wild lemurs disappear.