March 7, 2003 Search the Currents Archive

Comparing Genes with Our Fellow Primates

Drake’s Plate: The Final Chapter?

An Enlightening Sabbatical at Chabot
Washington Report
Alexis Bell Awarded Burwell Lectureship
Eugene Myers Elected to National Academy of Engineering
LDRD Call for Proposals for FY 2004
In Memoriam: Iran Thomas
Berkeley Lab Currents
ProteinShop: A New Approach to the Protein Folding Problem
Workshop Points to Big Future for Nanoscience Research
A Better Way to Build a Detector?
Science Glossary
TEID Publications Win Awards
Blackberry Canyon Stairs Get a Facelift
Bancroft Bus Route to Include New Campus Stop
Foreign Travel Resources
Employee Referral Program
Paul Alivisatos to Give “Friends of Science” Presentation: Nanocrystals and Solar Cells
Bulletin Board
Flea Market

Comparing Genes with Our Fellow Primates

By Lynn Yarris

Berkeley Lab scientists have developed a powerful new technique for deciphering biological information encoded in the human genome. Called “phylogenetic shadowing,” this technique enables meaningful comparisons between DNA sequences in the human genome and sequences in the genomes of apes, monkeys, and other nonhuman primates. With phylogenetic shadowing, scientists can now study biological traits that are unique to members of the primate family.

“The ability to compare DNA sequences in the human genome to sequences in non-human primates will enable us in some ways to better understand ourselves than the study of evolutionarily far-distant relatives such as the mouse,” says Eddy Rubin, M.D., director of DOE’s Joint Genome Institute (JGI) and Berkeley Lab’s Genomics Division. “This is important because as valuable as models like the mouse have been, there are many physical and biochemical attributes of humans that only other primates share.”

Rubin led the development of the phylogenetic shadowing technique. He and his colleagues used it to identify the DNA sequences that regulate the expression of a gene that is an important indicator of the risk for heart disease and is found only in primates. The results of this research were reported in a paper published in the Feb. 28 issue of Science. Coauthoring the paper with Rubin were Dario Boffelli, Dmitriy Ovcharenko, Keith Lewis, and Ivan Ovcharenko of Berkeley Lab, plus Jon McAuliffe and Lior Pachter of UC Berkeley.

Comparative genomics compares DNA segments in the human genome to DNA segments in the genomes of other organisms, such as the mouse or the puffer fish. It has proven to be an effective means of identifying genes, the DNA sequences that code for proteins, and gene regulatory sequences, the DNA sequences that control when a gene is turned on or off.

“The rationale for comparing the genomes of different animals to identify those sequences that are important is based on the understanding that today’s different animals arose from common ancestors tens of millions of years ago,” Rubin explains. “If segments of the genomes of two different organisms have been conserved (meaning the sequences are the same in both) over the millions of years since those organisms diverged, then the DNA sequences within those segments probably encode important biological functions.”

In order for comparative genomics to work, the conserved functional sequences have to stand out as distinct from the nonfunctional sequences which were not conserved. This requires the passage of time — lots of it — in order for the nonfunctional sequences in the two genomes to drift apart.

For example, mice and humans last shared a common ancestor about 75 million years ago, plenty of time for the nonfunctional sequences in their respective genomes to go their separate ways. Only about five percent of the two genomes are conserved, and most of the genes and regulatory sequences that have been discovered lie within these conserved DNA segments.

Humans and nonhuman primates, on the other hand, shared common ancestors as recently as 6 to 14 million years ago for apes, 25 million years ago for Old World (African) monkeys, and 40 million years ago for New World (South American) monkeys. This is insufficient time for much genetic divergence to have taken place. Consequently, nonhuman primates have been largely ignored in the effort to interpret the human genome.

Explains Boffelli, who works with Rubin at both Berkeley Lab and JGI, “There is only about a five percent difference between the human and the baboon genomes. When you run comparisons between the two, all of the sequences look just about the same. We can’t distinguish functional from nonfunctional sequences.”

Rubin’s group overcame this lack of distinction by comparing segments of the human genome to segments of not one but anywhere from 5 to 15 different genomes of nonhuman primates, including chimpanzees and gorillas, orangutans, baboons, and Old World and New World monkeys. By sequencing specific segments within each of the genomes of the different primates being analyzed, the researchers found enough small differences from genome to genome in the nonhuman primates that could be combined to create a phylogenetic “shadow” which could then be compared to the human genome.

Eddy Rubin (left) and Dario Boffelli led the development of phylogenetic shadowing.

“The additive collective sequence differences or divergence of these nonhuman primates as a group was comparable to that of humans and mice,” Rubin says.

The phylogenetic shadow that Rubin and his colleagues created was distinct enough for them to see the boundaries between exons (protein-coding DNA sequences) and introns (noncoding DNA sequences) for several genes, in addition to discovering the regulatory elements for a gene named “apo(a),” which is associated with low-density lipoproteins (LDLs) in the blood stream of humans. An evolutionary new-comer, apo(a) is found in humans, apes and Old World monkeys but appears to be lacking in nearly all other mammals.

“We couldn’t study apo(a) by comparing human DNA sequences to the sequences of evolutionarily distant species because those species don’t have apo(a),” Rubin says.

Rubin believes that the ability to do comparative genomic studies with nonhuman primates will prove especially beneficial to human medical research. Data from this study suggests that sequencing the genomes of as few as four to six primate species in addition to humans may be enough to identify much of the conserved functional DNA sequences in the human genome.

“The argument for sequencing a broad variety of evolutionarily distant species, like the mouse and puffer fish, has been that they would be needed for us to gain a good understanding of the human genome,” Rubin says. “These evolutionarily distant creatures have been incredibly useful, but maybe now we should be focusing our effort on sequencing the genomes of not one but several different non-human primates. Their collective sequences will tell us things about the human genome that we will never to able to learn from our more distant relatives in the animal kingdom.”

Drake’s Plate: The Final Chapter?

By Allan Chen

For years, California schoolchildren were taught that “Drake's Plate,” a brass marker discovered in 1936, recorded the 1579 California coastal landing of English explorer Francis Drake and his ship, The Golden Hind. That was the case until 1977, when Berkeley Lab’s Helen Michel and Frank Asaro used neutron activation analysis on the brass plate and found that it was manufactured no earlier than the eighteenth century — and most likely in the early part of the twentieth. They found that what had been one of California history’s greatest archaeological finds was not authentic. Although Michel and Asaro confirmed that it was modern, no one knew at the time who had made the Plate.

Now the final chapter in the Plate’s history seems to have been written. At a press conference on Feb. 18 at UC Berkeley’s Bancroft Library, researchers claimed that the Plate was devised as a practical joke by several friends of Herbert E. Bolton, director of the Bancroft Library from 1920 to 1940. Fascinated by stories about Drake posting the Plate to mark his California landing, Bolton often told his students to look for it in Marin County. The researchers’ evidence suggests that the Plate was meant to be a practical joke among friends, but the hoaxers lost control of their prank when Bolton authenticated the find publicly before they could tell him the truth.

Although it was historical evidence that completed the story, it was science performed 30 years ago by Michel and Asaro that confirmed what a few historians had suspected all along about the Plate’s dubious origins. Neutron activation analysis showed that its chemical impurity levels were too low for sixteenth century English manufacturing techniques. They estimated that the artifact was made no earlier than the eighteenth century, and probably between the last half of the nineteenth century and the early part of the twentieth — perhaps even as late as 1936, when the forgery was created.

Frank Asaro

In the mid 1970s, then-director of the Bancroft Library, James Hart, commissioned a new study of the Plate, in anticipation of the quadricentennial of Drake’s Landing. As part of this study, he asked the Research Laboratory for Archaeology and the History of Art at Oxford University in England to chemically analyze small fragments of the Plate, and also asked Nobel laureate Glenn T. Seaborg if someone on his staff would drill small samples from the Plate to send to England. Seaborg in turn asked Asaro. “I discussed this with my colleague Helen Michel, and we agreed to drill the Plate,” Asaro says. “But we also said we’d like to make some measurements too. This was acceptable to Professor Hart.”

Although they started with the expectation that the Plate was authentic, right away Michel and Asaro began seeing things that made them suspicious while drilling through the plate. For instance, they expected to find corroded material, but instead saw fine strips of metal. The thickness of the plate was too homogeneous for something that would have been hammered out. Most importantly, the neutron activation analysis revealed not only higher levels of zinc than expected for an alloy made in Drake’s time — zinc hadn’t yet been identified in the sixteenth century — but much lower levels of other metals such as nickel, cobalt, silver, gold, lead, and iron, suggesting that it was made from high-purity copper and zinc not available at the time. These and other clues led Michel and Asaro to conclude that the plate was probably made in the late nineteenth or early twentieth century and certainly no earlier than the eighteenth century.

Michel and Asaro wrote up their results and sent them to Hart: “He had wanted a four-page letter,” says Asaro. “We sent him a 45-page paper.” Hart published 16 pages of the report and Michel and Asaro later published the complete report in the journal Archaeometry

An Enlightening Sabbatical at Chabot

By Monica Friedlander

Rick Norman

Rick Norman was 17 years old when he first fell in love with particle physics while on a field trip here at the Laboratory. His chemistry teacher at Skyline High School in Oakland brought a group of students to the Hill and showed them the “Frankenstein machines,” which scanned bubble chamber pictures back when the Bevatron was running.

“They were showing us the tracks of the bubble chambers, and that made such an impression on me,” Norman said, his face lighting up as he recalled his first encounter with nuclear science. “In the old days there used to be a cloud chamber outside the library in Building 50. The Bevatron was running across the street and you could see the tracks coming in from the Bevatron. I’ll never forget that. That’s what made me think I really want to be a physicist.”

In the years since Norman has become a renowned nuclear physicist, but he never forgot the joy of that first discovery. And over the ensuing decades he would go out of his way to share it with others, mentoring youngsters and teachers alike, both on his own time and as part of a educational programs such as those sponsored by the Lab’s Center of Science and Engineering Education. A few years ago Norman also served on the Curriculum Framework and Criteria Committee that developed science content standards for California public schools.

72-inch bubble chamber

But most of all he loves to work with children to light a spark in them and put them on the path to scientific discovery. That’s what he decided to do last year as part of his sabbatical, which he split between  research at Lawrence Livermore Lab (see sidebar) and teaching at the Chabot Space and Science Center in Oakland.

“Public schools these days do so little in the way of science, and Chabot is a tremendous resource,” Norman says.

His charges at Chabot were “Galaxy Explorers,” high school interns who work as docents at the Science Center, explaining exhibits and performing demonstrations for the public. Their required training includes two hours a week of science enrichment. Norman took responsibility for that for three months, teaching them a course in nuclear particle physics and astronomy entitled “What is the Universe Made Of?”

“The idea was to start with big things — galaxies — and work down to smaller and smaller building blocks and see how it all fits together.”

Along with some of the students he developed websites on radioactive decay, x-ray spectroscopy, and neutron activation analysis. He used nuclear physics data from Berkeley Lab experiments, posted it on the web, and showed students how to analyze it. “It’s the kind of thing you can’t do in a school,” he says.

Also as part of the course Norman performed the type of experiments that first drew him to his profession. He brought in cloud chamber components from the Lab and had the students put them together and do experiments. The effect on the young generation was not unlike his own so many years ago.

“Somehow, seeing the tracks come in makes it much more real,” he said. “Kids these days have grown up with video games and computers. Nothing you show them on the air is going to wow them. But to see those tracks right in front of you — that makes them think a little bit. “

As fascinating as cloud chambers may be, Norman knows better than to spring nuclear science on young people from day one. Instead he greeted them with something a little more conducive to breaking the ice – literally:

“We made ice cream in one minute using liquid nitrogen,” he said. “Just to see their faces was worth everything. I had them do the mixing and I would pour the liquid nitrogen in. They were a little reluctant to eat it until I did. “

On another occasion he entranced youngsters from an elementary school in Fremont with a demonstration of vacuum chambers. He brought in a vacuum pump and had a child come up and flip the lid off. Then he’d pump the air out and ask the kids to try again. “Of course he couldn’t do it. I tried to explain why that happened and the kids were fascinated,” Norman said.

Chabot, however, was not Norman’s first choice for a sabbatical education venture. As a graduate of Skyline High, he decided he would give something back to his alma mater.

“I realized that there’s a real shortage of science teachers in the public schools, in particular in physics. So my plan was to go teach or help physics teachers,” he said.

He wrote to the principal of Skyline and volunteered to work with them. He even explained that his salary would be entirely paid for.

“I’ll come do whatever you want,” he said. His offer, however, fell on deaf ears. Norman received no response and called the principal repeatedly.

“She said she talked to the physics teacher and the chair of department and that they felt they had things under control and didn’t need my help and that my talents would be better used elsewhere.”

His second choice was Chabot. During his previous visits to the Science Center, Norman admits, he was a little underwhelmed.

Rick Norman (center) and his “Galaxy Exporer” class on a tour of Berkeley Lab.

“They have some nice exhibits, but not as much as I would have expected of a new, $70 million facility,” he said. “The reason I thought of them is that I knew the folks who ran the education department there — Eileen Engel (who used to work with the Center of Science and Engineering Education at Berkeley Lab), and now Molly Field. When I approached them about coming up the response was very different.”

Once at Chabot, Norman realized there’s a lot more to the program than meets the eye. About 200 to 500 children from all over the Bay Area and beyond attend classes there every day. Courses are offered in chemistry, physics, biology, and astronomy. Norman spent time with the teachers and sat in on classes.

“That’s what really convinced me that it’s a fantastic place. The teachers are all first rate and do a remarkable job working with all age groups.”

The course for the Galaxy Explorers was so well received that Chabot decided to buy some Geiger counters and a big cloud chamber to develop yet a new course in nuclear physics. Norman will continue working there on a part-time basis and encourages other scientists at the Lab to follow suit.

“A place like Chabot would welcome more participation from folks at Berkeley Lab,” he says. “They value having our people as a resource. Ideally this would be something the Lab would sponsor, in the sense that this would not be seen as something outside of your job but part of your job. And it’s good PR for the Laboratory as well.”

Norman views these activities not only as a means to impart a specific set of skills to students, but perhaps even more importantly as an opportunity to trigger their love of science and set them on a course of learning that can last a lifetime.

“Kids may go to Chabot once or twice a year,” Norman says. “In a few hours, how much can you cover? But you gets them to feel that science can be fun, nonthreatening, and inspire them to learn more.”

Washington Report

Abraham defends hydrogen fuel cell research

In an address to the National Hydrogen Association’s annual conference in Washington D.C. this week, Energy Secretary Spencer Abraham said the Bush administration is committed to the development of hydrogen fuel cells, and he blasted lawmakers who have criticized the president’s broad plan to create a hydrogen economy. The Secretary said the administration’s “bold” fuel cell plan has been “attacked not on the basis of what it is, but on inaccurate assertions of what it is not.” Abraham said that lawmakers who have called for a much larger effort have not studied the issue to determine what is needed to establish a fuel cell market.

“Unlike those who make unexamined calls for more spending, we devoted an entire year to developing a hydrogen roadmap,” he said. The administration has proposed to spend $1.7 billion on fuel cell R&D over the next five years.

Dingell wants more funds for Yucca Mountain

Rep. John Dingell (D-Mich) has written a letter to Secretary Spencer Abraham expressing his concern that funding for DOE’s construction of a nuclear waste repository at Yucca Mountain in Nevada is “inadequate.”

“I have concerns about the adequacy of the proposed FY 2003 appropriation and President Bush’s budget request for FY 2004 funding, both of which appear to be lower than the amounts you previously indicated would be needed,” Dingell wrote in a letter dated Feb. 12. Congress provided only $460 million of the $591 million DOE sought for the nuclear waste program in FY 2003. The president’s request stayed the same in FY04. Congressman Dingell said he is worried that the cuts could “cripple the Department’s efforts to finish site characterization and, if appropriate, apply to the Nuclear Regulatory Commission for a license to operate a permanent waste repository.” An even greater concern, he said, is “the need to restore to the program the billions of dollars contributed over a nearly 20-year time period to the Nuclear Waste Fund.”

Study says tech transfer laws are just fine

Federal technology transfer laws are working and should not be tampered with, according to a draft report that a presidential advisory committee discussed at a meeting in Washington D.C. this week. The draft document presented to the President’s Council of Advisers on Science and Technology also recommended that PCAST work closely with the newly created Homeland Security Department to “rapidly develop technology transfer policies and capabilities,” said PCAST member Kathleen Behrens, who headed the group that prepared the report. The draft report will be available for comment on the PCAST website at — Lynn Yarris

Alexis Bell Awarded Burwell Lectureship

Alexis Bell, who holds joint appointments with the Lab’s Chemical Sciences Divisions and U.C. Berkeley, has been awarded the 2003 Robert Burwell Lectureship in Catalysis by the North American Catalysis Society. The lectureship is given in recognition of substantial contributions to the field, with emphasis on discovery and understanding of catalytic phenomena, catalytic reaction mechanisms, and identification and description of catalytic sites and species. Bell is known for his research in the field of heterogeneous catalysis and is recognized as one of the pioneers in developing in situ spectroscopic techniques and isotopic tracer techniques for the study of catalyzed reactions. He is a member of the National Academy of Engineering a Fellow of the American Association for the Advancement of Science.

Eugene Myers Elected to National
Academy of Engineering

Eugene Myers, a guest in the Lab's Life Sciences Division and a professor of computer science at UC Berkeley, has been elected to the National Academy of Engineering. The election is considered one of the highest professional honors for an American engineer. A prominent researcher involved in the sequencing of the human genome, Myers is a former vice president of informatics research at Celera Genomics in Rockville, Maryland.


LDRD Call for Proposals for FY 2004

Submission deadline: April 18

Director Charles Shank has issued the call for proposals for the FY 2004 Laboratory Directed Research and Development (LDRD) program, which provides support for projects in forefront areas of science that can enrich Berkeley Lab’s R&D capabilities and achievements.

Multi-investigator and multidivisional initiatives that address problems of scale are especially encouraged. All projects should have a clearly-stated problem (e.g., DOE mission or addressing a national need), coherent objectives, and a well-considered plan for leadership, organization and budget.

The call for proposals has been distributed to division directors and business managers. Principal investigators must submit proposals to division directors by April 18.

After an internal divisional review and evaluation, division directors will forward the proposals to the Director’s office. They will then present the proposals from their respective divisions to review committees comprised of the Director, deputy directors, associate laboratory director, and other division directors. The Director will make the final decisions.

The complete call, schedule, guidance, and forms are available for downloading off the Lab home page under the heading “Publications” and then “LDRD” (or directly at

In Memoriam: Iran Thomas

A memorial service will be held tomorrow in Maryland for Iran Thomas, the Department of Energy’s director of Materials Sciences and Engineering in the Office of Science’s Basic Energy Sciences (BES) program. Thomas died last Friday. He was a deputy to associate director for BES Pat Dehmer and a highly regarded science administrator for 15 years.

Thomas’ legacy includes creation of a large fraction of major BES user facilities, including the Advanced Light Source. He was also a champion of the BES initiative on nanoscience technology, which has resulted in the federal commitment for five nanocenters, including the Molecular Foundry at Berkeley Lab.

“Iran Thomas will be sorely missed by all of us,” said Director Charles Shank. “We at Berkeley Lab have benefited from his extraordinary vision, competence, and dedication to Basic Energy Sciences programs. Most of all, he loved the science.”

Dehmer was equally complimentary in her memo to friends last week. “Iran thought big, often really big,” she wrote. “And, as a result, his accomplishments were many and great. He personally created a host of scientific programs and a large fraction of the BES major scientific user facilities that now dot the nation.

“During his 15-year reign in the division of materials sciences and engineering,” she continued, “he became synonymous with its programs and facilities. However, his most enduring legacy will be his philosophy and spirit of innovation, which he passed on to many of us.”

The memorial service will begin at 2 p.m. eastern time at the Cedar Lane Unitarian Universalist Church, 9601 Cedar Lane, Bethesda, Md. The family requests that memorial donations be made in Thomas’ name to one of following, or to the charity of one’s choice: Jobs Unlimited, Inc., 1075 Rockville Pike, Rockville, MD 20852; or Beacon House Community Ministries, Inc., P.O. Box 29629, Washington, DC 20017.

Berkeley Lab Currents

Published twice a month by the Communications Department for the employees  and retirees of Ernest Orlando Lawrence Berkeley National Laboratory. Ron Kolb, Communications Department head.

EDITOR: Monica Friedlander, (510) 495-2248, mailto:[email protected]

STAFF WRITERS: Lisa Gonzales, 486-4698; Dan Krotz, 486-4109, Paul Preuss, 486-6249; Lynn Yarris, 486-5375

CONTRIBUTING WRITERS: Jon Bashor, X5849; Allan Chen, X4210

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ProteinShop: A New Approach to the
Protein Folding Problem

By Paul Preuss

In a unique scientific competition called CASP, the Critical Assessment of Structure Prediction, teams of biologists and computer scientists from around the world try to beat one another to accurate predictions of the structures of recently found but as-yet unpublished proteins — starting with nothing more than their gene sequen-ces. Among the 187 teams in last year’s CASP5, Teresa Head-Gordon of Berkeley Lab’s Physical Biosciences Division headed a group with a special approach.

Most of the other teams used methods that depended heavily on knowledge of existing protein “folds,” three-dimensional structures already stored in the Protein Data Bank (PDB). But Head-Gordon’s Global Optimization Method used initial protein configurations supplied by a revolutionary visualization tool called ProteinShop.

Silvia Crivelli of the Visualization Group in the Lab’s Computational Research Division was a member of the CASP5 team and one of the developers of ProteinShop. She says a major step forward came when “we copied concepts from robotics. When you move a robot’s arm, you move all the joints, like your real arm.” After a year of work on ProteinShop, Crivelli says, “we were able to apply the same mathematical techniques to protein structures.”

Structure by the numbers

The one-dimensional string of amino acid residues specified by a gene’s coding sequences doesn’t reveal much about the protein’s three-dimensional shape.

But by locally forming energy-efficient bonds among acids, this primary structure quickly twists into secondary structures called alpha helices and flat beta strands. In turn these fold into a three-dimensional tertiary structure, which, for most proteins, represents the “global” minimum energy for the structure as a whole.

Sequences that are likely to form helices and flat strands are so well known they have become predictable; information on thousands of structures is stored in the PDB and can be applied to unknown protein folds. But the coil regions that link the secondary structures are not so easily predicted.

Moreover, the more amino acids in a protein, the more local energy adjustments must be made, and the harder it becomes to calculate the global energy minimum. The Global Optimization Method tackles the problem in two distinct phases.

During the setup phase, the program generates the most likely secondary structures in a given sequence and combines them into several approximate configurations; before ProteinShop, this phase needed computer runs of hours or days. During the second phase, the overall energy of the structure is reduced step by step, by optimizing many subsets of the structure.

Inverse kinematics

ProteinShop’s secret is inverse kinematics, a mathematical technique for analyzing movement in structures consisting of jointed segments — for example the fingers, arms, and shoulders of a robot or an animated figure. By taking into account the degrees of freedom permissible at each joint, contortions that don’t break limbs or penetrate bodies can be predicted.

“The difference is that with a robot you have maybe 10 or 20 joints, but in a coil we often have long regions, 80 amino acids,” Crivelli says, “and we want all of the angles among them to move in a concerted way.”

In ProteinShop the user can select a structure, like the helix in the box, and manipulate it to reduce the interference from atom collisions, marked by the spheres. Inverse kinematics calculates angles and helps keep all structures intact while the helix is moved.

Secondary structures and coils are built up by adding amino acids to the structure one at a time, treating each as a jointed segment of a flexible structure. Within seconds a “geometry generator” module incorporates predicted secondary structures, or fragments of them, in the string.

“The whole thing looks like you could just move it around like spaghetti,” says Crivelli. “But before we incorporated reverse kinematics, if you tried to move a protein configuration, it broke.”

Now the process works fast enough to be truly interactive, allowing the user to alter the angles between individual amino acids and to play with the entire “preconfiguration,” dragging whole secondary assemblies into new relationships without breaking previous structures. 

New worlds to conquer

The second phase of the global optimization method — seeking the global energy minimum — remains a computational challenge. The basic approach is to repeatedly tweak the energy budgets of many smaller regions until there is no further improvement.

In practice, energy calculations for every part of a structure would take much too long. The sophisticated procedures developed by Head-Gordon’s team optimize only randomly sampled, small regions. Thus, even after weeks of computer time, it may not be certain that the end result is the true global optimum.

Crivelli says the researchers are working on new methods to combine basic energy calculations with knowledge from the data base. “By recognizing structures and fragments that are known to work, we won’t have to calculate every angle from scratch. The tool will be highly interactive, displaying energies and saving minima as the user finds them.”

The results so far

In CASP4, in 2000, Head-Gordon’s team predicted the structures of only  8 folds, the longest containing 240 amino acids. With a ProteinShop jumpstart, the CASP5 team predicted 20 new or difficult protein folds ranging from 53 to 417 amino acids in length. The team ranked 16th overall in the competition — “great for a method that doesn’t use much knowledge from the PDB,” Crivelli says.

ProteinShop is already tooling up for CASP6. Many competitors are interested in what ProteinShop can contribute to their own methods in the race to the protein-prediction finish line.

Teresa Head-Gordon’s team at CASP5 included Silvia Crivelli and Bobby Schnabel, Richard Byrd, and Betty Eskow from the University of Colorado. ProteinShop was developed by Visualization-Group head Wes Bethel, Crivelli, Nelson Max of Livermore Lab and UC Davis, and UC Davis’s Bernd Hamann and Oliver Kreylos.

For more information about ProteinShop, see

Workshop Points to Big Future
for Nanoscience Research

By Lynn Yarris

More than 400 attendees of the first DOE Nanoscale Science Research Centers workshop held last week (Feb. 27-28) in Washington D.C., were treated to a blue-ribbon lineup of political as well as scientific speakers. The message they heard was loud and clear: nanotechnology research might involve the study of very small things, but it represents potentially very big things in federal funding for the physical sciences.

“It’s like we all have the same speechwriter,” observed John Marburger, director of the Office of Science and Technology Policy and science advisor to President George W. Bush, who delivered an address entitled “Nanoscience and the National Science Agenda.”

Marburger said that the governments of every major developed nation are now investing in nanotechnology research, seeking to gain a competitive advantage. “What gives our nation the edge are the five DOE Nanoscale Science Research Centers,” he said.

Under the National Nanoscience Initiative launched in FY 2001, DOE’s Office of Science announced it would establish five new centers that would “support the synthesis, processing, fabrication, and analysis” of materials at the nanoscale. These centers are Berkeley Lab’s Molecular Foundry; the Center for Functional Nanomaterials at Brookhaven National Laboratory; the Center for Integrated Nanotechnologies at Sandia National Laboratories and Los Alamos National Laboratory; the Center for Nanophase Materials Sciences at Oak Ridge National Laboratory; and the Center for Nanoscale Materials at Argonne National Laboratory.

Marburger was introduced by Office of Science Director Raymond Orbach, who proclaimed in his opening remarks that the five DOE nanoscience centers will be at the hub of national laboratory research efforts in nano-related fields.

“All five centers are in the President’s proposed FY 2004 budget and all are well on their way to becoming a reality,” Orbach said.

Before hearing from Orbach and Marburger, workshop attendees first heard from Congresswoman Judy Biggert, a Republican who represents the 13th District of Illinois and who chairs the Energy Subcommittee of the House Science Committee. Biggert recently introduced H.R. 34, the “Energy Science and Investment Act of 2003,” which calls for the Office of Science to receive an overall increase in funding of nearly 62 percent by FY 2007. This would mean an FY 2007 authorization level of $5.31 billion, compared to the $3.3 billion authorized for FY 2003. The American Institute of Physics has said her bill is “one of the most important physics-related research bills” that the new Congress will consider this year.

“Nanotechnology research is very important to our nation’s future economic competitiveness,” Congresswoman Biggert told workshop attendees. “The Office of Science is uniquely positioned to do nanotechnology research, and I am convinced its nano- science centers can only enhance our economic competitiveness.”

The congresswoman urged attendees to contact their congressional representatives and ask them to support H.R. 34, which now has 74 cosponsors. In addition to a substantial increase in funding for the Office of Science (SC), her bill would also make significant administrative changes in DOE. An Under Secretary of Energy and Research would be created with authority over all DOE-funded civilian science at the non-weapons national laboratories and research universities. A new assistant secretary of science would replace the current “SC director” position, and a science advisory board would be established which would consist of the chairs of DOE’s advisory panels.

“I am a scientist wannabee who has always thought that scientists were very cool,” Congresswoman Biggert said to enthusiastic applause.

The applause was also enthusiastic and vigorous for Congressman Zach Wamp, a Republican who represents the Third District of Tennessee and serves on the House Appropriations Committee and the Energy and Water Subcommittees.

Speaking at a Thursday luncheon, Wamp told attendees, “If we want a balanced federal budget we have to invest in technology. Investing in the physical sciences can give us another boom economy.”

Wamp, who has won a “Champions of Science” award bestowed by the Science Coalition (an alliance of more than 400 organizations dedicated to sustaining the federal government’s commitment to U.S. leadership in basic science) is a rousing speaker and his talk energized the audience. Arguing that the national economic slump is a reason for more investment in the physical sciences rather than less, he cited the example of the Japanese government.

“The economy in Japan is bad but that did not stop their government from investing in supercomputing and taking the lead in that technology,” he said. “New technologies are needed to solve problems not just today but for the long-term too. This takes leadership [in the physical sciences] and we’re just not there now.”

To get the resources needed to advance the development of nano and other technologies that can help solve persistent global problems, such as energy, Wamp said, “we need to do a much better job of marketing the physical sciences. We’ve got to brand the physical sciences in a different way. It is critically important to the vitality of your science and this country’s economy that we get people excited about and supportive of the physical sciences.”

Attendees also heard from Senator Pete Domenici (R-NM), another winner of the Champions of Science award. As chairman of the Senate Energy and Water Development Appropriations Subcommittee, Domenici has been a strong supporter of the physical sciences. He is especially keen on the promise of nanotechnology.

“Nanotechnology represents a new frontier, and it’s harder to guess exactly where these new ultra-miniaturized technologies will make the greatest contribution,” Domenici said. “Suggestions range from new generations of ultratough or ultralight materials to new approaches to hydrogen storage for a future generation of hydrogen-fueled vehicles. This is a truly exciting and revolutionary field.”

The senator also expressed confidence in DOE’s ability to lead the development of nanotechnology. “The Department has led the nation in other major scientific initiatives in the past, from high performance computing to the Human Genome Project,” he said. “Nanoscience provides another golden opportunity for the Department to again lead the way into an important new area.”

Scientific presentations were given by a number of the major names in nanotechnology research, including Berkeley Lab’s own Paul Alivisatos and Gabor Somorjai of the Materials Sciences Division (MSD). Alivisatos spoke on an “integrated view of the nanoscale science research centers,” and Somorjai spoke about “catalysis and nanosci-ence.” On the second day of the workshop, MSD’s Mark Alper gave an overview of Berkeley Lab’s Molecular Foundry.

It was Patricia Dehmer, director of DOE’s Office of Basic Energy Sciences, who perhaps best summarized the anticipated role of the five new nanosci-ence centers with respect to the National Nanotechnology Initiative and the country’s need to maintain economic competitiveness.

“The DOE centers are different from centers funded by the National Science Foundation and others in that they are patterned after the same philosophy that guides our national user facilities: they are there to be used by everyone, including researchers from universities and private industry as well as national laboratories,” Dehmer said. “We will partner aggressively with NSF and others to get the job done. The importance of nanotechnology research and development cannot be overstated.”

A Better Way to Build a Detector?

Rick Norman spent the first part of his sabbatical at Lawrence Livermore National Laboratory in a group that works on radiation detector development for applications. His task was to test various devices for the detection of weapons in things such as cargo containers, airplanes, and cars.

Along with colleague Stan Prussin, a nuclear engineer at UC Berkeley with whom he shared an office at Livermore, Norman looked at the systems being considered at Livermore and began to have some doubts.

“Stan and I did some calculations and convinced ourselves and eventually the folks at Livermore that what they were trying to do wouldn’t work,” Norman said. “So we looked for another approach. We came up with the idea of bombarding cargo containers with neutrons to try to induce fission in the bomb material, and then look for gamma rays emitted by the material. It turns out that this looks a lot more promising than what they were trying before.”

As a result, Norman was given time at the  88-Inch Cyclotron to test his theory and is in the process of running tests right now.

“Our lab can only run small scale experiments because we’re not allowed to handle bomb-size quantities of uranium and plutonium,” he explains. “So we’ll do feasibility testing here on small quantities and they’re going to do full-scale tests at Livermore.”

Norman expects initial results of the tests to come in by this spring or summer. “The first experiments look very positive,” he says.

Science Glossary

Amino acid

One of 20 kinds of small molecules from which proteins are assembled. When one amino acid joins another it loses a water molecule; what remains is an amino acid residue.

Alpha helix

The most abundant secondary structure in proteins, with exactly 3.6 amino acid residues per turn.

Beta sheet

Two or more flat chains (beta strands) of amino acid residues lying side by side in a plane.


A chain of amino acids not shaped like a helix or beta strand.


A particular configuration of helices, sheets, and coils. Some of the several hundred known folds are common, others are rare.


The mathematical relationships among linked objects. Forward kinematics calculates what happens to the last link when the first one moves (e.g., where the thumb goes when the shoulder moves); inverse kinematics calculates how other links must move to get the last link into a certain position.

TEID Publications Win Awards

The following materials published by the Technical and Electronic Information Department (TEID) won Touchstone awards this year:

Joint Genome Institute Progress Report
Distinguished, technical publications

Advanced Light Source Activity Report 2001
Excellence, technical publications

Computing and Communication Services News
Merit, online communication

Innovative Solutions to Better Support
Berkeley Lab's Science Mission
Merit, technical publications

NERSC Annual Report
Merit, technical publications

Blackberry Canyon Stairs Get a Facelift

Rising from Parking Lot F at the sharp bend of Cyclotron Road to just below the Blackberry Canyon Gate are the newly renovated Blackberry Canyon steps, which opened to pedestrians two weeks ago after months of being cordoned off due to their previous dilapidated state.

The scenic stairway now features custom steel handrails with stainless steel cables, pressure treated wood stair treads, and safety lighting. The work is the result of a talented team of design, engineering, archi-tectural, and facilities professionals. Photo by Robert Couto

Bancroft Bus Route to Include New Campus Stop

No change to offsite Hearst route to BART

One of the major offsite Laboratory bus routes, the Bancroft Run, has been altered beginning this Monday to incorporate a stop at the west campus entrance and pickups at Buildings 62, 66 and 74.

The changes follow the completion last Friday of a trial van route to the West Circle entrance to the Berkeley campus off Oxford Street. The Bancroft bus will continue to leave every 30 minutes at 15 and 45 minutes past the hour from the main Building 65 bus stop. But it will no longer turn from Oxford onto Center and to the downtown BART station. Instead, it will continue on Oxford after the campus stop, turn right at Hearst and proceed to the Laboratory.

The Bancroft bus will actually begin and end its run at Building 74, the life sciences area. Departure times there will be at 10 minutes and 40 minutes past the hour. First departure time is 6:40 a.m., and last departure is 7:10 p.m.

The offsite Hearst bus, which leaves every 10 minutes and has the downtown BART station as one of its destinations, will remain unchanged. Employees at Building 937 downtown can either board the Hearst bus at Oxford and University or the Bancroft bus at West Circle on campus. The West Circle stop will be on the hour and the half-hour.

The new Bancroft bus stops, which start at Building 74, are: Building 48, Building 65 (downhill), East Gate (Donner, on campus), Calvin Lab (campus), Bancroft at Piedmont, Bancroft at College, Bancroft at Bowditch, Bancroft at Telegraph, Bancroft at Ellsworth, Oxford at Kitteridge, West Circle (campus), Hearst at Oxford, Hearst at Euclid, Hearst at Leroy, Building 65 (uphill), Buildings 62/66, and Building 74.

On the uphill stop across the street from Building 65, the Bancroft bus will also pick up passengers who wish to proceed uphill to Buildings 54, 48, 77, 62/66, and 74 (pull cord to signal stop). This is in addition to the regular onsite bus shuttle routes, which remain unchanged.

Comments may be addressed to Tammy Brown of Bus Services at mailto:[email protected] or X4165.

Foreign Travel Resources

The Counterintelligence (CI) Office at Berkeley Lab is providing information to employees to assist them in making decisions regarding official and unofficial travel during the current period of tensions. The information comes from the United States Department of State, Bureau of Consular Affairs.

The U.S. Department of State issues travel warnings whenever it recommends that Americans avoid a certain country. Countries currently deemed inadvisable for travel are: Afghanistan, Algeria, Angola, Bahrain, Burundi, Central African Republic, Columbia, Congo-Kinshasa, Cote d’Ivoire, Indonesia, Iran, Iraq, Israel, Gaza and the West Bank, Jordan, Kuwait, Lebanon, Liberia, Libya, Macedonia (former Yugoslav Republic of), Nigeria, Pakistan, Qatar, Saudi Arabia, Somalia, Sudan, Syria, Tajikistan, Venezuela, Yemen, and Zimbabwe.

This list could be augmented from day to day.

The State Department also issues public announcements to disseminate information quickly about terrorist threats and other relatively short-term conditions that could pose significant risks or disruptions to Americans. For current public announcements see

Questions regarding the information listed above or about future travel plans may be directed to Bill Cleveland at the CI Office at X4988 or mailto:[email protected].

Paul Alivisatos to Give “Friends of Science”
Presentation: Nanocrystals and Solar Cells

Materials Sciences Division Director Paul Alivisatos will be the featured speaker at the next “Friends of Science” presentation. His talk, entitled “Control of Nanocrystal Shape Boosts Efficiency of New Hybrid Solar Cells,” will be held on Monday, March 10 from 5:30 to 7 p.m.

To make a reservation send an email to mailto:[email protected] or contact the Community Relations Office at X7292. Reserved parking will be available after 5 p.m. in the Building 54 lot.

Employee Referral Program

The Department of Energy has approved Berkeley Lab’s Employee Referral Incentive Program (ERIP), allowing it to become a permanent component of the Laboratory’s recruitment strategy. ERIP was launched as pilot program in 2001 and has proven to be highly successful.

“Having ERIP as a permanent program acknowledges that our employees are among the best recruitment sources for new hires,” said a spokesperson for the Human Resources Department. To date, HR says, the Lab has received more than 800 employee referrals which resulted in 65 hires.

Employees whose referral lead to a new hire are awarded a net amount of $1,000.

To make a referral and ensure eligibility for the award, complete an ERIP form and send it along with the referral’s resume to the ERIP coordinator either by email (mailto:[email protected]) or through Lab mail (MS 937-600), addressed to “ERIP Coordinator.” Please note that submitting a referral directly to a hiring supervisor does not guarantee eligibility for the award.

The ERIP referral form and additional information about the program can be found online at

Flea Market


‘01 MAZDA MIATA MX-5 SE, blue metallic, hard top, 6 spd, 7.8K mi, ac, all pwr, cruise, am/fm/cd, Bose premium sound, dual front air bags, abs, tan leather, premium wheels, sport suspension, like new, $21,500, Geoffrey, X4626

‘93 FORD MUSTANG convertible, >74K mi, runs perfect, cruise, at, ac, pw, ps, more, $4,000/bo, Feng, X5304

‘92 MAZDA MINIVAN, 160K mi, new brakes/batt, cruise, all pwr, rear ac, am/ fm/cass, runs great, $3,200/ bo, Gustavo, X4473, 525-6680

‘91 VW JETTA, 92K mi, sunrf, runs very well, good miles, new tires/brakes,  cd/ radio, $2,500, Greg, 527-4757

‘83 HONDA PRELUDE, Coupe 2D, 5 spd, navy, 120K mi, am/fm, sliding sunrf, exc cond, clean, $1,000, Greg, X7706, 527-7644

‘83 HONDA ACCORD,  4 dr sedan, charcoal grey,  5 spd, 117k mi, am/fm/ cass, exc cond, $1,000/bo, Jimmy, (925) 296-5649, (925) 798-4645


BERKELEY HILLS, 2 bdrm/ 2 bth duplex, fp, bay view, gourmet kitchen, w&d, security syst, no smoking/ pets, walk to Lab, $1,860/ mo, Tennessee, 848-0166

BERKELEY HILLS, bay view, furn rm 17'x15', priv bth/ent, cooking facil in adj rm, w&d, pool table, workout mach, quiet neighbrhd near UC/pub trans/shops, $850/mo incl linens, dishes, util, phone, internet, use of garden/ BBQ, wkly b&b, no smoking/ pets, $300/wk, Carol, 524-6692

BERKELEY HILLS, by wk/mo, quiet furn suite, sleeps up to 3 in 2 bdrm/1 bth, quiet, eleg, bay views, DSL, cable, microwv, walk to UCB, Denyse, 848-1830, mailto:[email protected]

BERKELEY HILLS, fully furn rm w/ sep entry, full kitchen priv, w&d, quiet neighborhd, lovely backyard, near bus, $890/mo incl util, Arun, 524-3851, mailto:[email protected]

BERKELEY HILLS, house for rent behind Claremont Hotel, Alvarado Rd, great view, 3 bdrm + lge play rm, 3.5 ba, AEK, din rm, lge liv rm, hardwd flrs, avail now, $2,500/mo, 1st/last + $1,250 dep, Shmuel, 908-3102

BERKELEY, 1914 Woolsey St, rm avail now in 3 bdrm house, clean, peaceful, share kitchen/bth, close to BART, shops, females only, Sumita, 541-2358, mailto:[email protected]

ELMWOOD, share eleg 11 rm house w/ 2 professionals, 35+, nonsmoking, lge bdrm w/ fp & big closet, avail now, weekly shared dinners, yellow Lab, sauna, guest rm, fishpond, $850/ mo+dep, shared expenses, Tony, 841-4480

KENSINGTON, furn 3 bdrm house avail for visiting scholar, view, patio, very quiet, $1500/mo, Ruth, 526-2007, 526-6730

NORTH BERKELEY, by wk/mo, furn lge sunny  1 bdrm apt, walk to campus/shuttle, many amenities, priv garden, gated carport, avail after 8/1, Geoff, mailto:[email protected], 848-1830

PIEDMONT, furn 1 bdrm apt w/ liv rm, study, kitchen & patio in secluded area, $1,350/mo incl utils, avail now for short-term or until end of June, Julie, 452-0790

PLEASANT HILL, townhouse, 1,400 sq ft, 3 bdrm/ 2 bth, 2 car garage, comm pool & facilities, $1,800/ mo avail now, Derun, X5053, mailto:[email protected]

ROCKRIDGE AREA/OAK, master bdrm in priv house, nice quiet area, walk to College Ave/BART/Lab shuttle, $495, smaller rms also avail, 655-2534

WALNUT CREEK, 1601 Alvarado Ave, lge 1 bdrm apt, grnd flr of 4plex, patio, carport, pool, laundry, $850/mo, Bob, (925) 376-2211, mailto:[email protected]


BABY GRAND piano & bench, Harrington, mahogany, plays well but could use refinishing, $600/bo, Ginny, X7413

CELLPHONE, Nokia 5190, standard batt, hi-cap batt, desk charger, more, $50, Joe, X5374, (505) 710-3998

DOUBLE FUTON & foldable pine frame w/ extra support planks, great shape, $100, Elisa, X7863, 665-9091

GAS RANGE G.E. XL44, with self cleaning oven, digital timer, clock, thermostat, 1 low, 2 med., 1 high output stovetop burners, $200, Peter, X7653

MOVING SALE, 3/16, wooden desks, $25; baby crib, $10; basinett, $7; misc items incl chairs,  tables, books, glasses, wine decanters, Margaret, X7550

OAK BED, full size, beautiful antique circa 1910, tall carved headboard, $800/ bo, new matt avail; oak 5-drawer dresser, close color to bed, $500, Ken, X7739

SMITH-CORONA portable manual typewriter in good cond, $10; mahogany, wood record cabinet in exc cond, $20, Ray, 525-2436

SPA: 5-person Coleman, self-contained spa, hook to 220V & ready to go, 3 yrs old, good cond w/ insulated cover & steps, $2,500, Max, X4022


CARPOOL from Fairview/ Eastern Hayward area, Doyle, X4568

HOUSESITTER in Richmond area, 2 bdrm w/ fp & 2 pets, 3 yr old beagle & 6 mo old cat, both are sweeties, 3/6 – 12, Trina, X4645, 215-7698


PETS: 7 doves & 5 gray male cockatiels, not tame, live in an outside aviary; 2 spayed female outdoor cats, 1 blk/wht short-hair, 1 gray/wht long-hair, Marcy, X6448, (415) 381-4822


PARIS, FRANCE, near Eiffel Tower, furn elegant sunny 2 bdrm apt, avail all year round by wk/mo, Denyse, 848-1830

TAHOE KEYS, S. Lake Tahoe, 3 bdrm/2.5 bth house, fenced yard, quiet, sunny, great view of water & mtns, $195/night, 2 night min, Bob, (925)  376-2211.

Bulletin Board

Flea Market Policy

Ads are accepted only from LBNL employees, retirees, and onsite DOE personnel. Only items of your own personal property may be offered for sale.

Submissions must include name, affiliation, extension, and home phone. Ads must be submitted in writing via e-mail (mailto:[email protected], fax (X6641), or delivered/mailed to Bldg. 65.

Ads run one issue only unless resubmitted, and are repeated only as space permits. They may not be retracted once submitted.

The deadline for the March 21 issue is Thursday, March 13.

Advanced Windows 2000 Security Course

An advanced course in Windows 2000 security will be taught from 9 a.m. to 5 p.m. on Friday, March 14 in the Building 50 auditorium. Geared primarily to Windows 2000 system administrators, webmasters and programmers, the course will cover issues such as securing active directory and advanced network security considerations. The instructor will be Gene Schultz. To enroll see

Vulnerability Scanning

Jay Krous’ presentation on “Vulnerability scanning at LBNL,” originally scheduled for Feb. 12, has been rescheduled for noon on Wednesday, March 19 in Perseverance Hall. The brown bag is sponsored by the Computer Protection Program.

Fidelity Retirement Consultations

Fidelity Investments is offering employees free individual consultations about retirement investment options. The 45-minute, one-on-one sessions with a Fidelity representatives may be scheduled on March 12, April 9 or May 14. They will be held in Building 70, Room 191. Appointments can be arranged by calling Fidelity at (800) 642-7131.

Anne Fleming Retirement Reception

Following a 43-year tenure on campus and on the Hill, Anne Fleming, report coordinator for the main library, is about to retire from Berkeley Lab. In recognition of her service, Fleming’s colleagues are planning a retirement reception on Monday, March 31 from 3 to 4:30 p.m. in Perseverance Hall.

Fleming joined the Lab in 1974 as executive assistant to then-director Andrew Sessler. But it was in 1983 that she embarked on what was her dream career — as a librarian. She started at the Donner Library, moved on to the Engineering Library, and in 1985 to what was then the Technical Information Department (ID). Since 1994 Fleming has served in her current role of report coordinator.

Reservations for the reception can be made through Yen Manikin (MS 50B-4230, mailto:[email protected], X7580.) The cost is $20 and includes a gift, hors d'oeuvres and soft drinks. Make checks payable to Yen Manikin.

EH&S Schedule Online

The most up-to-date EH&S schedule of classes is available online on the EH&S training website at To enroll, contact Valarie Espinoza-Ross at mailto:[email protected]or enroll via the web at Preregistration is required for all courses except EHS 10.

2003 LBNL Golf Club Tournament Schedule

Roddy Ranch, Antioch, March 15
Chardonnay, Napa, April 12
Mare Island, Vallejo, April 26
Boundary Oak, Walnut Creek, May 17
Delta View, Pittsburg, June 15
Lone Tree, Antioch, July 19
Oakland Metropolitan, Aug., TBA
Windsor Golf Club, Sept. 13
Red Hawk – Reno, Oct. 11
Wolf Run – Reno, Oct. 12
Poppy Ridge, Nov. 2

For information about joining the Golf Club or participating in tournaments, contact membership chairman Dave Plate at X7232 or mailto:[email protected].