College of Natural Resources, UC Berkeley

News & Events

June 30, 2010

Spring 2010: Chris Johns, Editor-in-Chief, National Geographic Magazine

The April 2010 issue of National Geographic will be devoted to a single topic: fresh water. With striking visuals and in-depth reporting, we will focus on the emerging challenge of global freshwater shortages and the choices ahead as the world manages a limited supply. This coverage continues the magazine's tradition of documenting key environmental issues and educating readers to care about the planet. Chris Johns will provide insight into key freshwater issues facing us today as reported by a team of renowned National Geographic contributors.

Johns's career in photojournalism began while studying animal science at Oregon State University. He graduated with a degree in technical journalism and a minor in agriculture. He worked as a teaching assistant while studying for a master's degree in photojournalism at the University of Minnesota.

In 1975 Johns became a staff photographer at the Topeka (Kansas) Capital-Journal and in 1979 was named National Newspaper Photographer of the Year. In 1980 he joined the Seattle Times as a picture editor and special projects photographer. Three years later Johns became a freelance photographer largely working for Life, Time and National Geographic. National Geographic made him a contract photographer in 1985, and Johns joined the magazine staff in 1995.

In 1990 Johns photographed and wrote the critically acclaimed book Valley of Life: Africa's Great Rift. He followed with a National Geographic Society book, Hawaii's Hidden Treasures, which dealt with Hawaii's extinction crisis.

--As posted at National Geographic

June 25, 2010

Professor Awarded Prestigious Overton Prize in Computational Biology


Professor Steven E. Brenner has been awarded the International Society for Computational Biology (ISCB) Overton Prize. The Overton Prize honors early- to mid-career scientists who have achieved a significant and lasting impact in bioinformatics and/or computational biology.

Brenner has contributed to the understanding of genomes, and to protein and RNA function. His most important contribution to the RNA field was the discovery of the prevalence of RNA surveillance and alternative splicing as a novel mode of gene regulation. He continues to work in this area and has extended his work in RNA regulation as a member of the modENCODE consortium, which aims to identify all the functional sequence elements in the Drosophila and Caenorhabditis elegans genomes.

Outside pure research, Brenner has contributed to the computational biology community at large. He served as an ISCB director from 1998 to 2000 and again from 2002 to 2006. As a dedicated advocate of the open-access and open-source movement, he was one of the founders of the BioPerl open-source software project. Later, he became a director of the Open Bioinformatics Foundation, which aims to put the creation of open-source software libraries such as BioPerl on a secure financial footing. And he is a founding editor of PLoS Computational Biology, the first open-access journal focused on advancing the understanding of living systems through the application of computational methods.
Brenner remembers being interested in computers and biology even as a small boy. But, rather than having a dual major, he chose the flexibility of Biochemical Sciences for his undergraduate studies at Harvard, and followed his advisor's encouragement to take computer science courses as well. As an undergraduate, he was able to work in Walter Gilbert's lab, “maybe the very first genome lab in the world.” Gilbert and his colleagues were sequencing the genome of the bacterium Mycoplasma genitalium. While in Gilbert's lab, Brenner met colleagues who introduced him to the idea of combining both his interests into the study of computational biology.

After graduation, Brenner obtained a fellowship for graduate study at the University of Cambridge, and studied for his PhD in the MRC Laboratory of Molecular Biology under Cyrus Chothia. As one of the original authors of the SCOP: Structural Classification of Proteins database, Brenner presented it at the second ISMB meeting in 1994. While initially having an uncertain reception, SCOP has since been cited over 4,000 times and remains widely used today.

After leaving Cambridge, Brenner obtained a fellowship to the National Institute of Bioscience, Japan, to work on genome analysis, but he was soon back in the US as a postdoctoral research fellow in Michael Levitt's lab at Stanford University. In Levitt's lab, he continued to work on genome and protein sequence analysis and the detection of distant evolutionary relationships between proteins.

In 2000, Brenner moved to the University of California, Berkeley, as an assistant professor, and became a faculty scientist at Lawrence Berkeley National Laboratory that same year. In 2009 he was appointed as an adjunct professor at the University of California, San Francisco, and is promoted to full professorship at UC Berkeley this year. His lab now includes experimental as well as computational biologists.

The Overton Prize is given in memory of G. Christian Overton, a young bioinformatics researcher and ISCB director who died suddenly in 2000.

More on this story is featured on the Public Library of Science (PLoS) website.

June 23, 2010

Wild Neighbors: Local Spider Makes Good

By Joe Eaton

A couple of weeks ago, Ron and I went to the Bone Room to hear UC-Berkeley entomologist Rosemary Gillespie discuss her research on the spiders of the Hawai’ian Islands.


Gillespie and her students get to spend a lot of field time in Polynesia. At least one, a weevil specialist if I recall correctly, decided to stay there.

Gillespie has worked with several groups of Hawai’ian spiders, including the spectacular evolutionary radiation of long-jawed orbweavers. Her marquee species, though, is Theridion grallator, better known as the happy-face spider. It’s a small, furtive, nocturnal creature, found in primary forest on all the major islands except Kaua’i. (The only spiders we encountered during our visit there were exotics, including a sizable huntsman that shared the kitchen of our vacation rental.) In one color morph of the happy-face, the arachnid’s abdomen has two black dots above a curved red smile.

Not all happy-face spiders sport happy faces, though; see Gillespie’s web site for variations. On all the islands where she’s studied them, two-thirds of the happy-faces have plain unmarked yellow abdomens. The others are patterned with spots and blotches of red, black, and white. Each of the 20 or more morphs is genetically determined, although the mechanism in Maui spiders is different from that in Big Island spiders. One of her graduate students is teasing out the details.

Although Maui and Big Island individuals can interbreed, there’s normally no movement between islands. The whole array of color morphs has evolved independently on Oahu, Maui, and the Big Island. For a lucid explanation, with diagrams, go to UC’s Understanding Evolution site

What’s the point of all this polymorphism? Gillespie and Geoff Oxford of the University of York hypothesize that it has to do with predator avoidance. These spiders co-evolved with birds that feed on small arthropods, like the famous Hawai’ian honeycreepers and the ‘elepaio flycatcher. Happy-face spiders hide under leaves; against that background, the all-yellow forms are the most cryptic.

But rather than rely on that, the spider has hedged its bets—diversified its portfolio of colors and patterns. The variation keeps avian predators from developing a consistent search image; as shown in experiments with blue jays, visual multitasking makes for less efficient foraging. So more spiders go uneaten, and the genetic variety is preserved.

Yes, there is a California connection here. During her Bone Room talk, Gillespie said that a similar case of defensive polymorphism had been documented close to home—in Tilden Park, among other places. This involves another spider called Theridion californicum (no common name.) First described from Mill Valley in 1904, T. californicum occurs in coastal habitats from British Columbia to southern California. Like grallator, it lives under leaves, frequently those of poison oak.

Continue reading "Wild Neighbors: Local Spider Makes Good " »

June 15, 2010

Trees shift upward as climate warms

By: David Perlman

The world's warming climate is forcing trees and the plant life around them into new territories where the environment is more like the areas where they normally thrive, scientists report from a new global survey.

Some forests and groups of vegetation have begun moving upward to higher elevations, or northward to higher latitudes to meet the climate change, while others in areas that are drying are shifting southward toward greater sources of moisture, the researchers say.

In California, for example, a detailed forest census along the west side of the Sierra in the Tahoe National Forest by UC Berkeley scientists found that the warming climate is shifting growth patterns uphill among many species of shrubs, oaks, firs and pines that for hundreds of years have been thriving at lower elevations.

Similar forest changes are being found on every continent by biologists working around the world, according to a report published this week in the journal Global Ecology and Biogeography.

The global report was compiled by Patrick Gonzalez, a visiting scholar at Berkeley's Center for Forestry in the College of Natural Resources, together with U.S. Forest Service researchers at Corvallis, Ore.

Gonzalez is also leading a research group that has surveyed hundreds of trees and shrubs along a 12-mile transect of the Tahoe National Forest, ranging from the foothills at 2,300 feet to the High Sierra at 6,900 feet.

The researchers measured more than 1,000 trees and took 197 corings of the larger oaks, pines and firs to determine their ages. They found that in the past century, the oaks and Douglas firs that were normally found at lower elevations are beginning to be seen "upslope" in areas dominated by white firs and sugar pines, Gonzales said.

"Those species, in turn, may be moving into the higher elevations, where red fir thrives in the deep winter snow," he said in an interview.

Gonzalez said climate data for the Sierra transect have been clear because records taken at a National Weather Service station that has been operating in nearby Downieville since 1948 show that average annual temperatures there have been increasing at seven times the global rate. There has been no heavy logging, burning or grazing in the transect area, so climate change could be the primary cause of the changes in vegetation, Gonzalez concluded.

In their survey of observed changes in vegetation reported by other scientists around the world, Gonzalez and his colleagues noted that trees and shrubs in northern Africa's Sahel region have been dying where drought has increased as the climate warms, and have moved further south where rainfall is more abundant.

Similar changes have been taking place in the high Arctic, he said, where warming has brought new shrubs encroaching on the tundra, where caribou and other wildlife could be threatened.

The report on Sierra tree seedlings moving to higher elevations because of a warming climate reflects earlier evidence that many mountain-dwelling animals are also moving their ranges upward to cooler areas.

James Patton and Craig Moritz of UC Berkeley's Museum of Vertebrate Zoology surveyed 28 species of mammals living at sites from the San Joaquin Valley across Yosemite to Mono Lake and found that as average annual temperatures warmed by 5 degrees Fahrenheit during the past 90 years, more than half the species had shifted their ranges upward by as much as 1,600 feet. The two biologists published their survey in the journal Science on Oct. 10, 2008.

June 9, 2010

Desperate Female Spiders Fight By Different Rules


If you thought women's pro wrestling was a cutthroat business, jumping spiders may have them beat.

In most animals the bigger, better fighter usually wins. But a new study of the jumping spider Phidippus clarus suggests that size and skill aren't everything – what matters for Phidippus females is how badly they want to win.

Found in fields throughout North America, nickel-sized Phidippus clarus is a feisty spider prone to picking fights. In battles between males, the bigger, heavier spider usually wins. Males perform an elaborate dance before doing battle to size up the competition. "They push each other back and forth like sumo wrestlers," said lead author Damian Elias of the University of California at Berkeley.

This fancy footwork allows males to gauge how closely matched they are before escalating into a full-blown fight. "Males rarely get to the point where they solve things by fighting," said co-author Carlos Botero of the National Evolutionary Synthesis Center in Durham, NC. "Before the actual fight there's a lot of displaying. This allows them to resolve things without injuring themselves."

But when the researchers watched female fights, they found that females fight by different rules. They skip the preliminaries and go straight for the kill. "Males have a more gentlemanly form of combat, whereas in females it's an all-out fight," said Elias. "At the drop of a hat they start bashing and biting each other."

And unlike male combat, female feuds were often fatal. "They don't give up, even when their opponent is beating them to a pulp," said Botero. "They keep going until one of them is dead, or severely injured."

The researchers were unable to predict which female would win based on size or strength. "Nothing we could measure predicted which one would come out on top. That was really unexpected," said Elias.

At first, the researchers wondered if victory went not to the bigger fighter, but to the owner of the battlefield. "In a lot of animals one of the things that determines whether they win a fight is whether they're on their own territory," Elias said.

Continue reading "Desperate Female Spiders Fight By Different Rules" »

June 7, 2010

Viewpoints: We can harness green energy by managing California forests

By: William Stewart

Forest management can lead to cleaner air, safer communities and lower firefighting costs, yet its greatest value may lie in addressing climate change and what it keeps hidden underground.

Managing forests helps reduce greenhouse gas emissions. It lowers the threat and severity of wildfire, a significant source of avoidable emissions. It also keeps fossil fuels underground.

When forests are thinned, the harvested biomass or branches, brush and small trees can be chipped and used to produce energy. Biomass energy takes carbon that is above ground – wood chips – and keeps it above ground by burning it in power plants to produce electricity. Biomass energy is carbon neutral because no more carbon is released producing energy than would be if the vegetation were to simply decay.

Research has shown that active forest management can provide significantly greater carbon benefits than management strategies that set forests aside in reserves. While young reserved and managed forests sequester, or remove from the atmosphere and store, roughly the same amount of carbon in standing trees, actively managed forests can provide the additional benefit of offsetting fossil-fuel use by producing low-carbon energy from forest and sawmill residues.

Managing forests to reduce fuel loads provides immediate dividends. Fewer fuels means less-intense wildfire, greater firefighter safety, lesser environmental consequence and fewer greenhouse gas emissions. There's great carbon benefit right there – emissions avoided and standing carbon protected – by capturing the thinnings that might otherwise have gone up in smoke and using them to generate energy can be an added plus.

Continue reading "Viewpoints: We can harness green energy by managing California forests" »

Climate change leading to major vegetation shifts around the world

By Sarah Yang, Media Relations

BERKELEY — Vegetation around the world is on the move, and climate change is the culprit, according to a new analysis of global vegetation shifts led by a University of California, Berkeley, ecologist in collaboration with researchers from the U.S. Department of Agriculture Forest Service.

In a paper published today in the journal Global Ecology and Biogeography, researchers present evidence that over the past century, vegetation has been gradually moving toward the poles and up mountain slopes, where temperatures are cooler, as well as toward the equator, where rainfall is greater.

Moreover, an estimated one-tenth to one-half of the land mass on Earth will be highly vulnerable to climate-related vegetation shifts by the end of this century, depending upon how effectively humans are able to curb greenhouse gas emissions, according to the study.

The results came from a meta-analysis of hundreds of field studies and a spatial analysis of observed 20th century climate and projected 21st century vegetation.

The meta-analysis identified field studies that examined long-term vegetation shifts in which climate, rather than impacts from local human activity such as deforestation, was the dominant influence. The researchers found 15 cases of biome shifts since the 18th century that are attributable to changes in temperature and precipitation.

"This is the first global view of observed biome shifts due to climate change," said the study's lead author Patrick Gonzalez, a visiting scholar at the Center for Forestry at UC Berkeley's College of Natural Resources. "It's not just a case of one or two plant species moving to another area. To change the biome of an ecosystem, a whole suite of plants must change."

The researchers calculated that from 1901 to 2002, mean temperatures significantly increased on 76 percent of global land, with the greatest warming in boreal, or subarctic, regions. The most substantial biome shifts occurred where temperature or precipitation changed by one-half to two standard deviations from 20th century mean values.
Some examples of biome shifts that occurred include woodlands giving way to grasslands in the African Sahel, and shrublands encroaching onto tundra in the Arctic.

"The dieback of trees and shrubs in the Sahel leaves less wood for houses and cooking, while the contraction of Arctic tundra reduces habitat for caribou and other wildlife," said Gonzalez, who has served as a lead author on reports of the Intergovernmental Panel on Climate Change (IPCC). "Globally, vegetation shifts are disrupting ecosystems, reducing habitat for endangered species, and altering the forests that supply water and other services to many people."

Continue reading "Climate change leading to major vegetation shifts around the world" »

U.S. Climate Satellite Capabilities in Jeopardy

By Alexis Madriga


The United States is in danger of losing its ability to monitor key climate variables from satellites, according to a new Government Accountability Office report.

The country’s Earth-observing satellite program has been underfunded for a decade, and the impact of the lack of funds is finally hitting home. The GAO report found that capabilities originally slated for two new Earth-monitoring programs, NPOESS and GOES-R, run by the National Oceanic and Atmospheric Administration and the Department of Defense have been cut and adequate plans to replace them do not exist.

Meanwhile, up until six months ago, NASA had 15 functional Earth-sensing satellites. Two of them went down in the past year, and of the remaining 13, 12 are past their design lifetimes. Only seven may be functional by 2016, said Waleed Abdalati, a longtime NASA satellite scientist now teaching at the Cooperative Institute for Research in Environmental Studies at the University of Colorado Boulder.

Taken together, American scientists will soon find themselves without the ability to monitor changes to key Earth systems at a time when such measurements could help determine the paths of the world’s energy and transportation systems.

“Can you imagine if we’ve passed the apex of our Earth-observing capability right at a time when we realize that, ‘Hey, we need to understand what’s going on’?” said Abdalati. “We’re talking about less than half the capability in the coming five years than we’ve had in the previous five years.”

While President Obama’s 2011 budget has gone partway to restoring money for Earth observations, a decade of neglect has left the nation’s agencies — the National Oceanic and Atmospheric Administration, NASA and the US Geological Survey — without the resources they need to do the job.

Despite this, the agencies put together a consortium to come up with a coordinated strategy for Earth observations, the United States Group on Earth Observations. The group readied a report on the state of the nation’s Earth-observation capabilities, but it’s been stuck in review for the past year.

The GAO’s very first recommendation is that this report be released to the public.

“We’ve been told that it proposes continuing observations in 15 to 20 areas. We’ve been told that it doesn’t involve costs and schedules,” said GAO auditor David Powner, lead author of the GAO report. “We think that what’s really important is that we need to get these initial findings and reports. Everyone is telling us that there are good things to build off of in there.”

Continue reading "U.S. Climate Satellite Capabilities in Jeopardy" »

June 3, 2010

Exploring the Sierra with Naturalist John Muir Laws

* Date: 6/29/2010
* Event Location: Berkeley REI
* Event Fee: Free

* Time: 7:00 p.m. - 8:30 p.m. (PDT)
* Presenter: John (Jack) Muir Laws
* Group Size: 75


Award-winning naturalist, environmental educator, and author/illustrator of The Laws Field Guide to the Sierra Nevada, John (Jack) Muir Laws has spent countless days backpacking the Sierra, observing the fascinating behavior, adaptations, and interactions between species.

Join Jack for an illustrated lecture on the remarkable relationships between plants and animals you're likely to encounter on a hike in the Sierra. Whether you're a botanist, birder, or backpacker, come discover the subtle and essential threads, which connect species. Find out about stewardship efforts underway to address species conservation challenges.

Following his talk, Jack will sign copies of his field guide, which was produced in collaboration with the California Academy of Sciences and contains 2,710 original watercolor paintings of more than 1,700 Sierra species. Please note: Registration is optional for our free in-store presentations. If you register, you will receive an email reminder and any program updates. Seating is limited and is first-come, first-served. Additional Dates: 6/30 (Corte Madera)

Click here to register for the event

To find out more about John Muir Laws, visit his website

Berkeley Butterfly Walk

by Steven Finacom
About a dozen people joined eminent UC entomologist Jerry Powell on Saturday, May 29, 2010 for a leisurely butterfly-watching walk along trails at the top of Berkeley’s Panoramic Hill.

Views from the higher southeast elevations of Panoramic Hill were stupendous. The Bay spread out, visible from Santa Clara County to San Pablo Bay, sunny skies prevailed, and light breezes made for a pleasant ramble through meadows along the crest, then back along one of the fire trails on the shady north-facing slope of Strawberry Canyon.
A coyote, hawks and songbirds completed the wildlife cameos along the walk.The late rains meant that much of the seasonal landscape is still green.

More than a dozen butterfly species were spotted and identified by Powell and others on the walk.They included the California Ringlet, Lorquin’s Admiral, Umber Skipper, Sara Orangetip, Field Crescent, Mournful Duskywing, Red Admiral, Chalcedon Checkerspot, Anise Swallowtail, Pipevine Swallowtail, Pale Swallowtail, and Western Tiger Swallowtail.

Powell said that there were fewer species than he expected of this time of year, possibly due to the cooler weather earlier this spring.

Powell is a Professor in the Graduate School at UC Berkeley and Director Emeritus of the Essing Museum of Entomology, where he started working in 1961.His primary research interest is certain types of small moths.
When the group finally spotted a Sara Orangetip—a white butterfly with vivid orange patches on the wing ends—fluttering along the trail in Strawberry Canyon, I thought of Berkeley native David Brower hiking these same hills as a boy in the 1920s, and looking for butterflies, including the Orangetip.

At that time the Berkeley hills were undeveloped in their upper reaches, but also largely unprotected.Residential development would eventually sweep to the summit, north of the UC campus and south of Claremont Canyon.In the 1970s a sustained, and ultimately successful, struggle began to protect most of Claremont Canyon from residential development.

Hundreds of residential lots had already been subdivided for development, but almost all were eventually bought and incorporated into the East Bay Regional Park District.
The walk was sponsored by the Claremont Canyon Conservancy, a non-profit that grew out of that land use struggle and now works to protect and restore the natural environment of the canyon behind the Claremont Hotel.

This Saturday, June 4, the Conservancy is sponsoring another free walk, a “geology ramble” led by Martin Holden, from 10 am to noon.Meet at the Stonewall Road trailhead to the Claremont Canyon Regional Preserve.A vigorous climb is involved.

For more details see the Conservancy website

See Professor Powell’s website, and if you want to know more about butterflies, visit the North American Butterfly Association (NABA) website


CNR Calendar

Monthly Archives

Recent Posts

Spring 2010: Chris Johns, Editor-in-Chief, National Geographic Magazine
Professor Awarded Prestigious Overton Prize in Computational Biology
Wild Neighbors: Local Spider Makes Good
Trees shift upward as climate warms
Desperate Female Spiders Fight By Different Rules
Viewpoints: We can harness green energy by managing California forests
Climate change leading to major vegetation shifts around the world
U.S. Climate Satellite Capabilities in Jeopardy
Exploring the Sierra with Naturalist John Muir Laws
Berkeley Butterfly Walk


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