Volume 1, Issue 6
The Toughest Shrimp Around
When a tiny mantis shrimp is hungry, it lines up a snail and delivers a lightning fast and powerful whack to the shell, cracking it open for easy feasting. The amazing thing is that the shrimp's smashing move delivers over 200 pounds of force, hundreds of times more than its own body weight. According to UC Berkeley integrative biologist Sheila Patek, that impressive impact comes from the speed of the motion, decidedly the swiftest kick in all of the animal kingdom.
Sheila Patek, pictured here with a Mantis Shrimp, also studies the biomechanics and physiology of how lobsters communicate. (photo copyright John B. Carnett/POPULAR SCIENCE MAGAZINE)
"The speed of the limb far exceeds most biological systems," says Patek, who last month was named one of Popular Science magazine's "Brilliant 10" for 2004.
To calculate the power of the shrimp's kick, Patek outfitted her shrimp tank with load cells, piezoelectric sensors that measure force. She then coated the devices with shrimp paste, a treat that attracts the predators to the snail stand-ins. Each kick to the load cell squeezes the sensor, generating a measurable electrical signal. It's not unlike the old carnival game where a player smashes a target with a sledgehammer to ring the bell and prove his strength.
Patek's research on the particular crustacean's predation began with a short film starring a peacock mantis shrimp (Odontodactylus scyllarus). The pummeling motion of the shrimp's clublike heel is far faster than the eye, or traditional videotape can follow, Patek explains. Last spring though, Patek, professor Roy Caldwell, and graduate student Wyatt Korff collaborated with the BBC to capture the shrimp's strikes using a high-tech camera shooting at 5,000 frames per second.
For the first time, the scientists could watch the attack in slow motion and really see the biomechanical forces at work.
"The first time I saw the video, I was impressed by how incredibly extreme, energetic, and fast this motion is," Patek says.
Patek's measurements revealed that the shrimp can release its front leg at speeds of 23 meters per second. Previously, scientists thought that the shrimp stored the energy for such speeds by contracting its muscles and latching the leg, essentially cocking it until the energy is released during an attack. However, Patek doubted that the latch-based mechanism was enough to generate such speeds. A spring would do the trick, but if the shrimp was equipped with one, where was it?
"I went to the National Museum of Natural History where they have the world's largest collection of these critters," she says. "I noticed that on the front limbs of every single stomatopod species, there's a beautiful and unique saddle-shaped structure."
The stiff saddle is what's known as a hyperbolic paraboloid. Similar in appearance to a Pringles potato chip, the shape is used by some avant-garde architects to design cement roofs resistant to buckling. This saddle in the shrimp's exoskeleton proved to be the missing spring, bending enough as the muscles contract to store the energy needed to propel the leg with the extreme speed and force required to shatter a tough snail's shell.
"The shrimps wear down their own heel with each attack," Patek says. "Luckily for them, they molt every three months."
A peacock mantis shrimp takes a whack at a Tegula snail with its front leg, which can reach speeds of 75 feet per second. (Sheila Patek, Wyatt Korff/UC Berkeley)
The video also revealed a secondary physical phenomenon of the speedy strike. Negative pressure near the point of impact results in cavitation, erosion caused by the implosive collapse of vapor bubbles. A half-millisecond after the shrimp's heel hits its target, the cavitation bubbles finish the job.
Now that the magnificence of the mantis shrimp's eating habits have been caught on film, Patek is eager to unravel the evolutionary mysteries behind their impressively brutal weapon. For example, she'd like to understand what factors led to the diversification of the limb and how the underlying model of the saddle has evolved in different kinds of mantis shrimp.
"The best part of biology is teasing apart the evolutionary history that goes into something as incredibly powerful and biomechanically complex as this single limb," she says.
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Chilling News About Glaciers
Every couple of years or so, Kurt Cuffey spends two months in Antarctica conducting fieldwork. (courtesy the researcher)
When most people look out over the Golden Gate Bridge, they're awe-struck by the majesty of the San Francisco Bay. Not UC Berkeley professor Kurt Cuffey. Staring out at the Pacific Ocean, the first thing that pops into his mind, he says, is the sea level. Meanwhile, visions of glaciers dance in his head. Cuffey, who last month was named one of Popular Science magazine's "Brilliant 10" for 2004, studies polar ice sheets to understand the history of climate change and predict future shifts in our planet's physical environment.
"The polar ice sheets are the primary control on global sea levels and also impact the temperature of the planet quite profoundly," says Cuffey, a professor in both the Department of Earth and Planetary Science and the Department of Geography.
The massive ice sheets are affected by the climate in several ways, Cuffey explains. Snowfall causes them to grow while a rise in temperature leads to melting. Meanwhile, the ice sheets flow like a viscous fluid, similar to "honey dumped on a counter," Cuffey says. For example, the Antarctic ice sheet, more expansive than the continental United States and several miles deep, moves hundreds of meters annually. While the size of the ice sheet is affected by temperature, it's also part of a climatic feedback loop.
"The snow covering the sheets causes them to be very reflective," Cuffey says. "If the climate cools and the ice sheet grows, it will reflect more sunlight causing a further cooling of the climate. With global warming, the inverse is true."
In Antarctica during the summer, there are periods of 24-hour sunlight. In winter, there are weeks where the sun does not rise. (courtesy the researcher)
Cuffey employs several techniques to gather his data, most of which involve suffering the sub-zero centigrade temperatures of Antarctica. His survey work involves mounting Global Positioning Systems on glaciers to monitor the ice flow and collecting atmospheric data from an array of weather stations. Cuffey's most interesting insights often come from ice cores, samples extracted by drilling a mile-long bore hole into a glacier. Bubbles trapped in the ice contain atmospheric air from tens of thousands of years ago.
"The ice and the bubbles act as chart recorders of climate, atmospheric composition, and other environmental properties over periods of millennia," he says.
For example, by chemically analyzing the ice cores and temperature readings taken from a Greenland bore hole, Cuffey and his colleagues determined that in the 20,000 years since the last ice age was its coldest, the Greenland ice sheet warmed approximately 15 degrees centigrade, much more than previously thought. Amazingly, 10 degrees of that warming occurred over a single decade. Cuffey's results hammered home the fact that climate change can occur much more abruptly than most scientists suspected.
When he's not trudging through the snow, Cuffey crunches his data on a computer to create numerical models of ice sheets. These mathematical models of ice flows reveal how the ice sheets behave over time in response to climate and sea level changes. The models are also essential in predicting future climate changes. For example, Cuffey asks, how would the ice sheet change if global warming raised the temperature by, say, five degrees centigrade?
The recent Hollywood blockbuster "The Day After Tomorrow" depicts global destruction caused by a nearly-instantaneous ice age. While the film is based purely on science fiction, Cuffey says that the Greenland ice sheet could plausibly melt in the next few thousand years, raising sea levels enough to drown most major coastal cities.
"What if we determine that global warming in the next century could induce a rapid climate change that will decimate some societies around the globe?" Cuffey says. "How does society act on that information? Part of what I'd like to do is provide data that can help determine public policy."
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From Crime Scene Clues To Life On Mars
UC Berkeley chemist Richard Mathies designs high-tech tools for two very different kinds of detectives. On Earth, his group is developing instruments that will be used by forensic scientists to help solve crimes using DNA analysis. A similar system could also aid astrobiologists in hunting for life on Mars without ever stepping foot on the red planet.
Richard Mathies, whose work is funded with both public and private grants, leads a multi-disciplinary research group consisting of physical chemists, biophysical chemists, mechanical engineers, bioengineers, and chemical engineers. He is also the director of the Center for Analytical Biotechnology in the College of Chemistry.
Mathies is the inventor of capillary electrophoresis arrays and energy transfer fluorescent dye labels, common technologies in today's DNA sequencers. Now he's combining those innovations with a microscale plumbing system to build an entire genetics laboratory on a chip.
The chip is the key component in the Mars Organic Analyzer, an instrument that will probe the Red Planet's soil for amino acids, the building blocks of organic life. The Mars Organic Analyzer may travel to the Red Planet as early as 2009 aboard either NASA's Mars Science Laboratory, the European Space Agency's ExoMars mission, or possibly both. Funded by NASA, the system was developed in collaboration with the Jet Propulsion Laboratory at the California Institute of Technology and UC San Diego's Scripps Institution of Oceanography.
"Up until now, chemistry has been done on microliter or milliliter scales," Mathies says. "But there's actually more than enough molecules in a few nanoliters, or billionths of a liter, to do most of today's chemical assays."
Still, the big hurdle in designing a lab-on-a-chip has not been integrating the chemical analyzers in such a small device, but rather controlling the flow of the tiny sample through the system. To that end, Mathies and graduate student Alison Skelley built a multi-layer plastic chip containing a complex system of etched channels. Fabricated with the same processes used to manufacture computer chips, the four-inch diameter device is outfitted with myriad plastic membranes and valves that control the flow of the sample.
"It's essentially a microfluidic microprocessor that runs very complex 'programs,'" Mathies says. "By activating the various pneumatic lines, you can react the samples, process them, mix them, and present them to analyzers all on this one chip."
The valves and pumps on this lab-on-a-chip are moved up and down using a pressure or vacuum source. (courtesy the researcher
On Mars, the chip will run a program that seeks out a specific characteristic of amino acids that Mathies says would be "strong proof of extraterrestrial life."
"The question we asked was if you were sitting on Mars right now, what experiment would you run to determine if a little bit of dirt contains evidence of life?" he says. "The challenge is to come up with a methodology that's not totally Earth-centric without it being so general that you don't learn anything."
The experiment they developed is based on the fact that amino acids are optically active molecules. They can exist as mirror-images, designated either "left-handed" or "right-handed" depending on their stereoisomeric structure. When amino acids are accidentally created in space without any basis in life, they're an equal mix of left and right-handed. So if a sample taken on Mars shows a "chiral excess" of one optical isomer versus the other, the amino acids are biological in origin.
Inside the Mars Organic Analyzer, the capillaries on the chip are filled with one of two kinds of chemical "gloves" that mate with either left- or right-handed amino acids. If a mix of amino acids moves down a capillary filled with left-handed mitts, the left-handed amino acids flow through the system more slowly because they'll slip inside the left-handed chemical gloves along the way. Meanwhile, the right-handed amino acids won't fit inside the gloves at all. The speed and mobility of the amino acids can then be analyzed to determine whether there's a prevalence of one optical isomer over the other. Such a prevalence, Mathies says, would provide evidence of life.
Recently, Mathies and his collaborators successfully demonstrated the system in the arid Panoche Valley near Fresno, California. The next field-test will take place in Chile's Atacama Desert, the driest, most Mars-like environment on our planet.
"If an instrument can't detect life there, it has no business going to Mars," says Mathies, who is also affiliated with the California Institute for Quantitative Biomedical Research (QB3).
While the researchers perfect their system for the rigors of space travel and robotic deployment, Mathies is applying a similar approach to solve a terrestrial problem. He's the recipient of a large National Institute of Justice grant to develop a compact, high-throughput genetic identification system. The goal is to build a machine, based on his lab-on-a-chip, that would allow forensic investigators to quickly analyze DNA evidence from crime scenes and known felons at very low cost.
"Forensic laboratories have hundreds of thousands of DNA samples that have never been analyzed or compared because it's too expensive and slow to run the tests," Mathies says. "With our integrated and automated system, you could place a sample in the machine and very rapidly and cheaply amplify and analyze the markers in our DNA that distinguish us as individuals."
That capability is especially important now, he adds, given the passage in the recent election of California Proposition 69. The proposition mandates that DNA samples be collected "from all felons, and from others arrested for or charged with specified crimes."
Eventually, Mathies says, a portable version of the machine could enable DNA tests right at the crime scene. This on-location testing would eliminate questions of whether a sample was tainted or mislabeled during handling, processing, or analysis, and provide crime scene investigators with immediate information on possible suspects.
"These lab-on-a-chip technologies motivated by such things as Mars exploration and forensic identification have larger applications in all areas of chemical and biochemical analysis, from genetic sequencing to pathogen detection," Mathies says. "This technology will lead to a real paradigm shift in chemistry."
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Berkeley's Scientific Legacy
1960: Donald Glaser and his bubble chamber
Nobel Laureate Donald A. Glaser, Professor of Physics and Neurobiology in the Graduate School
A pressure cooker with windows? That was the basic idea behind the bubble chamber, a powerful instrument for the study of atomic particles that led to a 1960 Nobel Prize in Physics for its inventor, UC Berkeley professor Donald Glaser.
Glaser first conceived of the bubble chamber in 1952, at the age of 25, while a faculty member at the University of Michigan. According to scientific lore, Glaser was enjoying a cold beer when he observed the stream of bubbles in his brew. It was a moment of saloon science that inspired a tool second only in importance to the cyclotron for atomic physicists.
The first bubble chamber, no bigger than its inventor's thumb, contained a clear, super-heated liquid in the path of charged atomic particles accelerated by an atom smasher. As the particles pushed through the liquid, they created a trail of tiny bubbles that could be photographed through the window of the chamber. Analyzing the bubbles provides physicists with insight about the particles and related forces.
Donald Glaser with Xenon Bubble Chamber. (courtesy LBL)
Over the years, bubble chambers increased in size--surrounded by a magnet the size of a bus to control the particles--and capability as scientists around the world embraced the instrument. Indeed, Luis W. Alvarez, another Berkeley Nobel Laureate (Physics, 1968), and his colleagues, expanded on Glaser's work to develop their own hydrogen bubble chamber. The device enabled the researchers to discover many new resonance particles, subatomic particles with incredibly short lifetimes.
After consulting during the summers at the Lawrence Radiation Laboratory, Glaser joined the University of California faculty in 1959. Five years later, he became a professor of physics and molecular biology at the university. Now a Professor of the Graduate School, Glaser's research has shifted to the construction of computational models that shed light on the physics and physiology of human perception.