Wednesday, October 28, 2009

No bones about it: A great place to work

The Scientist magazine's readers ranked Emory as the 5th Best Place to Work in Academia in the United States. The ranking was based on a survey of more than 2,350 life scientists with a permanent position in an academic, hospital, government or research organization. The scientists represented 94 US institutions and 25 institutions from the rest of the world.

Emory ranked especially high in the categories of "peers" and "job satisfaction." The top four institutions were Princeton University, University of California-San Francisco, Albert Einstein College of Medicine, and University of Oklahoma Health Sciences Center. The top international institution was the Max Planck Institute of Molecular Cell Biology and Genetics.

Read the full survey results.

Monday, October 26, 2009

A new twist on an ancient story

“Evolution is a theory that we have more experimental evidence for than any other theory, and yet 50 percent of the population of the United States doesn’t accept it,” said David Lynn, professor of chemistry and biology, during a recent Creativity Conversation with choreographer David Neumann. “Maybe we’ve taken the wrong path in talking about evolution. In science we do a good job of conveying facts, but not a good job of telling the stories – what makes it human.”

Lynn’s research focuses on the origins of life. His desire to find new ways to explain science to the public inspired him to collaborate with Neumann, and the Seattle troupe Lelavision, as they developed dance performances. Their works, including Lelavision's "Warm Pond" (see photo), recently premiered in Atlanta.

“I was deeply influenced by the manner in which evolution operates and using those structures – contingencies and chance operations – in the structure of the dance,” Neumann said. “Sometimes when you utilize chance there’s a fantastic discovery.”

Watch a video of the conversation between Lynn and Neumann:


Related story:
Dancing with the scientists

Wednesday, October 21, 2009

The Cascade Range: Chemistry to climbing

Can you combine a high-powered career in chemical cascade research with a mountaineering hobby and still have time to form human bonds? Sure, if you rope colleagues into both adventures.

Emory’s Albert Padwa (above at Mount Rainer in 1984) gives a perspective of his 48-year career in a recent issue of the Journal of Organic Chemistry. The cover (see below) was designed by Emory chemist Stefan Lutz and features Annapurna, Nepal, the site of Padwa's latest climb.

What makes for excellence in science? “To me, it’s pushing out into completely new territory,” Padwa says.
Here’s an excerpt from the JOC article:

“I associate the top of mountains with success, achievement and freedom. In contrast, the lower part of the mountain possesses many obstacles and challenges which need to be overcome. This is really not so different from bringing a chemical project to fruition and getting it published…

“Because of the rate at which they increase molecular intricacy, cascade reactions have received considerable attention from my research team over the past 25 years. The development of sequences that combine transformations of differing fundamental mechanisms broadens the scope of such procedures in synthetic chemistry and provides me with continuing challenges for reaching an ‘ideal summit.’”

Tuesday, October 20, 2009

Bug splatter study is data driven

The next time you take a road trip, think before you clean the bug splatter off your car. Those insect remains may actually be more interesting than your vacation photos.

“It turns out that your car is a sampling device for understanding the biodiversity of all the places you’ve been,” says James Taylor, a computational biologist at Emory.

Genome Research recently published a paper by Taylor and collaborators that applied advanced DNA sequencing techniques that are traditionally used on microbial samples to look at insect biodiversity. “We were curious whether these techniques would work for more complex organisms,” Taylor says.

To collect genetic material for the study they used the bumper and windshield of a moving vehicle. Two samples were collected: on a drive from Pennsylvania to Connecticut, and on a trip from Maine to New Brunswick, Canada.

“We found that there is a huge amount of insect diversity, but what was really surprising was to see the enormous amount of novel sequence,” Taylor says. “It’s indicative of how poorly we have sampled the whole tree of life in genome research so far. There’s an enormous amount of species out there.”

Road tested

Taylor is a co-developer of Galaxy, an open-source software system for analyzing genetic data. The Galaxy developers recently refined the system, creating the Galaxy metagenomic pipeline that allows a research team to integrate all of the data, analyses and workflows of a study, and then publish this material as a live online supplement.

The bug splatter paper served as the first test of the metagenomic pipeline.
“I believe that this study is one of the most transparent and reproducible bioinformatics papers ever,” Taylor says. “Anyone can go online, follow links and see every step of our analysis and exactly what parameters were used. And they can take our data and do their own analysis of other questions.”

No computational experience is required to use the free Galaxy system, Taylor says. “All of science is becoming computationally intensive, so tools like this are needed to improve transparency.”

DNA sequencing technology is getting cheaper, opening more doors for research by small investigators, and Taylor is focused on serving this niche.

“Nowadays, you can have a crazy idea like studying bug splatter and without a lot of money or work, you can go out and do it just to see what’s there,” he says.

Related story:
Mapping genomics of complex ant system
Plug your data into the Galaxy

Monday, October 19, 2009

Icons of evolution

Nancy Lowe goes to church more often than most. All she has to do is step outdoors, where she finds the sacred in nature. During breaks from her job as a lead research specialist in biology, you might see her sketching a leaf or a bug somewhere on campus.

“I’m an artist and a naturalist,” she says. “Working as a lab technician is my day job.”

Lowe’s art is featured in the ongoing exhibit at Emory Library’s Schatten Gallery, marking the 150th anniversary of the publication of Darwin’s “On the Origin of Species.” The eclectic show includes original editions of “Origin,” panoramic “nanoscapes” captured by electron microscopes and a retrospective of how poet Ted Hughes’ work evolved.

Lowe’s contribution is a series of luminous paintings called “Species Icons.” On canvases glinting with gold leaf, a pitcher plant wears a halo and tube worms are strung with jewels.

“Medieval religious icons seem to glow with a certain power,” Lowe says. “They’re old and precious. I wanted to combine that feeling with the careful attention to detail in scientific illustration of organisms. For me, that’s what’s sacred – the amount of geological time that it has taken to evolve these species.”

The paintings also grew out of a question that Lowe says she’s pondered for years: “Now that evolution has become our primary creation story, what should we put on our stained glass windows?”

After graduating from the Art Institute of Chicago, Lowe worked in video and film before discovering her love of illustrating nature. She volunteered as an artist for a species inventory project in the Great Smoky Mountains National Park. She regularly teaches art, in addition to making her own. The name of her web site, "look at your fish", comes from 19th-century naturalist Louis Aggasiz. He would give his students a pan containing a pickled fish and leave them alone to stare at it for hours.

Careful observation is important to art, as well as science, she says. “I want my students to ask, ‘What’s this little bristle for on this bug?’ and realize that every structure is connected to some function. It all comes back to evolution.”

A microscope can distance scientists from their subjects, Lowe says. “We’re looking at things now through a molecular and a genetic lens. That is a more cerebral pursuit. I think we’ve lost something about teaching students to love the organism.”