Volume 5, Issue 37 May 2008
Underground Astronomy
Professor of physics Bernard Sadoulet has designed a sophisticated set of equipment to search for particles of dark matter. Image credit: CDMS
Most scientists who study the cosmos keep their eyes fastened firmly on the sky. Not so Bernard Sadoulet. A Berkeley professor of physics, Sadoulet is stalking dark matter, the elusive material that forms the scaffolding of the universe. And the place he's laid his traps is just as shadowy-a former iron mine more than 2,300 feet underground.
Sadoulet admits that the bowels of the earth make for an unconventional place to study the universe. But the particles that are the leading candidates for dark matter are most easily detected far from the cosmic rays that rain down from space.
"We have good reasons to believe that only about five percent of the energy in the universe is made of ordinary matter. So 95 percent is unknown. And we are trying to determine experimentally what that is," Sadoulet says.
Roughly 75 percent of the mystery material is known as dark energy-a force that behaves like anti-gravity, pushing galaxies apart. The remainder is called dark matter, and cosmologists believe it provides the gravitational mass that holds the universe together.
An elaborate cooling and shielding system surrounds the dark matter detectors, preventing interference from heat and other types of radiation.
The jury is still out on what dark matter is. About all scientists know is that it has mass, clumps under the influence of gravity, and can't be seen because light passes right through it.
"It is interesting to observe that the most inert component in the universe is ultimately responsible for the formation of structure and, ultimately, stars, planets, and life," Sadoulet says.
Speculations about dark matter's identity range from the side effects of additional dimensions to ultralight particles known as neutrinos. But several lines of thinking have converged on heavy particles known as WIMPs (weakly interacting massive particles).
Despite their acronym, WIMPs are atomic behemoths, approximately 100 times the mass of a proton. Their great mass would explain why they have not yet been seen in laboratories; previous generations of particle accelerators weren't powerful enough to produce them. In nature, these giant particles would have formed in the early universe in the burst of energy released by the Big Bang.
"If these particles are the dark matter, they form a dark halo around the galaxy. We are in this halo, and there are billions of these particles going through us all the time," Sadoulet says.
One of the detectors used to identify candidate particles of dark matter known as WIMPS. Silicon and germanium atoms coating the detector's surface will emit a distinctive pattern of vibrations and electrons if hit by a WIMP.
Sadoulet leads an experiment to find these particles within Minnesota's Soudan Mine. His Cryogenic Dark Matter Search employs detectors made of silicon or germanium crystals cooled to nearly absolute zero. Any WIMPS or other particles crashing into the crystals will trigger a distinctive set of vibrations called phonons and extract electrons. The ratio of the electrons and phonons generated distinguishes a bona-fide WIMP from other forms of radiation such as gamma-rays. Sadoulet is already working on the next generation of this experiment, which will involve caching more sensitive and efficient detectors in a Canadian physics laboratory nearly three times deeper than Soudan.
Other scientists are tackling the problem of dark matter with a satellite capable of detecting the gamma rays emitted by colliding WIMPS, and a powerful new particle accelerator called the Large Hadron Collider that will attempt to manufacture WIMPs from scratch. Sadoulet's detectors will be essential for confirming whether any of these artificial particles match the profile of a WIMP.
"Within five years, three totally different approaches to catching WIMPS should be in operation, and we may be at the brink of a discovery" says Sadoulet. "It's an interesting time to be searching for dark matter."
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Distant Relatives, Common Genes
Glance through any family's photo album, and you're likely to home in on a few outstanding ancestral traits. The shape of a nose or the arch of an eyebrow can be passed down for generation after generation.
Biologists have long studied commonalities such as these to infer ancestral relationships between animals. But the more distant the relationship, such as between humans and sponges, the trickier it is to establish connections through simple comparisons of anatomy.
A Berkeley professor of both physics and cell and molecular biology, Dan Rokhsar is also a member of Berkeley's Center for Integrative Genomics and a faculty scientist at the Department of Energy's Joint Genome Institute. Photo credit: courtesy Dan Rokhsar
Dan Rokhsar, a Berkeley professor of both physics and molecular and cellular biology, and a faculty scientist at the Department of Energy's Joint Genome Institute, is sidestepping this problem via a different aspect of inheritance: genes. Genes shared by distantly related animals are likely to have originated in their last common ancestor. So by sequencing and comparing the genomes of creatures ranging from sea anemones to sea squirts, limpets to pufferfish, Rokhsar and his research team hope to reconstruct characteristics of the great-great grandparents to all animals.
"We're interested in that transition from being a unicellular organism to being multicellular-when it happened and how it happened," Rokhsar says. "The fossil record can't tell you much because the animals at the time were soft-bodied."
Instead, Rokhsar studies the genomes of its living descendants. His approach has already yielded many surprises. For example, sea anemones, which lack a brain or any other type of central control, have long been considered to have a correspondingly primitive nervous system. But Rokhsar has discovered genes that code for different types of neurons to grow in various regions of an anemone's body.
"By looking at where and when these genes are expressed, we're finding patterns you can't see just by looking at the animal," Rokhsar says.
Rokhsar's work is also giving scientists a broader perspective on popular model organisms such as fruit flies and nematode worms. Their genes are relatively simple in structure, with few of the intervening segments that break up human genes. Some scientists speculated that this genomic complexity is what gave humans an evolutionary edge. But Rokhsar has found that the genomes of sea anemones and limpets are equally complex.
"We're learning that the human genome is more typical than we thought," Rokhsar says. "It also gives us hints about why fruit flies and nematode worms have been so useful. By clearing away all that other complexity, they've stripped away a lot of the stuff that makes it harder to work with vertebrate systems, and have laid bare the basic system."
Rokhsar is sequencing the genomes of organisms as diverse as the starlet sea anemone (left) and choanoflagellates (right). His work is encouraging comparative research in a broader variety of organisms and improving our understanding of animal evolution. anemone photo credit: Nicholas Putnam, UC Berkeley; choanoflagellate photo credit: Nicole King lab, UC Berkeley
By diversifying the types of organisms with available genomes, Rokhsar hopes to encourage interest in these species as laboratory models. The resulting knowledge can only improve understanding of how animals evolve and adapt to challenges such as a changing climate.
Recently, the skyrocketing price of petroleum and the threat of global climate change have turned Rokhsar's attention toward greener subjects: plants. Now, he is not only providing new insights into our genetic heritage but also clearing a path toward a cleaner, greener future.
"The cellulose and lignin in plant walls is where all of the carbon goes from photosynthesis. That's the carbon we want to convert to fuel. How do they do it? One way to find an answer is to look at genomes," Rokhsar says.
He is now working to sequence the genome of switchgrass, a native plant and strong candidate to produce biofuel. Scientists want to understand which switchgrass genes promote positive traits such as fast growth or minimal fertilizer requirements. With these in hand, they can screen sprouts for desired characteristics and hasten the development of useful varieties.
"We need to collapse the 5,000 years it took to breed maize into an edible plant into 10 years for switchgrass, because we don't have a lot of time to develop renewable fuels," Rokhsar says. "And we'll need to do this sustainably and as a solution for the long term."
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The Living Story of Sulawesi
Jim McGuire during the nighttime capture of a reticulated python in Central Sulawesi, Indonesia. He is a professor of integrated biology and curator of herpetology at the university's Museum of Vertebrate Zoology. Photo credit: Ben Evans
The Indonesian island of Sulawesi is a 12,000-square-mile jigsaw puzzle. During the past 25 million years, drifting tectonic plates tore four separate paleo-islands from the far corners of the South Pacific and smashed them together in a steamy corner of Southeast Asia.
This turbulent history has turned Sulawesi into a complex biological cipher. Today, it houses a mélange of species with confusing origins: some may have been passengers on the original islands, some may have arrived afterward, and some may have evolved from the mix.
McGuire collects snakes, lizards and frogs throughout Sulawesi in areas such as Bogani Nani Wartabone National Park. Photo credit: Jim McGuire
Jim McGuire, curator of herpetology at Berkeley's Museum of Vertebrate Zoology and a professor of integrative biology, is studying how these species evolved and came to be distributed on Sulawesi today. McGuire first visited Sulawesi while collecting flying lizards of the genus Draco. When he sat down to analyze specimens collected from across the island's four peninsulas, he was astonished by what he found. Based on body shape, the reptiles could be sorted into three morphologically distinct species. But the genes carried by their mitochondria, the powerhouses of cells, told a different story. This data suggested that the three groups could be comprised of multiple "cryptic" species identical to the naked eye but apparently unable to interbreed.
"It was as if they were cut off from each other at some point. But in many cases we don't know what the underlying mechanism would be," McGuire says. The story becomes even more complicated when species from neighboring islands are considered. Many of the "cryptic" Sulawesi species have given rise to new species on off-shore islands. As a consequence, they are more closely related to anatomically distinct lizards now living on other islands rather than to their apparently identical next-door neighbors on Sulawesi.
Flying lizards such as Draco beccarii are one of McGuire's primary interests. These tropical lizards can glide through the air with remarkable accuracy by expanding their ribs into a patagium, or wing. Photo credit: Jim McGuire
Then McGuire read about Sulawesi's macaque monkeys, which comprise seven distinct species. The ranges of many meet at the same localities where the genetically distinct but morphologically identical flying lizards meet.
These findings inspired McGuire to compare the genetics of nine different types of Sulawesi fauna and analyze their origins. His goal is to piece together the story of when each animal group arrived on the islands and how they have fragmented to produce today's range of species.
A Draco beccarii male clinging to a tree. Photo credit: Jim McGuire
It's hard to imagine a more challenging problem. "It is the most difficult place in the world, I think, to do this sort of biogeographical analysis because the tectonic history has been so complex," he says.
Nearly every year since 2004, McGuire has visited the island for months at a time, hacking through thick foliage and traveling bone-rattling jungle roads to collect lizards, frogs, and other island species. Along the way, he has collected in areas few scientists have visited before.
While collecting, McGuire roughs it in field camps such as this one in Gunung Karua, Central Sulawesi, as his home base. Photo credit: Jim McGuire
"On every one of these trips, we find all sorts of new species that haven't been documented before. And a lot of those species are in primary forest habitats," he says. "I feel that I have a moral obligation to explore and document this species diversity before we wipe it all out."
Back at Berkeley, McGuire compares the species' mitochondrial and nuclear DNA, which evolve at different rates. With this approach, called coalescent-based population genetic analysis, he can determine whether the animals are still genetically isolated or whether genetic differences detected in the mitochondrial DNA are merely artifacts of a previous period of isolation.
An animated movie of the formation of Southeast Asia based on tectonic plate movements. Sulawesi is located at the intersection of the central latitude and longitude lines.
Based on these data, he uses computer simulations to reconstruct the evolutionary history of these animal groups. He then plans to go back and study contact zones between species more closely to try to identify any environmental or ecological barriers, such as past flooding or the presence of a predator, that are enforcing species isolation.
"Once we've completed this, I think we could have a better understanding of biogeography in Sulawesi than virtually anywhere else in the world," McGuire says.
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