Duke Research Blog

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

Author: Becca Bayham (Page 2 of 3)

Solving the world’s humanitarian problems

By Becca Bayham

What will the world of 2050 look like?

Popular fiction tells us we’ll have hoverboards, spaceships and artificial intelligence. According to USAID advisor (and Duke alum) Alex Dehgan, we’ll also have new ways of addressing humanitarian challenges — and we’ll need them. Dehgan kicked off the Student International Discussion Group‘s Water & Energy Symposium, Feb. 10.

“We know that climate change is going to affect the U.S., the Middle East, Central Asia and North Africa. This is actually a national security issue for us,” Dehgan said. “One thing that I think has been forgotten is, it’s not just climate, it’s climate times the environment. It’s the interaction of these two pieces.”

Dehgan described a patch of tropical forest where all the trees had been cut down. Trees send moisture back to the atmosphere via transpiration. No trees, no rain. The ground dried up, and the area is now 30 degrees warmer than it was before.

The world of the future may look different in other ways. According to Dehgan, 51 countries will lose population between now and 2050, largely due to declining birth rates. Other countries such as India, Pakistan, Nigeria, Bangladesh, the Democratic Republic of the Congo, China, Uganda, Ethiopia and the U.S. will experience massive population growth. Some of those countries already face problems providing their people with sufficient food, energy and clean water.

“[USAID] sees the developing world as the future of the U.S. economy,” Dehgan said. “Many of these challenges aren’t just bad news. They’re challenges we can take on to develop our markets.”

To that end, Dehgan cited five trends that will help organizations tackle humanitarian challenges in the future:

  1. Democratization of Science
    It took researchers 13 years and 2.7 billion dollars to sequence a single human genome for the first time. Now a company can sequence 100 genomes a day for less than $100 each. Lower costs allow humanitarian groups to deploy innovative technologies (such as vaccines) on a large scale.
  2. Increase in Computing Power
    “The power of computing is increasing exponentially, while the cost is decreasing exponentially. This provides us with exceptional ability to use computer power to help understand and solve problems,” Dehgan said.
  3. Data, Data, Data
    “A kid in Africa has more power and knowledge in his hand with a smart phone than President Clinton had 15 years ago,” Dehgan said. Technologies such as remote sensing, crowd sourcing and bioinformatics will add new types of data to our pool of knowledge.
  4. Connectivity
    Cellphones act as gateways to human knowledge, providing people with access to information they didn’t have before.
  5. Decentralization of Manufacturing
    Certain 3D printers, for example, now have the ability to produce 70 percent of the parts needed for another 3D printer. Online course materials such as iTunesU and MIT OpenCourseWare help support individuals that are trying to solve their own problems.

Dehgan also says he hopes that a sort of “humanitarian X Prize” could identify solutions to our changing world by catalyzing new research.

In 1996, the X Prize Foundation announced a $10 million reward for the first group to launch a manned, reusable vehicle into space twice within two weeks. The foundation hoped to spur innovation that would make low-cost space flight possible, and they succeeded. The winning team claimed the prize in 2004, after investing $100 million in new technologies.

“With grants, you don’t know what you’re going to get,” Dehgan said. “If you have a prize, you only win the prize once you’ve actually solved the problem. And one of the great things about it is that you get more than one solution.”

Max Leung, Caped Crusader Against DNA Damage

By Becca Bayham

His lab colleagues call him Batman, the Toxic Knight.

To the rest of the world, he is Maxwell Leung, a PhD candidate in Duke’s environmental toxicology program. For the past five years, Leung has worked in the lab of Joel Meyer (AKA “Super-enviro-man”) fighting for environmental justice with pipettes and PCR machines.

Leung spoke about his research Jan. 27 as part of the Nicholas School’s continuing series on toxicology. Leung studies how exposure to certain environmental chemicals can affect organisms’ later-life development by damaging their DNA.

Cells contain two types of DNA: nuclear DNA (found in the nucleus) and mitochondrial DNA (found in mitochondria, which generate most of a cell’s energy).

“When people talk about DNA damage, they are usually referring to DNA damage and revision occurring in nuclear DNA,” Leung said.

A ligase enzyme repairs damage to nuclear DNA (National Institute of General Medical Science)

For the most part, special packaging and multiple repair mechanisms protect nuclear DNA from harm. However, mitochondrial DNA lack certain repair mechanisms, and little is known about their packaging. In the lab, Leung evaluated damage to both types of DNA by exposing worm larvae to short bursts of UV radiation. He found that, while nuclear DNA damage was partially repaired during the 24 hours between exposures, mitochondrial DNA damage continued to accumulate.

Further study of the exposed worms suggested that mitochondrial DNA damage at an early life stage can cause adverse effects such as reduced energy production, DNA transcription and oxygen consumption in adults. Given this connection, Leung sought to identify environmental chemicals that are capable of damaging mitochondrial DNA. Of the six chemicals he tested, one targeted mitochondrial DNA over nuclear DNA, and caused visible neurological effects: paraquat, a widely-used herbicide.

Which raises the question: if one out of six tested chemicals had this effect, then how many other environmental chemicals could cause that type of damage?

Unfortunately, mitochondrial DNA damage disproportionately affects neurological tissues; neurons require a great deal of energy and thus contain large amounts of energy-producing mitochondria. Studies have found strong associations between genes in mitochondrial DNA and neurodegenerative disorders such as Parkinson’s disease.

After the lecture, I spoke to Leung about why he decided to study science, and how he came to Duke.

“When I was in junior high, there was a TV show called ‘Success Stories’ in Hong Kong, featuring a number of famous Chinese scientists pursuing scientific careers in U.S. They went on to become National Academy members, win Nobel Prizes, and make important contributions to science and our world. That left an impression on me.”

Now, Leung hopes to write his own success story. He received his undergraduate degree in Food and Nutritional Science from the University of Hong Kong, and a master’s degree in Food Toxicology from the University of Guelph in Canada.

Leung came to Duke in 2007, following a visit to Joel Meyer’s newly-established environmental toxicology lab. At the time, the lab was “literally empty,” with just four PCR machines and a lab technician from Canada. Fifteen researchers work in the lab now, and each has been christened with their own superhero nickname including such characters as “Terror Byte,” the “Nano Ninja,” and “Wonder Worm Woman”.

“I enjoy the people I come across in science more than the science itself,” Leung said. “I enjoy doing experiments, giving talks and writing papers, but it is always the interesting people that I get to know through these activities that keep me going everyday.”

‘Knowsphere’ could solve climate problems, Revkin argues

By Becca Bayham

Does the world seem a little angsty-er to you? It should, it’s got way more adolescents.

“There were only a billion people [on Earth] in 1800; now we have a billion teenagers,” said Andrew Revkin, a prize-winning journalist and New York Times blogger, during a lecture on Jan. 18.

“Is this a sign of overpopulation?” someone in the audience joked, referring to the jam-packed classroom.

Likely not, but, as Revkin discussed, resource limits and an explosive human population growth may eventually cause population or economic declines.

“We don’t seem to have distinguished ourselves from bacteria on a plate of agar yet,” Revkin said. “Science is saying hey, hey, there’s an edge to the dish! But we’re still in go-go-go mode.”

The fact that we will reach the edge of the dish is undeniable — and it won’t be pretty. To illustrate, Revkin showed a picture of Black Friday shoppers fighting over a sale item.

“Can you imagine everyone doing this?” he said.

Unfortunately, we humans are historically bad at confronting problems that don’t affect us here-and-now. If in doubt, see our lackluster response to the national debt. Or global climate change, for that matter (a topic Revkin often blogs about).

“There’s a big chunk of everyone who just doesn’t want to deal with global warming, to tell you the truth… it’s hard, it’s complex, it’s laden with layers of complicit uncertainty. What is it and what do you do about it?”

Revkin believes that global connectedness, powered by the internet, offers a solution to the many problems humanity will face in coming years.

Communication between people — sharing information and exchanging ideas — has long fueled our economy and fostered human progress. According to Revkin, a network of collaborating schools, libraries, businesses and other institutions (a “knowsphere”) could help combat problems ranging from natural disaster preparedness to the treatment of diseases.

“Much of human progress can be charted in relation to our linkages with others,” he said.

In the 1920s, philosophers Vladimir Vernadsky and Teilhard de Chardin conceptualized the idea of a “noosphere” (from the Greek “nous”, mind and sphaira, “sphere”), a philosophical sphere of intelligence around the Earth that humans could draw from — a planet of the mind. Back then, it was just an idea.

“But now, it’s happening,” Revkin said.

EPA regulation adds jobs, despite partisan myths

By Becca Bayham

“Environmental and health threats are unambiguously non-partisan concerns,” EPA administrator Lisa Jackson said during a Dean’s Series lecture at Duke, Dec. 6. “The quality of our air and our water has an effect on our way of life whether we live in a red state or a blue state.” (View Jackson’s talk at Duke on Demand)

And yet, Republican leadership has orchestrated 170 votes against environmental protection laws since the beginning of this year. According to Jackson, these votes were mostly in response to myths. She cited one false, but commonly used statistic that the EPA plans to triple its budget and hire 230,000 new regulators (a 1,200% increase over its current 17,000).

“It’s striking how easy it is to get information to the American public that is scary or misleading,” Jackson said.

Back in 2009, an anonymous source leaked a series of emails exchanged between British climate researchers, setting off a controversy dubbed “Climategate” by one climate skeptic blogger. The emails were the subject of intense media coverage, even though later investigations found no evidence of fraud. However, when a leading climate skeptic recanted his beliefs earlier this year, the event received very little media attention.

“Right now there are two visions competing for the future of our country and our economy,” Jackson said.

The first is a trust in science and a belief that our country can institute changes that will both protect the environment and create a surge of new jobs. The second vision, according to Jackson, is that “moving forward requires rolling back.” Namely, that the U.S. should maintain policies that protect polluters, thereby preserving a small number of jobs.

But, “a strategy to grow our economy by doing less is not sufficient to deal with the problems we have now,” Jackson said.

Furthermore, actions that benefit the environment can also benefit the economy, she argued. Contrary to belief, smart regulations generate jobs rather than eliminate them. Congress will soon pass a mercury standards act to limit toxic emissions from smokestacks. This legislation will create an estimated 31,000 short-term construction jobs and 9,000 long-term jobs. The EPA predicts that the standards will save 17,000 lives a year (via reduced incidence of heart attacks, asthma and acute bronchitis).

Most Americans have grown up in a country regulated by the EPA. Thus, people may underestimate how much the agency has done during its 40-odd years of existence, Jackson said. Americans enjoy clean air and water, things that are not a given in other countries. However, budget cuts threaten enforcement while toxic substances such as mercury, lead, VOCs and nitrous oxides still pose a threat.

“The future of the environmental movement is educating the public that the threat is not done,” Jackson said.

However, she finds ample reason for hope in the actions that communities — red and blue alike — are taking to improve efficiency and reduce their environmental impact.

“I think that if we do our jobs right, we will keep moving forward,” she said. Not quickly, “but we’re not moving backwards either.”

Solving problems with iPad (or Android) apps

eCLIP iPad applicationBy Becca Bayham

When a patient comes into the E.R. with a lung problem, doctors usually put them on a ventilator. Unfortunately, this procedure helps some patients, but hurts others. Doctors have difficulty predicting which will be the case, due to a lack of data on risk factors. A predictive model was recently developed to solve this problem, but the calculations require more time and information than E.R. doctors usually have.

Enter Raquel Bartz, an emergency room doctor at Duke Hospital. She envisioned an iPad application where doctors and family members could input the necessary medical information, and the app would spit out the treatment protocol for a particular patient. Bartz turned to Richard Lucic and Robert Duvall’s Software for Mobile Devices class (COMPSCI 196) to make her idea a reality.

The result? An application called eCLIP, developed by students last Fall and available now in iTunes’ App Store. (See photos at left)

eCLIP is one of five applications created by students during the two semesters COMPSCI 196 has been offered. Lucic and Duvall described the course — and its various student-produced applications — at last week’s Visualization Friday Forum, sponsored by the Visualization Studies Initiative (http://visualstudies.duke.edu/) and Duke’s computer science department.

“We’re trying to teach students about the mobile app world,” Lucic said. “In addition, we’re trying to teach students about the software development process, from conception of an idea to delivering a product to a client.”

Lucic emphasized the importance of teamwork, as well as the value of visual design skills for increasing a product’s appeal. Furthermore, user testing is a critical step for identifying problems.

This semester, nine clients pitched their application ideas. Students voted for their favorite projects, and three were ultimately chosen:

  • Ajay Patel, IT Manager in the Duke Cancer Center, wanted a way to track medical samples during processing and reduce human error
  • Allison Besch, educational curator for the North Carolina Maritime Museum, wanted a fun, educational tool for teaching marine resource conservation to 4th graders
  • Rachel Cook, Duke alumna and former futures trader, wanted an app to encourage microlending and bridge the gap between lenders and borrowers

Each client worked with a team of 3-4 students, and met with them every other week to discuss the team’s progress.

“A lot of students are learning how to code mobile apps for the first time, so there’s only 6-7 weeks of actual coding time,” Duvall said.

Despite the time crunch, students try to present a finished product to their clients by the end of the semester. But who keeps the app going after the course’s conclusion?

“What we’re trying to do is have the students provide enough documentation and write their code well enough that the app can be maintained by the client’s organization,” Lucic said. “Clients have been thrilled with the experience. I think we’ve done a superb job of meeting their needs, as much as you can in a one-semester course.”

Sharing is caring, when it comes to scientific data

By Becca Bayham

Worms don’t typically evoke a sense of awe. But C. elegans nematode worms — all 558 cells of them — played an important role in how scientific data is shared today.

Scientists Robert Waterston and Sir John Sulston described this connection during the James B. Wyngaarden Distinguished Lecture on Nov. 14, sponsored by the Institute for Genome Sciences and Policy. [Watch the whole lecture – 1 hour, 9 minutes)

During the 80s, Waterston and Sulston were unraveling the nematode genome at their University of Cambridge lab. Worms make good subjects for study because they are finite, transparent and genetically manipulatable.

The Worm Breeder's Gazette - Volume 8, Issue 2When Waterston moved from Cambridge to Washington University in St. Louis, he felt isolated from the research community he’d left. However, an informal and creatively-covered publication — the Worm Breeder’s Gazette (see photo at left) — helped bridge that physical divide. Researchers used the Gazette to share short summaries of their discoveries.

“Through this very informal means, the community was made aware of what was going on, and invited to share in it,” Waterston said. “Indeed, it worked spectacularly. Now we knew not just these anonymous pieces of DNA, but where they belonged. And that made [the data] much more useful for us and the community.”

Waterston and Sulston were the first to sequence a multi-cellular organism’s genome. Following their success with worms, the two moved on to the holy grail of science at the time: the human genome.

In terms of data sharing, “human genetics was the polar opposite of the worm field. Human geneticists held things very close to their chests,” Waterston said.

In 1996, the two scientists joined other researchers at a conference in Bermuda to discuss how human genome data should be handled. Should it be stored in proprietary databases, with limited access? Or shared freely with the world? Waterston and Sulston advocated for the latter, and this opinion ultimately prevailed. If it hadn’t, the humane genome story might have ended differently — or not at all. Data sharing “kept the lines of communication open” between researchers, Waterston said, and greatly facilitated the sequencing process.

Sure enough, following the human genome’s completion in 2000, the entire sequence was released into the public domain. Public data sharing has become standard practice for other animal genomes and other areas of science. However, even though Waterston and Sulston’s efforts encouraged data sharing on a massive scale, the tendency towards secrecy still exists.

“Pushing for more open science continues to be important,” Waterston said. “The nature of science is that private initiatives continue to push on public domain. If we don’t push back, we’re going to be the poorer for it.”

Page 2 of 3

Powered by WordPress & Theme by Anders Norén