Volume 2, Issue 12
A Shrimp's Eye View
In the deep blue ocean a tropical mantis shrimp puts on a fantastic show for its brethren. Patterns on its sides and back light up in fluorescent yellows and greens while its legs flash red and white. The shrimp opens its mouth appendages and reveals a brilliant blue glow. These dazzling displays are invisible to the naked human eye, but UC Berkeley marine biologist Roy Caldwell has seen them. In fact, he discovered most of these secret signals.
Roy Caldwell on a boat headed to a research site on Lizard Island, Australia. (Gloria Caldwell photo)
"The mantis shrimp has the most sophisticated eyes of any animal on the planet," Caldwell says. "But we simply didn't know why they needed such a complex eye."
After nearly two decades studying the intricacies of stomatopod eyes, Caldwell and his colleagues recently determined that the eye has evolved to see things that human beings need special filters and lights to observe. Mantis shrimp, from the order Stomatopoda, use fluorescent markings and polarized patterns to signal and perhaps warn each other. After all, Caldwell and UC Berkeley integrative biologist Sheila Patek have shown that the mantis shrimp has the swiftest kick in the animal kingdom. Its calcified club appendage is a deadly weapon, capable of killing prey with one blow.
"Once they evolved that lethal weapon, it was imperative that they be able to recognize each other," Caldwell says. "One mistake and you could lose a head."
The mantis shrimp Lysiosquillina glabriuscula in threat posture, photographed near Key Largo. The stomatopod was photographed in blue light with a yellow filter (above) to show only the fluorescence, similar to what other mantis shrimp see at depth. (Roy Caldwell photo)
In late 2003, Caldwell and his collaborators reported the first documented case of sea creatures using fluorescence to signal. The breakthrough came when Caldwell and Thomas Cronin of the University of Maryland analyzed video shot by Physical Sciences Inc.'s Charles Mazel. Using a fluorescent lighting system to capture the colorful undersea life off the Bahamas, Mazel had accidentally filmed a mantis shrimp displaying two unusual "headlights." In shallow water, the yellow-green spots enable tropical mantis shrimp to recognize members of its own species. However, the animal also lives at depths of 40 meters where there's no yellow light to reflect off the spots. The video revealed that the stomatopod uses fluorescence to keep up the signal.
"At those depths, the animal does a neat trick of taking in the blue light in the ocean and fluorescing yellow," Caldwell says. "So the fluorescent pigment enables it to maintain its species-specific signal. In fact, its eyes are tuned to pick up on that color."
As he investigated further, Caldwell observed similar fluorescence in most of the species in the superfamily Lysiosquilloidae, but the story of the stomatopod signaling gets even stranger.
"I was taking photos of a mantis shrimp in our aquarium and there was a reflection I couldn't get rid of," he says. "So I grabbed a polarizing filter to knock out the reflection and as I turned it, the animal started flashing red and white at me."
This Haptosquilla banggai from Sulawesi, Indonesia has bright blue polarized patches on its first pair of mouth appendages that send a clear, but highly directional signal identifying the species and saying "This cavity is taken!" (Roy Caldwell photo)
It turned out that some mantis shrimp in the superfamily Gonodactyloidea also display and detect strong polarized signals, light waves that are oriented in a particular direction. Think of polarized sunglasses that reduce glare by blocking horizontally-oriented light. In the case of a stomatopod, the polarized patches on parts of its body look pinkish to the unaided human eye. But seen through a polarized lens, light reflected off those patches reads as bright red or white depending on the orientation of the animal.
"We already knew stomatopods had excellent polarized vision," Caldwell says. "But they see at least three angles of polarized light. It's the equivalent of wearing three different pairs of polarized sunglasses at various angles. Any time the animal moves, the eye will pick up these signals as flashing."
In May, Caldwell received a very special care package from his former graduate student Mark Erdmann, now working in Indonesia. Inside was a living stomatopod that Erdmann picked up on a deep dive near Sumatra. Much to Caldwell's surprise, the animal, a Squilloid, exhibited more polarized signaling than any of the Gonodactyloids the researchers had studied.
"Those two superfamilies are very far apart," Caldwell says. "So that suggests that this ability to produce polarization came from their common ancestor. It's a trait that's been around for a very long time."
This pair of Odontodactylus latirostris are courting. Only the male (left) has a polarized patch of cuticle on a scale near his head. The red signal is exposed by viewing the animals with the aid of a polarizing filter. (Roy Caldwell photo)
Currently, the researchers are surveying an array of stomatopod eyes and identifying the myriad polarized and fluorescent signals the animals display. Of course, the long-term goal is to deduce the purpose of each signal, if there is one, and how the signals and eyes co-evolve. The stomatopods live in a rough environment where hiding places are few and predators are many, Caldwell explains. In some cases, a stomatopod might use a polarized signal to let another shrimp know that a cavity is occupied.
"The polarized blue signal on the first pair of mouth appendages is hidden unless the animal shows it," he says. "And even then it can only been seen from a narrow angle. It's like having a spotlight you can flash at a specific individual to say: 'Hey, I'm in here. The cavity is occupied!''"
In other cases, the combination of fluorescence and flashing could signal another stomatopod's sexual intentions. A fluorescent male shrimp spinning its polarized legs like an eggbeater is not easily missed, Caldwell says.
"As we pick up little bits and pieces about these animals, we can put together an entire narrative about their evolution and how it all can be tied back to the innovation of that dangerous weapon 300 million years ago," Caldwell says.
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Change Agent
Organic chemistry depends on catalysts to spur the transformation of molecules during chemical synthesis. Like the catalytic reactions that are his specialty, UC Berkeley chemist Dean Toste is an agent of change. Toste develops new catalysts that could someday transform some forms of chemical synthesis, perhaps even streamlining drug discovery and pharmaceutical production.
While completing his PhD at Stanford, F. Dean Toste received the Nobel Laureate Signature Award of the American Chemical Society, the highest honor a chemistry graduate student can receive.
"Our catalytic reactions are less like the difficult transformations people often associate with organic chemistry and much more like cooking," Toste says.
Chemists employ catalysts to accelerate the rate of chemical reactions. These catalysts provide a pathway between the reactants and the end product that requires far less energy than the transformation would take on its own. During the last several decades, metal catalysts have emerged as a powerful tool for organic synthesis in the pharmaceutical and materials science. These highly reactive metals enable transformations that may not be possible using traditional methods. The problem, Toste explains, is that the metals are often in low-oxidation states, making them incredibly sensitive to air and moisture.
"It's a double-edged sword," he says. "You add a lot of reactivity but the reactions become so sensitive that they react with the environment around them. That limits the catalysts' practical utility."
The pharmaceutical industry already uses metal catalysts when it's seeking out new possible medicines during drug discovery. The high reactivity requires chemists to purify the solvents involved in the process and remove the air from the reaction vessels. Toste's novel metal complexes and catalytic reactions negate the need for those steps.
"Medicinal chemists might use our catalysts to make the discovery phase much easier, but our reactions may also be able to further streamline the production of drugs," says Toste, who has won numerous awards from pharmaceutical companies for his basic research successes.
One of the novel catalysts in action, catalyzing a reduction in an open test tube. (courtesy the researchers)
For example, Cytochrome P-450 is a high oxidation state metal enzyme that the human body uses to make cholesterol, steroids, and lipids. Toste and his colleagues have engineered catalysts based on Cytochrome P-450 that are non-oxidative.
"We took something that nature uses for oxidation and reversed it so now it does reduction," he says. "Since it's already oxidized, it isn't sensitive to the environment. You can just drop it into your flask and stir it up."
Along with the benefits of being tolerant of air and moisture, the catalysts coming from Toste's lab promise to have less impact on the environment. The reactions primarily are additions to the molecular product, or isomerizations, in which the organization of the atoms is changed but not the constituency of the molecule.
"Nearly everything you put in ends up in the final product, so the waste stream becomes very small." Toste says.
The researchers are also developing catalysts based on gold. Most of us think of gold as an inert substance that's perfect "for a wedding band," Toste says, the fact that gold is a low oxidation-state metal makes it interesting as a catalyst, but it's historically been very difficult to demonstrate very many useful reactions based on the element. Recently though, the Berkeley researchers have developed myriad gold complexes that work well as "open-flask" catalysts.
"Even if we don't discover the groundbreaking fundamental reaction that produces a new drug for pennies, we hope in the future that our catalysts could lead someone to those kinds of opportunities."
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Mathematics of Everything
Edward Frenkel is on a search for symmetry. Most simply, an object is symmetrical if it can be reflected, rotated, or "slid" from one area to another seemingly without changing it. Snowflakes are symmetrical. So are butterfly wings. And the human body. Indeed, the beauty of symmetry surrounds us. But the symmetries sought by Frenkel, a UC Berkeley mathematician, are hidden within esoteric branches of math and physics. In his eyes though, those symmetries are just as stunning.
"In mathematics, symmetries play a very important role in such diverse subjects as geometry, number theory, and algebra," he says. "And in physics like quantum field theory and string theory, symmetry is a focal point of research. I look at the fundamental properties of symmetry and how they play out in different domains so we can understand the underlying concepts and patterns."
As a high school student in Moscow, Edward Frenkel wanted to be a physicist. Then a mathematician friend of the family introduced Frenkel to the beauty of numbers. Frenkel's research enables him to pursue both passions.
Mathematical symmetry means that an expression remains unchanged even when certain operations are applied to it. For example, the formula a2c + 3ab + b2c is symmetrical because even if the "a" and "b" are swapped, the expression stays the same. Mathematicians study those kinds of symmetries by grouping together all of the operations that don't change a particular expression. In geometry, objects can be symmetrical. If an equilateral triangle is rotated 120 degrees or reflected along a vertical axis down the center, the shape stays the same.
Of course, much of the symmetry in geometry, algebra, and mathematics is far more difficult to spot. Frenkel's stomping ground is the Langlands Program, something of a "unifying theory" of mathematics based on symmetries. First proposed in 1967 by Robert Langlands of the Institute for Advanced Study, the conjectures boldly linked together seemingly unrelated objects in branches of mathematics like number theory and algebraic geometry. (British mathematicians Andrew Wiles and Richard Taylor built upon the Langlands Program to famously solve Fermat's Last Theorem in 1994, three hundred years after Fermat scribbled it in the margin of a book.)
Frenkel is co-managing a multi-university research project sponsored by the Defense Advanced Research Projects Agency (DARPA) to investigate the Geometric Langlands Program. As part of the effort, the researchers are applying Langlands' lessons to two of the most cutting-edge research thrusts in physics today--quantum field theory and superstring theory.
Quantum field theory is a framework to study elementary particles and their interactions. Superstring theory attempts to unite Einstein's general theory of relativity and quantum mechanics under one umbrella, or "theory of everything." According to superstring theory, all elementary particles are tiny vibrating strands of energy. Every matter particle also has a "superpartner," a particle that carries a fundamental force of nature such as gravity. The theory posits that superpartners are paired by supersymmetry.
"The question we're asking is, can we see the Langlands program in string theory like we do in number theory or geometry?" Frenkel says. "For me, the excitement of mathematics is recognizing when a phenomenon appears in many different contexts unexpectedly. First you admire that. Then you ask why."
Of course, string theory has not been experimentally confirmed. But postulating theories about theories is all part of the game, Frenkel adds.
"We don't know if string theory describes the universe, so this research may touch on something fundamental about reality or it may not," he says. "But at the very least, it produces very beautiful mathematics."
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Berkeley's Scientific Legacy
Jerzy Neyman and the start of Berkeley Statistics
When Jerzy Neyman arrived at UC Berkeley in 1938, he was thrilled to be faced with what he called a "tabula rasa" of statistical studies. During the previous two decades, statistical methods had bloomed as a tool of science and engineering and courses. Neyman was brought to Cal to launch the University's curriculum and research in the area. Called "a principal architect of modern statistics," Neyman directed what would become one of the preeminent hubs of statistical research in the world.
Neyman was born in 1894 in Bendery, Russia to Polish parents and earned a PhD at the University of Warsaw. A mathematician first, Neyman explored statistics during a job as "senior statistical assistant" at the National Agricultural Institute in Bydgoszcz, Poland. In 1925, he was awarded a fellowship to study mathematical statistics with the famed mathematician Karl Pearson in London. There he met Pearson's son Egon S. Pearson. During the next decade, the younger Pearson and Neyman jointly developed a groundbreaking and controversial theory on the testing of statistical hypotheses. It's now a core concept in elementary statistics textbooks.
"It is widely felt that in spite of the existence of a large number of special problems for which perfect solutions exist, statistical theory in general in its present state is far from being completely satisfactory from the point of view of its accuracy," they wrote at the time. Our intention is "to contribute toward the establishment of a theory of statistics on a level of accuracy which is usual in other branches of mathematics."
In 1937, a subcommittee established by the University of California's Committee on Courses urged the University to bring a professional mathematical statistician to campus to create a program within the Department of Mathematics. Neyman, then on the faculty of the University College London's Department of Applied Statistics, was recruited for the job.
Neyman's first achievement at Berkeley was the foundation of the Statistical Laboratory, a research center within Department of Mathematics. Once the Lab was underway, Neyman spearheaded a symposium of mathematical statistics and probability "to mark the end of the war and to stimulate the return to theoretical research." The massive success of the first symposium led to its series, with one taking place every five years. The Sixth Berkeley Symposium, attended by 240 leading scientists, resulted in the publication of a six-volume, 3,397 page proceedings.
"These symposia supplemented the teaching programs and research academic activities normally carried out in universities and other academic institutions," professor emeritus Chin Long Chiang, Neyman's former student, wrote. "They also had a great deal of influence on the attitude of theoretical statisticians and research scientists, making them recognize the need and the advantage of applications of statistics.
In 1954, Chancellor Clark Kerr recommended that a separate Department of Statistics with Neyman at the helm be spun off from the Department of Mathematics. Enrollment rapidly increased at a rate of 20-25 percent per year. From the classroom to his administrative office, Neyman was always an advocate for his students. One day in1940 during a class, he wrote two well known but unsolved problems in statistics on the blackboard. Student George Dantzig, arriving late to class, assumed they were homework. So he solved them.
"A few days later I apologized to Neyman for taking so long to do the homework -- the problems seemed to be a little harder to do than usual," Dantzig recalled. "I asked him if he still wanted the work. He told me to throw it on his desk. I did so reluctantly because his desk was covered with such a heap of papers that I feared my homework would be lost there forever. About six weeks later, one Sunday morning about eight o'clock, Anne and I were awakened by someone banging on our front door. It was Neyman. He rushed in with papers in hand, all excited: 'I've just written an introduction to one of your papers. Read it so I can send it out right away for publication.'
Neyman died in 1981 at the age of 87.
"Neyman used to say 'Statistics is the servant to all sciences,'" Chiang once wrote. "In many ways Neyman had expanded the domain and improved the quality of the service."