Volume 4, Issue 25 February 2007
Evidence for Inflation
Astrophysicist Adrian Lee is developing POLARBeaR, an instrument designed to obtain the first concrete evidence of the Big Bang. He is standing before one of his previous projects, APEX, located on Chile's Atacama Plateau. Image courtesy of Adrian Lee.
In the beginning, there was the Big Bang. Traveling faster than the speed of light, the universe swelled from an unimaginably hot, dense speck into a vast cloud of elementary particles—all in a trillion-trillionth of a second, a period known as "inflation." Then, over the next 14 billion years, that ball of particles continued to spread and grow at a far more steady rate, evolving into the protons, atoms, elements, stars, planets, and galaxies we know today.
At least, that's the creation story that cosmologists currently believe. But the fact is, despite many hints implying that inflation occurred, and abundant theories describing how it might have happened, no one has detected any direct evidence of that singular, mind-boggling expansion.
If UC Berkeley astrophysicist Adrian Lee has his way, this dearth of data about the newborn universe should disappear very soon. Lee and colleagues have devised an experiment called POLARBeaR (Polarization of Background Radiation), designed to detect patterns in space that could only have formed due to inflation.
At present, the most compelling inflation evidence is the cosmic microwave background, or CMB. This faint radiation permeates the entire observable universe—evidence that it was present early on, about 400,000 years after the birth of the universe. The other striking aspect of the CMB is its remarkably consistent temperature. The simplest explanation is that at some point the entire universe was small enough to be at thermal equilibrium. "I like to think of finding pieces of a hot potato scattered around a house," says Lee. "All of those pieces are the same temperature. The logical conclusion would be that they all belonged to the same potato, and that someone heated that potato, cut it up, and spread the pieces from room to room."
Lee has engineered a way to miniaturize and mass produce the photon detectors needed to obtain signals about primordial gravitational waves. He can now fit 1,000 detectors, called bolometers, onto a 9" x 9" silicon wafer. Image courtesy of Adrian Lee.
Minute variations in the temperature of the CMB were found in the early 1990s by George Smoot of UC Berkeley and John Mather of NASA Goddard Space Flight Center. They won the 2006 Nobel Prize in physics partly for this work.
Lee, too, studies the CMB, but seeks an even more subtle pattern within it. If inflation occurred, it would have created ripples in the fabric of space-time called gravitational waves. These waves should have etched a distinctive pattern into the CMB
"Imagine you're looking at the sky with eyes that can see microwaves, but you're also wearing polarized sunglasses. If you looked from place to place, you'd see faint fluctuations in the polarization intensity of the sky. If you could see the lines of the polarization, you would see that they are pointing in different directions in different points of the sky," Lee says.
The patterns would resemble the lines of force around a magnet, or the celestial gyres depicted in Vincent Van Gogh's painting Starry Night. "If we see these swirling patterns of vectors, they would be a smoking gun that inflation occurred," Lee says.
The POLARBeaR instrument will be built at 17,000 feet on Chile's Atacama Plateau, where vicunas, wild relatives of the llama, run wild. Image courtesy of Adrian Lee.
But detecting these patterns will be astoundingly difficult. The signals are very faint—a difference of billionths of a degree atop the 2.7 Kelvin of the CMB.
The best way to read CMB signals is with supersensitive radiation detectors called bolometers. From all the photons in the night sky, a bolometer can pick out the few that that are the right wavelength to have come from the CMB. Only 20 bolometer pixels, each as wide as a finger and a foot across, were needed in the CMB temperature fluctuation experiments. Each was hand built, hand tuned, and chilled to minus 272.5 degrees Celsius to improve their sensitivity.
But the polarization signals Lee seeks are a thousand times fainter. That means he needs at least a thousand bolometers for POLARBeaR. Handcrafting that many bolometer pixels, and chilling each, would be daunting.
Instead, Lee has engineered a way to build bolometer arrays using photolithography, the way computer chips are made. This has enabled him to manufacture all 1,000 pixels at once, and shrink them onto a silicon wafer no larger than a brownie pan.
When photons from the night sky hit the lens of the POLARBeaR telescope, they will be focused on the bolometer detector array. A cryostat will keep the bolometers near -273 degrees Celsius. The multiplexor will both amplify the signals from each bolometer and assemble them into an image in a manner similar to that used in digital cameras. Image courtesy of Adrian Lee.
POLARBeaR itself will consist of a telescope with a 3.5 m diameter telescope sited on the Atacama Plateau of Chile. The telescope will focus an image of the sky onto the bolometer array. At 17,000 feet above sea level, staff must wear oxygen prongs to breathe. But the advantages of altitude are well worth the trouble. At sea level, 50 percent of photons are absorbed by atmospheric water vapor; that drops to 10 percent three miles up.
Lee and colleagues at Lawrence Berkeley National Laboratories, UC San Diego, the University of Colorado, McGill University, College de France, and Imperial College London have submitted a $9 million proposal to fund POLARBeaR to the National Science Foundation.
Signals obtained by POLARBeaR would be a phenomenal advance in our understanding of the early universe. "The earliest thing that man could conceive of seeing right now would be these gravitational waves," Lee says. "I'm hoping that this information will allow us to go back and discover things we haven't even predicted yet about that time."
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The Sands of Time
A live specimen of a larger foraminifera from Papua New Guinea. About 1/2 inch long, it and has extended its pseudopodia, or "false feet," in the direction it is moving. JHL image, 1986.
Jere Lipps has an extraordinarily fine-grained view of history. As a professor of paleontology at UC Berkeley, Lipps examines records of the past written in layers of sediments and fossils. His work has shed light on ancient earthquakes and extinction patterns, the evolution of early life and even astrobiology, and taken him to more than 160 countries over the last 40 years.
The common thread to Lipps's far-ranging research? Foraminifera: tiny marine creatures easily mistaken for sand. Single-celled and quite separate from animals, foraminifera live in virtually every marine habitat explored by man. Even among scientists, foraminifera are chiefly known by their shells. These come in a galaxy of forms—stars and coils, turbans and disks, bulbous cones and simple tubes—segmented into chambers and pierced by patterns of pores. Some are built from secreted calcium carbonate; others are glued-together coral or sand. Their shapes are often distinct enough for Lipps to identify at a glance.
A common foraminifera, Trochammina hadai, found in San Francisco Bay. Lipps and colleagues found it was introduced accidentally to the bay 30 years ago in ship ballast water from Japan and had spread throughout the bay within about 15 years. (Scanning electron micrograph by Michele Weber.)
That type of mastery, however, doesn't come easy. By some estimates, foraminifera may have evolved into more than 80,000 species during their 545 million years on Earth.
Several qualities make foraminifera ideal markers of geologic history. In addition to being present virtually since marine animals first arose, "they're superabundant compared to the remains of clams or snails or dinosaurs. In a sample the size of a teaspoon, you can have thousands," Lipps says. Commercially, foraminifera are used in petroleum exploration, to find rocks that formed during the right conditions and timeframe to contain oil.
Forams are very picky about where they live. Many species can only survive a very narrow range of conditions, such as water of a certain temperature and salinity, or waves up to a certain strength. Distinct groupings allow Lipps to make extrapolations about long-ago ocean conditions and even geologic events.
Jere Lipps (right) and his research team, Lorraine Casazza (left) and Michele Weber, working on the Richmond marsh collecting foraminifera. JHL Image, 2004.
Recently, Lipps and his international team used foraminifera to analyze earthquake and tsunami frequency around the Pacific Rim. Alongside scientists from Alaska and Canada, Lipps examined shoreline sediment cores laid down over the past 7,000 years, at sites from Alaska to Baja California. By tracking changes in foraminifera over time, "we can know when the land goes up or down very precisely. If the edge of a marine plate gets bent down and the continent springs up, a marsh will go from marine to fresh water—then we see no more foraminifera."
Their findings should give coastal dwellers new respect for the watery giant next door. "We estimate that along our coast, from Alaska to Baja, we get a really big earthquake and tsunami every 200 to 300 years," Lipps says. Lipps has since expanded the project to New Zealand, Tahiti, and Mexico with scientists from those places.
Mangroves trees and marsh on the island of Moorea, French Polynesia, where Professor Lipps studies foraminifera. JHL image, 2002.
Lipps is also using foraminifera to gauge the health of UC Berkeley's Richmond Field Station marsh, the site of two former chemical factories. The University removed mud contaminated by heavy metals from the site in 2002. Lipps took sediment cores before the project began and has continued to sample it since. The marsh's comeback has been agonizingly slow, Lipps says. "I'm absolutely flabbergasted we're still looking at this, because foraminifera reproduce by the thousands. Every spring there's a bunch of juvenile ones, but they don't grow up—they just disappear." He ascribes their struggle to the fact that plants, which help keep the mud cool enough for foraminifera, haven't returned yet either.
Lipps's work frequently takes him much farther afield. His research sites read like a brochure for adventure travel—he scuba dives for specimens in places such as New Guinea, the Caribbean, Abu Dhabi, French Polynesia, and Antarctica, where a small island now bears his name.
In Middle Eastern waters and elsewhere, Lipps encountered carpetlike bacterial mats containing rounded formations formed by bubbles. These shapes looked disturbingly similar to what other scientists were calling fossils from some of the earliest marine lifeforms known—the jellyfish-like Ediacaran fauna of 555 million years ago. This led Lipps to study Ediacaran habitats and fossil formation.
Jere Lipps studying the habitats available in icy environments on Iceland. JHL image, 2005.
Lipps's work in Antarctica has directed him toward a more forward-thinking branch of science: astrobiology. "When the images of [Jupiter's moon] Europa came back showing it was a moon covered with water ice, I thought, I know all about those habitats," Lipps says. Using his experience studying ice shelf biota, Lipps developed what he calls a "paleontological search strategy" for NASA. "I and my colleagues came up with a list of 25 or so different habitats where resources might be available where organisms could live." Lipps's expertise in taphonomy, the preservation of organisms in rocks and ice, allowed him to hypothesize how these habitats might be preserved in the ice and uplifted to the surface for observation.
Living on Europa would be no picnic, but any organisms would be hard pressed to surpass the survival skills of foraminifera. "They live from the deepest parts of the ocean to the supratidal, from the poles to the equator, even in environments that have very little oxygen," Lipps says. It's no wonder he admires versatility and breadth—those same qualities have been the lodestones of Lipps's own long and eventful career.
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Biomolecules in Motion
Haw Yang hard at work devising methods to study the chemistry of single molecules. Credit: Michael Barnes
Proteins are the parts that make living engines run. They supply cells with energy, build muscle and bone, and catalyze countless other reactions that let the spark of life burn bright. To do their jobs, proteins must curl around substrate molecules, stretch to let their substrates go, travel around cells and assemble into work crews.
Studying how proteins function, however, can be a major pain. Just billionths of a meter in size, they're too small to observe under a microscope. So scientists have resorted to more indirect methods, like mixing thousands of proteins together with other chemicals and observing the results.
While such averaging experiments have their uses, says UC Berkeley chemistry professor Haw Yang, "we are missing a lot of the interesting action" going on in individual biomolecules.
Now Yang is developing a better way to study biomolecules in motion. "What we hope is to visualize chemistry one molecule at a time."
For this feat, Yang uses a technique called single-molecule microscopy. The method employs probes that fluoresce red or blue when excited by a photon of light. The blue one can acquire photons from an external light source, while the red one only accepts photons from its blue counterpart. For his experiments, Yang affixes one blue and one red probe to opposite ends of a study enzyme. When the enzyme is relaxed, and both probes are far apart, the assembly glows blue. When the enzyme closes, the blue probe can pass along its photon, and the assembly glows red.
Glowing probes help Yang analyze the movement of enzymes. When the enzyme is open, the assembly glows red (left); when closed, the assembly glows blue (right). The color fluctuations reveal both an enzyme's activity rate and the number of positions, or conformations, it can assume. Credit: Lucas Watkins
"We can actually watch in real time as biomolecules such as enzymes open and close," Yang says.
The color fluctuations allow Yang to calculate how fast enzymes move and their range of motion. The amount of time they spend in various postures even indicates how many conformational states they have.
Scientists have long believed that when an enzyme is empty, it gapes open like a hungry alligator, and that after it has caught its substrate, it remains closed until the reaction has been completed. Yang's single-molecule microscopy studies have turned this notion upside-down. "Even when it has substrate, it doesn't just bind the substrate tightly and stop moving. It's still flapping," he says.
This constant motion makes perfect sense, considering how fast enzymes operate; some can process a million substrate molecules per minute. "Like a door, it has to be able to swing even without me going in and out. Its motion has to be inherent and already present in order to respond very quickly," Yang says. Relative instability enables enzymes to release substrate efficiently after a reaction is completed.
At present, Yang's single-molecule microscope is focused on an enzyme from the gut bacterium Escherichia coli. By comparing the behavior of the wild-type enzyme against enzymes with known mutations, he hopes to work out the design principles behind enzyme evolution.
The next step is to study how molecules work while inside a cell. To that end, Yang and his research group have invented a means to track the zigs and zags of a single molecule in three dimensions.
Yang and his group have developed a device capable of tracking the three-dimensional movements of a single nanometers-scale particle in solution. Above: an automated microscope keeps the target particle (encircled in red) in sharp focus as a neighboring particle (green arrow) drifts by. Below: The trajectory of the molecule plotted over time. Credit: Shan Xu
The system works much like the "missile lock" function on a fighter jet, though on a far smaller scale. Using a joystick connected to a powerful microscope and camera, Yang can target a gold nanoparticle, and the system will automatically keeps it in focus. On video, the target particle remains bright and sharp at the center of the screen, while other molecules drift in and out of focus like snowflakes in a storm. At present, Yang can record the three-dimensional location of a single 80-nanometer particle in water every 20 microseconds.
Meanwhile, a spectrophotometer records the light wavelengths refracted off the target as it rotates. This information allows Yang to calculate a particle's diffusion coefficient, which describes how easily it drifts in solution.
The device could help scientists better understand problems such as molecular self-assembly and protein translocation within a cell. For example, many different proteins are known to help manufacture proteins from RNA. But how and when they come together, and whether additional proteins are involved, remains unknown. The new focus-tracking microscope should provide new insights into this problem. Similarly, by observing the change in the diffusion coefficient that occurs when a protein lands on a strand of DNA, Yang will be able to measure the sequence and timing of transcription for the first time.
Ultimately, Yang's work could result in advances in disease research, drug design, turbulence, materials analysis, and even our grasp of basic biochemical reactions. Says Yang, "I hope that in doing these experiments, we will get the chance to know how nature makes these things happen, and take that understanding to improve our quality of life."
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