Where Cinema and Biology Meet


и видео http://video.nytimes.com/video/2010/11/15/science/1248069334...
When Robert A. Lue considers the “Star Wars” Death Star, his first thought is not of outer space, but inner space.
“Luke’s initial dive into the Death Star, I’ve always thought, is a very interesting way how one would explore the surface of a cell,” he said.
That particular scene has not yet been tried, but Dr. Lue, a professor of cell biology and the director of life sciences education at Harvard, says it is one of many ideas he has for bringing visual representations of some of life’s deepest secrets to the general public.
Dr. Lue is one of the pioneers of molecular animation, a rapidly growing field that seeks to bring the power of cinema to biology. Building on decades of research and mountains of data, scientists and animators are now recreating in vivid detail the complex inner machinery of living cells.
The field has spawned a new breed of scientist-animators who not only understand molecular processes but also have mastered the computer-based tools of the film industry.
“The ability to animate really gives biologists a chance to think about things in a whole new way,” said Janet Iwasa, a cell biologist who now works as a molecular animator at Harvard Medical School.
Dr. Iwasa says she started working with visualizations when she saw her first animated molecule five years ago. “Just listening to scientists describe how the molecule moved in words wasn’t enough for me,” she said. “What brought it to life was really seeing it in motion.”
In 2006, with a grant from the National Science Foundation, she spent three months at the Gnomon School of Visual Effects, an animation boot camp in Hollywood, where, while she worked on molecules, her colleagues, all male, were obsessed with creating monsters and spaceships.
To compose her animations, Dr. Iwasa draws on publicly available resources like the Protein Data Bank, a comprehensive and growing database containing three-dimensional coordinates for all of the atoms in a protein. Though she no longer works in a lab, Dr. Iwasa collaborates with other scientists.
“All that we had before — microscopy, X-ray crystallography — were all snapshots,” said Tomas Kirchhausen, a professor in cell biology at Harvard Medical School and a frequent collaborator with Dr. Iwasa. “For me, the animations are a way to glue all this information together in some logical way. By doing animation I can see what makes sense, what doesn’t make sense. They force us to confront whether what we are doing is realistic or not.” For example, Dr. Kirchhausen studies the process by which cells engulf proteins and other molecules. He says animations help him picture how a particular three-legged protein called clathrin functions within the cell.
If there is a Steven Spielberg of molecular animation, it is probably Drew Berry, a cell biologist who works for the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia. Mr. Berry’s work is revered for artistry and accuracy within the small community of molecular animators, and has also been shown in museums, including the Museum of Modern Art in New York and the Centre Pompidou in Paris. In 2008, his animations formed the backdrop for a night of music and science at the Guggenheim Museum called “Genes and Jazz.”
“Scientists have always done pictures to explain their ideas, but now we’re discovering the molecular world and able to express and show what it’s like down there,” Mr. Berry said. “Our understanding is just exploding.”
In October, Mr. Berry was awarded a 2010 MacArthur Fellowship, which he says he will put toward developing visualizations that explore the patterns of brain activity related to human consciousness.
The new molecular animators are deeply aware that they are picking up where many talented scientist-artists left off. They are quick to pay homage to pioneers in molecular graphics like Arthur J. Olson and David Goodsell, both at the Scripps Research Institute in San Diego.
Perhaps the pivotal moment for molecular animations came four years ago with a video called “The Inner Life of the Cell.” Produced by BioVisions, a scientific visualization program at Harvard’s Department of Molecular and Cellular Biology, and a Connecticut-based scientific animation company called Xvivo, the three-minute film depicts marauding white blood cells attacking infections in the body. It was shown at the 2006 Siggraph conference, an annual convention of digital animation. After it was posted on YouTube, it garnered intense media attention.
BioVisions’ most recent animation, called “Powering the Cell: Mitochondria,” was released in October. It delves inside the complex molecules that reside in our cells and convert food into energy. Produced in high definition, “Powering the Cell” takes viewers on a swooping roller coaster ride through the microscopic machinery of the cell.
Sophisticated programs like Maya allow animators to create vibrant worlds from scratch, but that isn’t always necessary or desirable in biology. A company called Digizyme in Brookline, Mass., has developed a way for animators to pull data directly into Maya from the Protein Data Bank so that many of the over 63,000 proteins in the database can be easily rendered and animated.
Gaël McGill, Digizyme’s chief executive, says access to this data is critical to scientific accuracy. “For us the starting point is always the science,” Dr. McGill said. “Do we have data to support the image we’re going to create?”
Indeed, while enthusiasm runs high among those directly involved in the field, others in the scientific community are uncertain about the value of these animations for actual scientific research. While acknowledging the potential to help refine a hypothesis, for example, some scientists say that visualizations can quickly veer into fiction.
“Some animations are clearly more Hollywood than useful display,” says Peter Walter, an investigator at the Howard Hughes Medical Institute in San Francisco. “It can become hard to distinguish between what is data and what is fantasy.”
Dr. McGill acknowledges that showing cellular processes can involve a significant dose of conjecture. Animators take liberty with color and space, among other qualities, in order to highlight a particular function or part of the cell. “All the events we are depicting are so small they are below the wavelength of light,” he said.
But he contends that these visualizations will be increasingly necessary in a world awash in data. “In the face of increasing complexity, and increasing data, we’re faced with a major problem,” Dr. McGill said.
Certainly, it will play a significant part in education. The Harvard biologist E.O. Wilson is leading a project to develop the next generation of digital biology textbook that will integrate complex visualizations as a core part of the curriculum. Called “Life on Earth,” the project will include visualizations from Mr. Berry and is being overseen by Dr. McGill, who believes it could change how students learn biology.
“I think visualization is going to be the key to the future,” Dr. McGill said.


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05 - Midnight Commander! а ещё там мелькает PyMOL
рад за линупс!
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