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Friday, 20 June 2008
1. Scientists with UC Berkeley ties win prestigious award
Contra Costa Times (*requires registration)
June 202008
The Bay Area can add the Kyoto Prize to a long list of prestigious awards garnered recently by local scientists.
TWO SCIENTISTS WITH TIES TO UC BERKELEY are among the recipients of the award, considered the Japanese equivalent of the Nobel Prize, one for his work in molecular biology and the other for his work in information science.
At 11:30 Thursday night, UC BERKELEY ELECTRICAL ENGINEER AND COMPUTER SCIENTIST RICHARD KARP and FORMER UC BERKELEY POSTDOCTORAL RESEARCHER ANTHONY PAWSON were to receive calls that they had won the prize, which includes a gold medal and 50 million yen, about $460,000 each.
Karp, 73, was recognized for lifetime achievement in the advanced technology category for work he has done since the 1970s in the theory of algorithms. The work has streamlined problem-solving algorithms and has influenced a wide range of scientific disciplines....
Pawson, 55, received the award in the basic sciences category for research in microbiology, some of which he began at Cal.
His work has advanced the understanding of communication between cells and is important in many biomedical fields, notably cancer research....
The prize is awarded by the Inamori Foundation, established by Japanese businessman Kazuo Inamori, who also founded Kyocera Corporation. He funds the awards with his own money.
"It is my hope that the Kyoto Prize will encourage balanced development of both our scientific progress and spiritual depth," Inamori said in a news release....
[Stories on this topic appeared in more than 100 sources worldwide, including the International Herald Tribune, New York Times Online, Washington Post, San Jose Mercury News, Contra Costa Times, Los Angeles Times, San Francisco Chronicle and Chronicle of Higher Education--link by subscription only] Full Story
2. Gene increase in evolution
Scientist Live
June 19, 2008
The newly sequenced genome of a dainty, quill-like sea creature called a lancelet provides the best evidence yet that vertebrates evolved over the past 550 million years through a four-fold duplication of the genes of more primitive ancestors.
The late geneticist Susumu Ohno argued in 1970 that gene duplication was the most important force in the evolution of higher organisms, and Ohno's theory was the basis for original estimates that the human genome must contain up to 100,000 distinct genes.
Instead, the Human Genome Project found that humans today have only 20,000 to 25,000 genes, which means that, if our ancestors' primitive genome doubled and redoubled, most of the duplicate copies of genes must have been lost. An analysis of the lancelet, or amphioxus, genome, being published in the June 19 issue of Nature, shows this to be the case.
"Amphioxus and humans had a common ancestor 550 million years ago, which allows us to use amphioxus as a surrogate for that ancestor in terms of understanding how vertebrate genomes evolved," said DANIEL S. ROKHSAR, A FACULTY MEMBER IN THE UNIVERSITY OF CALIFORNIA, BERKELEY'S CENTER FOR INTEGRATIVE GENOMICS and program head for computational genomics at the Department of Energy Joint Genome Institute (JGI) in Walnut Creek, Calif. Rokhsar and JGI post-doctoral fellow Nicholas H. Putnam performed the sequencing, assembly and genome-wide analyses of the amphioxus genome and are lead authors of the Nature paper....
[Stories on this topic appeared in more than a dozen sources around the world] Full Story
3. The Future of Energy: Grow your own
The biofuels of the future will be tailor-made
The Economist
June 21, 2008
Buried in the news a few weeks ago was an announcement by a small Californian firm called Amyris. It was, perhaps, a parable for the future of biotechnology. Amyris is famous in the world of tropical medicine for applying the latest biotechnological tools to the manufacture of artemisinin, an antimalarial drug that is normally extracted from a Chinese vine....
But that is not what the announcement was about. Instead, it was that Amyris was going into partnership with Crystalsev, a Brazilian firm, to make car fuel out of cane sugar.
...Where Amyris is leading, many are following. Some small firms with new and interesting technologies are trying to go it alone. Others are teaming up with big energy firms, in much the same way that biotech companies with a promising drug are often taken under the wing of a large pharmaceutical company....
Which of these approaches will work best is anybody’s guess. But their sheer number is proof that the most radical thinking in the field of renewable energy is going on in biofuels. It is in this area that the most unexpected breakthroughs are likely to come, says Steven Koonin, BP’s chief scientist. BP is backing one of the biggest academic projects intended to look into biofuels, the ENERGY BIOSCIENCES INSTITUTE (EBI), to the tune of $500m, which suggests that the company’s board agrees with him. The EBI is a partnership of the UNIVERSITY OF CALIFORNIA, BERKELEY, the Lawrence Berkeley National Laboratory and the University of Illinois.
One of the people involved, STEVEN CHU, the head of the Lawrence Berkeley laboratory [and UC BERKELEY PHYSICS PROFESSOR] , is a man with a grand vision. This vision is of a “glucose economy” that will replace the existing oil economy. Glucose, the most common monomer sugar, would be turned into fuels and maybe even the bio-equivalents of petrochemicals—bioplastics, for example—in local factories and then shipped around the world. That would be a boon to tropical countries, where photosynthesis is at its most rampant, though it might not play so well to James Woolsey’s security fears, since it risks replacing one set of unreliable suppliers with another.... Full Story
4. Researchers prepare to launch a submarine
CNet
June 20, 2008
If you reel in a small sub instead of a rainbow trout from the Sacramento River this summer, don't call Homeland Security.
It belongs to a TEAM OF RESEARCHERS FROM THE UNIVERSITY OF CALIFORNIA AT BERKELEY trying to learn more about the river currents in the delta.
The researchers are working with propelled 4-foot-long submarines and floating drifters equipped with GPS-receivers for positioning, GSM-modules for communication, and sensors inside for recording temperature, salinity, and currents.
"We are prototyping an infrastructure and testing it in the delta," said PROFESSOR ALEXANDER BAYEN, WHO LEADS THE TEAM AT UC BERKELEY'S CIVIL SYSTEMS DEPARTMENT.
The purpose of all this is to collect data to help the state better understand the river. And researchers have good reason to believe there's urgency to their work. With drought looming for most of California, understanding the state's water supply (much of the state's population drinks run-off from snow melting in the Sierra Nevada range) and how the system works is critical....
If the research project is successful, the innovations can be put to use in other parts of the world where there is a need for improved river management. The Berkeley team is already cooperating with Professor Linda Bushnell of the University of Washington on a project in the Mekong--the troubled river that floats through China, Laos, and Cambodia out in its delta in Vietnam. Full Story
5. UC gym's fate could rest on support beam
San Francisco Chronicle
June 20, 2008
The fate of UC BERKELEY's proposed athletic training center appears to hinge on a concrete beam intended to keep Memorial Stadium's west wall from collapsing, attorneys from both sides of the issue said Thursday.
In her preliminary ruling released Wednesday, Alameda County Superior Court Judge Barbara Miller said the university's plans for the $140 million training center adjacent to the stadium do not violate state earthquake laws because it would not sit on an active fault.
But she said the planned support beam on the stadium's foundation, which is needed to shore up that part of the aging stadium during construction of the training center, may be illegal. That's because its cost could be more than half the value of the stadium, which she said has not yet been determined....
The beam would cost between $600,000 and $700,000, but no one is sure what Memorial Stadium is worth. The university says it's so beloved by Cal fans that it is essentially priceless but would cost $593 million to replace, while plaintiffs say its dilapidated condition and position on the fault render it worthless....
[Another story related to this topic appeared in the Los Angeles Times] Full Story
6. Cal's Tedford cautiously optimistic after ruling
Contra Costa Times (*requires registration)
June 19, 2008
Berkeley — CAL FOOTBALL COACH JEFF TEDFORD is taking a cautious approach after Wednesday's ruling regarding the university's proposed Student-Athlete High-Performance Center and renovation to Memorial Stadium.
"I know a lot of specifics still need to be worked through," Tedford said. "I'm kind of in a holding mode to see what it all means. I know there are people working on it so we'll just have to wait and see."...
Tedford has said his program, along with others at the school, are in desperate need of upgraded facilities to compete on the Pac-10 and national level....
Although Tedford wasn't as quick as ATHLETIC DIRECTOR SANDY BARBOUR or VICE CHANCELLOR OF ADMINISTRATION NATHAN BROSTROM to claim victory, he said a conversation with Barbour was encouraging....
The proposed center, which is slated to be built next to Memorial Stadium, will feature training facilities, offices, conference rooms and locker rooms for 13 sports. About 450 staffers and athletes who work every day in the stadium would move to the new facility....
[This story also appeared in the Oakland Tribune] Full Story
7. Letters to the Editor
San Francisco Chronicle
June 20, 2008
...Go-ahead for UC
Editor -I am pleased, despite initial inaccurate media reports, in reading further about the ruling from Alameda County Superior Court that once several technical issues are resolved, UC BERKELEY may proceed in constructing its new STUDENT ATHLETE HIGH PERFORMANCE CENTER.
This ruling shows that a well-engineered, properly vetted project, which substantially complies with all applicable codes and laws, can be built regardless of reactionary politics.
I am impressed with the accuracy of the engineering and technical concepts noted in the ruling and am looking forward to a day where students and administrators are able to occupy the stunning new facilities.
Peter Symonds, Pleasant Hill Full Story
8. Leah Garchik: Good deeds all over the place
San Francisco Chronicle
June 20, 2008
...In the midst of the Oak Grove brouhaha, a Craigslist ad: "Mature Oak Firewood for Sale by the Cord. ... from 6- to 18-inch trunks, to be felled in the next week or so and available for pick-up or delivery ... Can cut to 12-, 18- or 22-inch lengths. Call Dan at (510) ..." The number provided is that of DAN MOGULOF, EXECUTIVE DIRECTOR OF THE UC BERKELEY PUBLIC AFFAIRS and in recent times, spokesman for the university about this controversy "probably because of sins I committed in the last life," he says....
[Stories related to the athletic center appeared in dozens of sources nationwide, including the San Francisco Chronicle, San Jose Mercury News, Oakland Tribune, KGO TV (link to video), San Francisco Chronicle, San Francisco Chronicle, San Jose Mercury News, and KGO TV (link to video). A correction to a previous story appeared in the New York Times] Full Story
9. Research Methods ‘Beyond Google’
Inside Higher Ed
June 20, 2008
When “Google” has become a synonym for “research,” how should faculty respond?...
Kathy Lee Berggren, a professor at Cornell University, teaches oral communication with a “heavy research component.” Still, she pointed out, “a lot of my students really [only] scratch the surface with the type of research they’re doing.”
“Research isn’t a Google search,” she said.
That sentiment was echoed by several others involved with the Cornell Undergraduate Information Competency Initiative, a program that kicked off on Monday....
The germ of the Cornell initiative started with a visit to the UNIVERSITY OF CALIFORNIA AT BERKELEY last spring, where faculty and librarians learned about the Mellon Library/Faculty Fellowship for Undergraduate Research, which for several years has tested a similar model but on the scale of an even larger research campus, and with funding from the Andrew W. Mellon Foundation.
During Berkeley’s accreditation renewal process several years ago, said ELIZABETH DUPUIS, THE PROJECT’S DIRECTOR, one of the campuswide goals was to define “what it means to be at a research institution.” Of course, she said, one of the fundamental aspects of that experience was research itself, but not just in lab courses or classes on research methods....
Berkeley’s Mellon-funded program, renewed after its initial grant for several years, is now in a hiatus phase in which the university is working with external evaluation consultants to conduct focus groups and interviews with participants. Last fall, a modified version of the program was established that focuses on full departments rather than on individual faculty members.... Full Story
10. Insidious Depictions of Barack Obama as a Monkey Draw More Attention – and Anger
Black America Web
June 20, 2008
You saw it coming: The suggestions of not enough brain power, the rumors about the “angry” spouse, the cartoons, the T-shirts....
Then there is the SockObama monkey sock puppet. Its creators said they didn’t mean to offend anyone -- and they question why people are upset by Obama’s portrayal as a monkey, but not when President George W. Bush is portrayed as a chimpanzee....
“A core American issue has been 'Are black people the same as everybody else?'” said diversity expert DAVID CAMPT, A VISITING SCHOLAR AT UNIVERSITY OF CALIFORNIA, BERKELEY, who teaches a course in American cultures. “We’re still dealing with the three-fifths clause (of the Constitution making male slaves equal to three-fifths of a man) and is the major issue we have been struggling with in our minds with the law and everything else.”
Campt, who also serves as a CONSULTANT TO THE UNIVERSITY’S VICE CHANCELLOR FOR EQUITY AND INCLUSION, said there has been progress when one considers that society in general tends to check its impulse to use loaded language, noting that comedian Michael Richards and radio show host Don Imus suffered consequences professionally when they made racist remarks in public.
The problem, however with trying to dismiss the strong reaction to black men portrayed as monkeys, especially with something like the Obama sock puppet, is what Campt called Mark Twain’s “too soon” theory.... Full Story
11. Book examines American policies post 9/11
Tom Engelhardt’s The World According to TomDispatch shed’s light on ‘new age of empire’ during rule of Bush administration.
Middle East Online
June 20, 2008
London – A comprehensive volume of essays that offers readers a chance to sample some of the finest political analysis of our age, focused on the wars in Afghanistan and Iraq has just been released.
Introduced and edited by TomDispatch's creator TOM ENGELHARDT, The World According to TomDispatch: America in the New Age of Empire is an essential primer for anyone seeking guidance along the highways and byways of our post 9/11 world....
It sheds light on subjects such as the US offshore Bermuda Triangle of injustice from Guantamano to the CIA "black sites," not to speak of extraordinary rendition, the response to Hurricane Katrina, global warming, Iraq's black gold and the energy crisis, and, above all, the Bush administration's misbegotten "smash of civilizations."...
Tom Engelhardt created and runs the website TomDispatch, a project of The Nation Institute where he is a Fellow. He is the author of a highly praised history of American triumphalism in the Cold War, The End of Victory Culture. Each spring he is a TEACHING FELLOW AT THE GRADUATE SCHOOL OF JOURNALISM AT THE UNIVERSITY OF CALIFORNIA, BERKELEY. He lives in New York City.... Full Story
12. Pioneer in field of molecular biology dies at 84
Washington Post
June 20, 2008
Berkeley, Calif. -- GUNTHER STENT, who helped pioneer the field of molecular biology as one of the first scientists to confirm the structure of DNA, has died. He was 84.
Stent died June 12 of pneumonia at his home in Haverford, Pa., according to the University OF CALIFORNIA, BERKELEY, where he served on the faculty for nearly 40 years.
The push to unlock the mysteries of human genetics in the years after World War II was led by the "phage group," a small collection of scientists that included Stent, James Watson and Francis Crick.
Watson and Crick discovered the double-helix structure of DNA in 1953. As a BIOCHEMIST AT UC BERKELEY, Stent performed experiments with bacterial viruses that confirmed Watson and Crick's results a year later.
"Gunther was part of the intellectual glue that kept this small band of pioneers together," said MICHAEL BOTCHAN, CO-CHAIRMAN OF UC BERKELEY'S DEPARTMENT OF MOLECULAR AND CELL BIOLOGY, which Stent helped found in 1987.
Stent also led the formation of the campus' department of virology in 1957 and the department of molecular biology in 1964....
[This and other obituaries of Professor Stent appeared in more than 100 stories around the world, including the International Herald Tribune, San Francisco Chronicle, Contra Costa Times, and San Jose Mercury News] Full Story
13. Playing for Keeps
Mental gymnastics: Lots of action, little money for three locals
San Francisco Chronicle
June 20, 2008
The Bay Area is packed with brainiacs; there are the obvious ones - Steve Jobs, Jerry Yang, the Google guys. But what about the lesser-known, yet enormously talented ones?
Daniel Naroditsky ranks first in the world in chess for boys ages 12 and under. Chester Santos holds the USA Memory Championship title....
How did these people develop their obsessions? What does it take to dominate a game?...
Imagine this: Adam Sandler is holding puffy, white pillows and saying, "What's up dude? Look at these pillows. They're crazy."
Razor blades start jutting out of the pillows and begin to slice off his arm. He shrieks, "This is crazy!"
This scenario could be straight out of a cheesy horror movie, but when CHESTER SANTOS conjures it up, he recalls the following playing cards: 10 of hearts, queen of spades and seven of diamonds. The technique of linking cards to people, objects and actions enables Santos to memorize the order of a card deck in 2 minutes and 27 seconds, helping him win this year's USA Memory Championship....
Santos, who grew up in Hanford, a working-class suburb 40 miles south of Fresno, was at the top of his high school class until his junior year, when his mother and stepfather divorced. Santos' grades plummeted, especially after discovering his stepfather wasn't his biological dad. He ended up going to Fresno City College before transferring to UC BERKELEY to study psychology. He rarely did homework or went to class....
After earning a 3.7 GPA at Cal (he lost points for attendance), Santos spent a year in law school....
Santos competes in memory mainly for the money....
In fact, Santos recently quit his $83,000-a-year computer engineering job at Wells Fargo in order to pursue memory consulting full time. He hopes to write a book, become the second American grandmaster memorizer and train for the World Memory Championships in Bahrain in October. He also wants to the most-well-known American memorizer.... Full Story
14. BART mug suggestion may whet commuter support
San Francisco Chronicle
June 20, 2008
Intent on overturning BART's ban on drinking in stations and on trains, BART board Director Lynette Sweet put on a demonstration Thursday to show off a travel coffee mug outfitted with a "dead man's trigger" engineered to keep the beverage from spilling even if the person holding it keels over and dies....
The agency recently teamed up with Metropolitan Coffee & Concession to place full-service Peet's Coffee & Tea, Inc. cafes in eight BART stations, and as part of the deal, the transit agency shares in the profits; the first cafe opened May 1 at the Embarcadero Station. Here's how Mark Lukin, president of Metropolitan Coffee & Concession, envisions money could be made if the (hopefully) spill-proof mugs were allowed:
His company would pay BART a licensing fee for the right to sell the mugs and then sell advertising on them....
His company is working with an INDUSTRIAL ENGINEER AT UC BERKELEY to design a cup with a screw-on lid - the lid on Sweet's model was attached to the cup by compression - that could withstand a tumble and not spill... Full Story