Volume 2, Issue 8
Boning Up On Human Evolution
Tim White, a UC Berkeley professor of Integrative Biology, is on what he calls "a planetary mission," but the planet he's exploring is Earth, albeit a very long time ago. White and an international team of scientists are digging deep into the geological record of remote Ethiopia to find clues about this planet as it existed 6 million years ago. What was the weather like? What kinds of plants thrived? What animals roamed the terrain? And, of particular interest to paleoanthropologists like White, what did our ancestors look like before evolution transformed them into us?
Fieldwork in southern sector, Main Ethiopian Rift. Left to right: Yonas Beyene, Tesfaye Yemane, Tim White, Berhane Asfaw. (photo © Gen Suwa)
"On one hand, we're explorers of lost worlds," says White, preparing to spend the fall at a bare-bones campsite in a dry, rocky rift 180 miles northeast of Addis Ababa. "On the other hand, we're forensic scientists. We don't have a lot of clues left from what happened in prehistory, so we have to assemble those clues from the fragmentary fossil record and study each one very intensively to extract as much information as we can."
White is no novice when it comes to this kind of detective work. In the early 1970s, he worked with the well-known Leakey family of anthropologists and later collaborated with Donald Johanson to link the famed Lucy skeleton in the chain of human evolution. Since that early work, White has continued to make many of the most significant strides toward completing human ancestry's family tree.
The oldest known fossil of modern humans, dating back 160,000 years. (© 2000 David L. Brill, Brill Atlanta)
For more than two decades, White has traveled back and forth to the Middle Awash region of Ethiopia where dramatic tectonic movement and rains shift the ground to reveal long-buried fossils. While the sediment of Oldevai Gorge, Lucy's burying place, is just the depth of a football field, the Middle Awash valley goes down a mile.
"The depth of the sediment there enables us to sample evolution across vast amounts of time," White says. "We're recovering and salvaging things within a geochronological context so we know their age, the most important piece of data when painting an evolutionary picture."
While White admits that the Afar rift is a tough place to spend the winter holidays, Middle Awash has treated White and his collaborators well. For example, early into a 1994 expedition, one of his graduate students spotted a palm bone on the ground that belonged to what was at the time the oldest hominid ever found.
"At the end of the scientific trail, if you look to the left instead of the right, you could miss something,"White says. "But the well-trained paleontologist always looks both ways."
Hominid fossils belonging to Ardipithecus ramidus kadabba, found in 1997-1999. The mandible of the subspecies is at upper left, the toebone is in the right upper row, and the hand holds a fragment of collar bone. (© 1999 Tim D. White \ Brill Atlanta)
Over the next few years, White's team--including his former graduate students Yohannes Haile-Selassie, now head of physical anthropology at the Cleveland Museum, and Gen Suwa, currently a professor at the University of Tokyo--delicately excavated the remains of that 4.4 million-year-old skeleton of a species since named Ardipithecus ramidus. The fossilized arms, legs, hands, feet, pelvis, skull, and teeth recently made a brief visit to Tokyo where Suwa has developed a special computed tomography (CT) scanner to enable digital reconstructions of the fragile bones.
"At the same time we're studying what we've found, we also want to continue gathering new samples," White says. "So every autumn, we head back into the field."
Between 1997 and 2000, the group excavated early hominid fossils from at least five other individuals who nearly six million years ago called the then-wooded Afar rift home. Last year, the scientists reported that newly-discovered teeth from those hominids indicate that it's a distinct species, not a subspecies of Ardipithecus ramidus as they previously believed. Dubbed Ardipithecus kadabba, it may represent the first human species to appear after the human branch on the family tree diverged from the branch leading to modern chimpanzees and humans.
Side view of the upper and lower dentition of a contemporary female common chimpanzee (left) and a comparative view of the fossil teeth from the hominid species Ardipithecus kadabba. (Tim White/UC Berkeley, courtesy Science Magazine)
This season, White and his team returned to Ethiopia where they'll continue to dig into the bottom of the rift for more fossil, geological, and paleobotanical samples. Paul Renne, directory of the Berkeley Geochronology Center, and one of his graduate students are on site to aid in dating the various layers of sediment. The group is also focusing attention on a higher spot where in 2003 they uncovered 160,000-year-old fossilized skulls, the oldest known remains of modern humans.
"There's so much knowledge we don't have that we can capture just by being there with the right people, the right tools, and at the right time," White says. "The secrets buried in the Afar keep pulling us all back to the field."
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Mining For Microbes
Every time UC Berkeley professor Jillian Banfield descends into the abandoned Richmond Mine in Iron Mountain, California, she's fascinated by the strange beauty of the pink films floating on pools of green water. Those highly-acidic films are what make Richmond Mine, one of the country's largest Superfund sites, such an environmental nightmare. For nearly a decade, Banfield has studied the communities of microbes in those films, the source of the hazardous acid mine drainage. Someday, her research might even lead to new ways to remediate the ecological damage.
Professor Jill Banfield is also affiliated with the Lawrence Berkeley National Laboratory's Earth Sciences Division.
"I was trained as a geologist and I'm very interested in the environment," says Banfield, a professor of Earth and Planetary Science and of Environmental Science, Policy and Management. "So I looked for an environmental problem that involves interactions between microorganisms and minerals, and I found the mine."
More than a quarter mile into the mountain's darkness, various species of microbes grow from the air, water, and minerals in the extreme environment. They form a self-contained ecosystem, Banfield says, with specific members of the community contributing particular functions.
The microbe community's metabolic processes transform the iron sulfide ore into sulfuric acid. Indeed, the drainage from the mine is the most acidic groundwater ever measured. Indeed, if it weren't for a massive on-site treatment effort by the Environmental Protection Agency, the runoff could eventually make its way into the Sacramento River. Meanwhile, the genetic secrets that control how the microbes form a community and interact with their environment to produce the acid mine drainage have been something of a mystery.
A researcher collects samples of the pink biofilm floating atop hot, green, acidic pools in the Richmond Mine at Iron Mountain, California. (Brett Baker/UC Berkeley)
"In the past we could really only study microorganisms by growing them in the lab and characterizing them in vitro," Banfield says. "The limitation is that we don't know how to cultivate most of them."
Last year, Banfield, graduate student Gene W. Tyson from UC Berkeley's Department of Environmental Science, Policy and Management, and their colleagues borrowed a technique from the Human Genome Project to reconstruct whole genomes directly from samples gathered in the mine. Rather than separate out each kind of microbe and sequence its genes, the scientists — including postdoctoral researchers Eric Allen and Rachna Ram, biologist Philip Hugenholtz, and collaborators from the U.S. Department of Energy's Joint Genome Institute (JGI) — used "shotgun" sequencing to obtain the genomes of the whole community at once.
"We break the DNA into small pieces, clone it, and sequence it," Banfield says. "It's like taking five jigsaw puzzles, mixing them all together in a box, and then reconstructing them. Doing that enabled us to pretty comprehensively sample the genomes of these communities' dominant populations."
Acid mine drainage in Spring Creek downstream from the Richmond Mine, part of the Iron Mountain Mine Superfund Site. (Gene Tyson/UC Berkeley)
The novel approach resulted in two microbial genomes that are almost entirely complete and three that are ninety percent there. The data enabled the researchers to identify many of the genes' functions and determine the role of each microbe in the community. For example, only one organism has the cellular machinery to convert nitrogen gas into biologically-available nitrogen that supplies the entire population. Another spews out the biofilm that the community calls home. The "community genomics" technique, published in the scientific journal Nature, was also lauded by Science magazine as a "Breakthrough of the Year."
With the genomes in hand, Banfield and her collaborators at Oak Ridge National Laboratory are studying the proteins encoded by the genes — a process called proteomics — to help unravel the biological processes at play in the mine. Banfield believes that this may be the first time that proteomics has ever been applied to natural communities.
A deep understanding of the metabolic dependencies and characteristics of the organisms could eventually aid environmental scientists in the development of remediation techniques, she says. For instance, adding certain organic constituents, comparable to increasing the community's food supply, might optimize the microbes' functions and speed up the formation of acid mine drainage.
The blue and yellow fluorescent dots represent two kinds of microbes in a sample from the mine.
"That would reduce the cost of remediation at the site in the long-term and make it more practical to extract the metal from the runoff to offset the cost," Banfield says.
Interestingly, the research is also informing scientists who are seeking life in other extreme environments, including Mars. Banfield is principal investigator on a large NASA grant to study the Mars biosphere. If life has existed on the red planet, or still does, it's feasible that the extraterrestrials might actually be microbes that thrive on the planet's iron and sulfur-rich surface, she says. The key is to know what the signs of life might look like.
"The mine provides us with a microcosm to study, and its simplicity makes it manageable," Banfield says. "This work is opening the door to understanding microbial function in the environment, almost in real time."
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Dealing with Cloudy Data
Looking up, it's easy to spot the clouds. The white fluff is strikingly contrasted by the blue sky. It's not so easy from space, especially above the Earth's poles. The clouds blend in against the vast expanses of snow and ice. This is a problem for scientists who use satellites to study clouds and climate. Recently though, UC Berkeley statistician Bin Yu, her graduate student Tao Shi, and their collaborators have devised a new algorithm that detects clouds even when the poles play tricks on the satellites' electronic eyes.
Professor Bin Yu's research is supported by National Science Foundation grants and by a Miller Research Professorship in 2004.
Understanding clouds is essential for scientists to computationally model Earth's current climate and make projections about the future. Historically, uncertainties about how clouds interact with radiation from the sun and the Earth have added to the difficulty of making accurate forecasts.
"Clouds have a cooling effect by reflecting the sun's radiation, but they also warm the Earth's surface by acting like a blanket," Yu says. "The tradeoff between cloud heating and cooling depends mainly on their thickness and height above the surface. So if you don't know where the clouds are and, as a result, the way they feedback on the global climate, the climate models don't really work."
Today's cloud detection systems that sift through mountains of satellite measurements are notoriously error-prone when it comes to the polar regions. The detection schemes usually rely upon visual or thermal contrast between the clouds and the surfaces below them. But conventional approaches fail if such contrasts are lacking. This commonly happens in the polar regions, where the ground may be as bright and as cold as the cloud above it.
NASA's Earth Observing System (EOS) Terra satellite, launched in 1999, carries a suite of next-generation instruments that aim to revolutionize cloud detection from space. One of these devices is the Multi-Angle Imaging Spectroradiometer (MISR) that views Earth across several bands of the electromagnetic spectrum using cameras pointed at nine different angles. No data like MISR's have ever been collected from space before, opening up possibilities for new cloud detection approaches.
Illustration of both the NASA EOS Terra Satellite and the view directions of the nine MISR cameras. (courtesy the researchers)
For example, the heights of reflecting surfaces can be derived from the multi-angle "stereo" views, and compared with the known elevation of the terrain below. If a surface is measurably higher than the terrain, it's classified as a cloud. When clouds are close to the ground though, as they often are at high latitudes, other approaches must be used.
Yu and Shi, in collaboration with Pennsylvania State University meteorologist Eugene Clothiaux and Amy Braverman, a statistician at NASA's Jet Propulsion Laboratory, developed an improved algorithm that leverages MISR's multi-angle capabilities in a novel way to dramatically improve cloud detection in polar regions.
"Instead of looking for clouds, we decided to look for ice," Yu says. "Since ice doesn't move, the data from MISR's multiple angles should be correlated when they're just viewing ice. The angles are filled with valuable information."
The researchers' new algorithm focuses on the reflective features of the surface. To distinguish icy terrain from clouds, this algorithm relies on correlations between such angular factors as the smoothness of the reflecting surface and its tendency to scatter light in a certain direction.
Using data from MISR, the researchers found their algorithm could classify polar-region clouds in the satellite data about as well as scientists laboriously identifying clouds in the images by hand, even for some of the most complex scenes.
Left: MISR image collected over Greenland on June 20, 2001. This is a difficult scence for cloud detection due to the presence of the fork-shaped frozen river and low thin clouds which are invisible in this image. (courtesy the researchers)
Right: Classification results from new algorithm. (courtesy the researchers)
The new algorithm will be among several to be tested extensively with MISR data in the coming year. When the results are in, MISR's cloud detection system will take advantage of the best qualities of each. Until then, Yu and her colleagues are devising Web software powered by their algorithm to encourage scientists to process images and put the algorithm through its paces along the way.
Meanwhile, Yu and Shi are considering other applications for MISR data. Already, they've launched a joint effort with Peking University and several environmental scientists in the U.S. to study the dynamics of air pollution in China.
"I'm fascinated by the huge amounts of data collected by new instruments that haven't been available before," Yu says. "The scientific fields that gather these data may be very different, but statistics is the common thread that connects them all together."
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Berkeley's Scientific Legacy
Shiing-Shen Chern and the New Geometry
In the esoteric world of pure mathematics, Shiing-Shen Chern was a 20th century champion. The professor emeritus of mathematics died in December at the age of 93, but his achievements as a world-renowned geometer live on through their impact on such high-profile fields as string theory and computer graphics.
Shiing-Shen Chern (China Daily photo)
Chern is known for his innovations in differential geometry, exploring the complexities of geometric figures by mathematically describing their shape. Differential geometry had its first heyday in the 19th century but the field was dormant by the time it caught Chern's eye during the 1930s. Chern's passion and genius reinvigorated the field, transforming it into a dynamic and vibrant area of study.
"By his stubborn trumpeting of the importance of geometry, people in the 1940s and '50s reluctantly acknowledged it — it must be, because Chern said so," Chern's friend and colleague, UC Berkeley mathematics professor Hung-Hsi Wu has said.
Early in his career, Chern devised a mathematical method using algebraic techniques of characterizing various kinds of shapes based on their curvature in more than three dimensions. The results of his work became known as characteristic classes, which everyone in the world (except for Chern) now calls "Chern Classes." Chern is also known for making great advances in algebraic geometry and topology. His advances in both areas have had a massive impact on the foundations of modern mathematics and many areas of theoretical physics.
Born in the Zhejiang Provence just southwest of Shanghai, Chern earned his doctorate from Hamburg University. At the beginning of World War II, Chern fled China, spending several years at the Institute for Advanced Study before moving back to his home country. During the 1940s and '50s, he established the Institute of Mathematics of the Academia Sinica in China as a training ground for a "glorious generation of Chinese mathematicians," Wu said.
IN 1949, Chern again relocated to the United States, eventually joining the UC Berkeley faculty in 1960. In 1979, Chern retired from the University but returned soon after to co-found and direct the Mathematical Sciences Research Institute (MSRI).
MSRI's home on the UC Berkeley campus will be named Chern Hall upon the completion of a new addition in late 2005. An esteemed teacher, Chern was honored by former student Bob Uomini in 1996 when Uomini inaugurated the Shiing-Shen Chern Visiting Professorships with his winnings from the California Lottery.
Chern died December 3 at his home in Tianjin, China, where he has lived since his wife passed away four years ago. He was still doing mathematics as honorary director of the Nankai Institute of Mathematics that he founded in 1984 at Nankai University.
"Anyone who wants to discuss differential geometry in the 20th century will have to mention two or three names, and Chern is one of them," Wu said.