December 21, 2001 Search the Currents Archive

New HR Head Brings Wealth of Experience, Leadership to his Job

Lose-Lose Theorem Challenges Standard Model of Physics

Why We Sequence the Critters: An Interview at JGI
Washington Report
Wozniak Recognized as Head of Safety Review Committee
Orbach Named Head of DOE’s Office of Science
Livermore Director to Step Down in 2002
New APS Fellows
Solved: The Elegant Architecture of a Cell-Membrane Water Channel
In Memoriam: Gil Shapiro
Thanks for Sharing
Bulletin Board
EH&S Classes – January 2002
Counter-Terrorist Expert to Speak at Berkeley Lab
Flea Market
Flea Market Policy

New HR Head Brings Wealth of
Experience, Leadership to his Job

By Ron Kolb

Think of Randolph R. Scott’s professional life as an extended day in the classroom and laboratory — learning and practice. And it’s not over yet. Next course: Human Resources at Berkeley Lab.

That’s how the Laboratory’s newest Operations manager looks at it. The head of HR, just two weeks into the job, has traveled a diverse and broadly experiential path to his present assignment. As he describes it, “I’ve had one career, and many jobs. This is the kind of setting that is ready for the things that leadership and partnership can make happen. My vision is that Berkeley Lab is not only the best place for science, but also a great place to work for all of us.”

Scott says he almost sees it as a lab within a lab, where he will be able to study and practice human resources. And he notes with emphasis, “The HR function has the capability to be a critical partner to the Laboratory’s scientific mission.”

“Randy brings a passion to his work that will serve the Laboratory well,” said Berkeley Lab Director Charles Shank. “We look forward to taking advantage of his knowledge of personnel issues and their impacts on a quality work environment.”

Deputy Director Sally Benson said the Lab is fortunate to be able to attract a person whose skill set is as broad as Scott’s. “Randy has been a proven success in the public sector, in private industry, and in retail,” she said. “He brings us a wealth of experience in management, employee and labor relations, compensation and benefits, training and development, and recruitment and employment. We look forward to taking advantage of these capabilities.”

Engaging and gregarious, Scott said he is “just this side of 50,” though he won’t say which side. When reviewing his resume, he is uncanny in remembering distant dates, facts and figures. (He recalls meeting his wife of 25 years, Bette, “on April 11 at 4:30 on a Sunday afternoon in Newark Airport on the shuttle to Washington.”)

He came to Berkeley Lab after six years at Kaiser Permanente in Oakland, where he was the health care company’s division director for employee relations and, before that, an area vice president for human resources. That experience, plus his six previous years as HR vice president at Blue Cross-Blue Shield in St. Louis and a year with JC Penney as its healthcare cost containment manager, gave him valuable exposure to the challenges of benefits and financing within managed health care systems.

Before that, he spent seven years as general manager of human resources for Diamond Shamrock Corp. in Dallas, a large energy and chemical company, where he learned the technical side of industry. It also gave him an opportunity to travel extensively and work in the company’s branches in Singapore, Jakarta, London and The Hague.

“One of the most important things to me is to be a generalist in HR,” he said. “In all of my job moves, I have tried to seek placement opportunities where I could strengthen my skills and knowledge in each of the human resource areas of practice. At Diamond, I became experienced in training and education, and then picked up compensation, benefits, and systems.”

It all started with a Vietnam-era stint as a personnel officer with the Air Force, and later with Boy Scouts of America, for which he served first as the associate national director for a new program called “Exploring.” A former Eagle Scout himself, Scott helped to develop this career-based program and joined his charges on adventures to places like the 1972 Olympic Games in Munich and week-long NASA space seminars.

More importantly, he said he “wanted to do something in education,” so he took leave to accept a faculty instructor appointment to teach Youth Agency Administration at Salem College in West Virginia while working on his masters degree at West Virginia University. At the conclusion of his work he was recognized as “professor of the year” by colleagues and students.

Upon his return, the Boy Scouts named him dean of their National Education Center, responsible for training adults entering the Boy Scouting profession. “It responded to that ‘teaching’ thing in me,” Scott recalled.

Now, 25 years later, he said, “I have most of the tools now. I’ve come almost full circle, back to research and academically based work. This is where I want to invest my career.”

In announcing Scott’s appointment, Benson also praised her executive administrator, Guy Bear, for his interim management of the Human Resources Department while the search proceeded for a new head.

Lose-Lose Theorem Challenges
Standard Model of Physics

By Lynn Yarris

What we know about the fundamental nature of matter is not enough to explain what has been observed in high energy physics experiments during the past decade, according to the “Lose-Lose Theorem” proposed by a Berkeley Lab physicist.

Michael Chanowitz, a theoretician with the Physics Division, says that a measurement of the breakdown or decay of Z particles — the carriers of the weak nuclear force — shows that the theory which has successfully explained fundamental physics since the 1970s, the Standard Model of Particles and Fields, is no longer quite so successful. In a paper published in the Dec. 3 issue of Physical Review Letters Chano-witz argues that whether scientists accept the measurement as valid or dismiss it as an anomaly, the Standard Model loses.

An artist’s conception of CERN’s future LHC dipole, where Michael Chanowitz’s theorem and the viability of the Standard Model are likeley to be tested in future years.

“An analysis of all relevant data, including searches for the Higgs particle, favors a breakdown of the Standard Model,” Chanowitz says. “This implies with a high probability that there is new physics beyond the Standard Model waiting to be discovered.”

The Standard Model provides a theoretical framework for describing the fundamental particles of matter and all of the forces that interact with them except gravity. It holds that there are two kinds of fermions — or matter particles — quarks and leptons (leptons include electrons and neutrinos), grouped into three distinct “generations” of increasing mass. Ordinary matter is composed of the lightest generation of fermions: up and down quarks, which combine to form the protons and neutrons of atomic nuclei; electrons, which bind atoms together into molecules; and electron-neutrinos which influence the stability of this matter.

Through the years, the Standard Model has been used to predict particle properties even before the particles were experimentally found. For example, it accurately predicted the mass of the top quark, which was found in 1994. The final particle needed to complete the Standard Model’s predictions is the Higgs, named after Peter Higgs of the University of Edinburgh who first proposed it. The Higgs particle is a boson, or force-carrier, thought to give mass to the elementary particles through its interactions with them. Among the measurements used to predict the mass of the Higgs particle is the direction of the decay of Z-particles into bottom and antibottom quarks (the bottom quark’s antimatter counterpart).

Says Chanowitz, “The result of this measurement disagrees significantly with the Standard Model’s predicted value. If genuine, the discrepancy implies a breakdown of the Standard Model.”

Michael Chanowitz of the Physics Division demonstrates how measurement of Z particles is incompatible with the Standard Model.

Because this measurement of Z-decay into bottom and antibottom quarks is extremely difficult, Chanowitz says the possibility that the discrepancy is the result of “subtle experimental error” cannot be excluded. However, under the terms of his Lose-Lose Theorem, the possibility of experimental error cannot save the Standard Model because, “the predicted value of the Higgs particle mass would then be so low that it should have already been observed at existing experiments.”

Chanowitz bases his conclusion on the fact that experiments at CERN (European Organization for Nuclear Research) on the Large Electron Positron collider have already set the lower limit for the mass of the Higgs particle at 114.1 GeV (billion electron volts). If the questionable Z-decay measurement is discarded, the Standard Model becomes an excellent fit with other important measurements. However, its predicted value for the Higgs mass then falls far below the established minimum.

“The Standard Model is caught in a Catch-22 dilemma,” Chanowitz says. “Whether the questionable Z-decay measurement is right or wrong, new physics beyond the Standard Model is required, either to explain the discre-pant measurement or to explain the failure to have already observed the Higgs particle.”

Some physicists have already speculated about new kinds of quarks, or a symmetry of fermions and bosons known as “supersymmetry,” as possible explanations. But Chanowitz says there is not enough evidence at this time to know what the new physics beyond the Standard Model might be.

“We need new particles or new forces at higher scales that can interact with the particles we already know about in order to explain those effects we’ve been seeing that cannot be explained by the Standard Model,” he says. “Until this new physics is known, we cannot predict the Higgs particle mass except for the general statement that it is at or below the trillion electron volt (TeV) scale.”

Chanowitz says that the Large Hadron Collider, which is scheduled to begin operations at CERN in 2005 and will smash together protons in the multi-TeV energy range, is likely to provide answers to the questions posed by his Lose-Lose Theorem.

Why We Sequence the Critters: An Interview at JGI

By Paul Preuss

“We evolved from other things, and evolution doesn’t fix what isn’t broken.”

Over the past year and a half the Department of Energy’s Joint Genome Institute has announced a string of remarkable events, including the sequencing of three human chromosomes, the sequencing of 15 microbes in a single month, the sequencing of the remarkable fugu fish, and the sequencing of the primitive chordate Ciona intestinalis, or “sea squirt” — among investigations of many other disparate organisms.

To find out what these creatures have to do with one another and with human beings, Currents interviewed JGI Director Trevor Hawkins, functional genomics head Paul Richardson, and computational genomics head Dan Rokhsar. Following are edited excerpts.

Currents: Why all these seemingly unrelated organisms? Is there a unifying theme?

Trevor Hawkins: It was known pretty early on that a lot of the sequences that are present in the human genome are also present within simpler organisms. We evolved from other things, and evolution doesn’t fix what isn’t broken.

If you look at the fugu, you say, okay, we have more cells than it does, and it has some tissues that we don’t have, like gills, but it has a liver, it has a circulatory system — all the things we do. You start to wonder, if it has all these functions and it shares them with us, isn’t it in fact using the same basic ‘construction kit’? And the answer is yes.

Paul Richardson: The overall reason for genome work is to gain insight into the function of the human genome. But you have to get far away from the human genome to get that insight. Evolution takes a very, very long time. To see significant changes in the genes, especially well conserved genes, you might have to go several hundred million years back in time to a common ancestor, to something like Ciona. In general we are looking for conserved function, and when we find genes that have the same sequence or very similar sequences, they are very likely performing the same biochemical reaction.

Dan Rokhsar: We use computer programs with the ability to look at multiple genomes and line them up and look for commonalities — which, if they’re there, indicate some functionality, even if we don’t know what it is. If it’s there in mouse, if it’s there in fugu, if it’s there in sea squirt, it must be doing something important.

Hawkins: One of the key goals of DOE’s Genomes to Life program is to understand regulatory networks. We’re starting to see these very short regions — maybe 50, 100, 150 nucleotide matches between the squirt, fugu, human, and mouse. One of the programs that we’ve set up has been centered upon taking these elements and proving through various assays that these are in fact regulatory structures.

Dan Rokhsar, head of Computational Genomics

It’s not obvious. You don’t have a gene, and here’s an element and you say aha! here’s the switch that turns this on.

Richardson: Promoter elements are typically two or three hundred bases upstream from the gene and may contain very small stretches of DNA, five or ten bases, that interact with specific transcription factors to turn on the gene. And oftentimes there are multiple transcription factors that we find upstream, which interact with the transcription machinery.

Hawkins: With a lot of diseases, our next level of understanding is going to be based upon how genes are interacting with each other within cells. The old notion of one gene, one protein, one disease — forget it! There are very few examples of that.

If you are trying to design a drug or a small molecule that affects a whole gene pathway or a network of genes switching on and off, you’ve got to know how all the genes are interacting with each other.

Currents: These kinds of scientific questions seem to involve a different approach from the one JGI was pursuing not so long ago.

Hawkins: At first it was sequencing of the human genome, nothing but sequencing. Today, about 50 percent of what we do is sequencing, although we produce about twice as many bases. Sequencing is becoming cheaper and cheaper all the time, and faster to do. Sequencing is a commodity. As we free up space, we can bring in more scientific programs to use the sequence.

Paul Richardson, head of Functional Genomics

Rokhsar: You can address a specific set of issues and have the programs drive the sequencing, rather than vice versa.

Hawkins: You can think in a different way. In the microbial community, for example, they were used to taking a microbe, spending a couple of years getting the sequence finished, and then they analyzed it and annotated it. We can sequence almost two of your average microbes 10 times in one day!

What’s coming out now is a different model, where in addition to your favorite microbe you also quickly sequence the half a dozen microbes that are related to it. We did this with Xylella [a bacterium spread by insects], where certain forms infect certain plants…and you could look through the sequences and pretty much identify the genes that one has and the other one doesn’t.

Currents: What major technical advances have allowed this new way of working?

Hawkins: It’s all been due to the Human Genome Project. We built these very large, industrial-scale processors because we were desperate to sequence the human genome, but now we’re sitting on the ability to sequence hundreds of bases every second. And that pretty much doubles every six months. We work closely with outside technology developers, and the spin-off for us is that we get their new machines and new reagents cheaper and faster.

There are two big areas we’re focusing on today. One is functional genomics; the other is the computing area.

JGI Director Trevor Hawkins

Rokhsar: Comparative genomics is like the Rosetta stone. You see these ancient texts, and you know they must mean something, but how do you know what they mean?

Currents: You mean by comparing those languages with languages you can understand?

Rokhsar: Yes, but the difference between the Rosetta stone and the genomic situation is that these aren’t dead languages. They’re living inside the bodies of these animals.

Now that we can generate all this sequence, it puts a lot more pressure on us to assemble it. Our JAZZ assembler [a computer program] was developed here over about a year. Its claim to fame is that it’s the only assembler in the public domain — and it takes into account aspects of the data that other assemblers simply ignore; for example the fact that we sequence from both ends of a piece of DNA, which is, again, a technology that JGI has employed from the very beginning.

Currents: And when you have that assembly, you have to figure out how it all functions.

Richardson: Trying to figure out the functions of genes includes looking at things like alternative splicing. Remarkably, there’s a single gene of Drosophila that has 38,000 different splice variants! It’s a very large gene with many exons [coding sequences], and it directs neuronal growth. By shuffling these exons around, and making different mRNA, which leads to different proteins, it’s able to direct those neurons to different parts of the body. You can say that’s one gene, but it’s performing many different functions.

Functional genomics also includes looking at gene expression: what are the cues that turn genes on. And we’re also getting into an area which is now called proteomics — the next step after functional genomics — actually getting right down to the biochemical function of the proteins.

One of the first things we’re doing, because we’re interested in regulatory translations, is looking at how expressed proteins bind to DNA, and getting an idea of what genes they might affect.

Currents: What are the next steps for these comparative-genome projects?

Hawkins: The squirt is just the start. We have other genomes in mind that will help us compare with some of the networks that we’ve found in the sea squirt. One of the next genomes that we’re seriously considering is the frog, Xenopus tropicalis.

When you look at a sea squirt you don’t think of human development, but when you look at a frog embryo, there’s a lot of similarity between a frog embryo and a human embryo. So if you begin to see something in the sea squirt, and then begin to see it in the frog, and then someone else starts to see it in the mouse, you can say, well this is probably going to be present in the human.

Richardson: In Ciona, we’re trying to get an idea of which genes function in the patterning of an embryo and the development of the notochord [a precursor of the spinal chord, found in some primitive animals and in vertebrate embryos]. And those will have homologs, or genes that are similar, in every other organism that has a similar body plan. In a more primitive organism the same gene may carry out the functions of, say, two, three, or four genes in a more specialized organism, because oftentimes those genes may have been duplicated or even reduplicated.

Rokhsar: In computation, the next hurdle is allowing people to make use of this comparative data — and all the other data. As people use those elements in their own experiments, they’re going to bring information back that’s much more diverse than just the sequence of As, Cs, Ts, and Ds [the nucleotide bases of DNA whose order determines genetic coding]. You want to be able to interrogate the whole system and ask questions at the meta-level, and not just be tied to finding a particular gene.

Hawkins: With sequence production, before now, only the “bravest and fittest” have been able to interpret this data. We want to make it so even your grandmother can use it.

As we look forward to producing other kinds of data, the burden is on us to produce tools to allow people to get the most out of the data sets.

The Joint Genome Institute, a consortium founded by Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Laboratories, now includes partners from several other institutions. Visit their website at

Washington Report

Merry Xmas for DOE’s IT Research

DOE would receive about $1 billion over a five-year period to conduct basic and applied research in networking and information technology (IT), under a measure the House Science Committee approved by a voice vote earlier this month. H.R. 3400, the Networking and Information Technology Research Advancement Act, amends the 1991 High Performance Computing Act, the law that coordinates federal IT research, to authorize a significant boost in basic research in IT at six agencies, including DOE and the National Science Foundation. All told, H.R. 3400 authorizes nearly $7 billion for IT research from FY03 to FY07 — a 46 percent increase. DOE’s funding would rise each fiscal year, from $193 million in FY 2003 to $212 million in FY04, followed by $234 million in FY05, $258 million in FY06 and $283 million in FY07.

Under this bill, DOE’s IT research would be directed to emphasize support for fundamental research in the physical sciences and engineering, and in energy applications; provide supercomputer access and advanced communication capabilities to scientific researchers; and develop tools for distributed scientific collaboration.

“The example of the Internet alone makes the case for the unexpected and often spectacular outcomes from federal long-term investments in information technologies,” said Eddie Bernice Johnson (D-Tex), who co-sponsored the bill.

Happy New Year for Science Says House Science Leader

House Science Committee Chairman Sherwood Boehlert (R-N.Y.) says that scientific research can expect a rosy future under the Bush administration, thanks in no small part to the influence of John Marburger III, the newly appointed director of the White House Office of Science and Technology Policy.

“Marburger made his mark from the start,” Boehlert said at a press conference in Washington, noting that Homeland Security chief Tom Ridge has relied on Marburger’s office to serve as the science arm of homeland security.

“There will be more funds for science across the board, both short-term and long-term.”

Boehlert acknowledged that many members of the Bush administration initially expressed public doubts about the benefits of basic research, especially Office of Management and Budget Director Mitchell Daniels. But the mindset at the White House has shifted, Boehlert said; as a result, federal spending for science rose in FY 2002 and “next year’s budget should be even better.”

Looking ahead, Chairman Boehlert said his Science Committee will have a busy agenda in 2002 that will include NSF reauthorization, climate change, and bioterrorism, including anthrax contamination. He also said he expects to see more cooperation among the various federal agencies that conduct science research.

Wozniak Recognized as Head
of Safety Review Committee

Nuclear scientist Gordon Wozniak shows Lab Director Charles Shank the inscribed desk clock he received in honor of his contributions as head of the Lab’s Safety Review Committee. The clock was a gift from the members of the SRC, and was presented to him earlier this month by Robin Wendt of EH&S. In recognizing Wozniac, Director Shank referred to his many accomplishments during his two-year tenure as head of the committee, such as revitalizing the role of the SRC to advise senior lab management on ES&H issues, improving ES&H programs and processes, and providing a forum for employees to work on EH&S related issues.

Orbach Named Head of DOE’s Office of Science

On Dec. 11 President Bush announced his intention to nominate Raymond L. Orbach, the current chancellor of the University of California at Riverside, to be director of the Office of Science at the Department of Energy. Orbach will remain at UCR pending confirmation by the U.S. Senate.

The third largest federal sponsor of basic research in the United States, the Office of Science exercises oversight over national laboratories, funds university research and helps set the U.S. scientific agenda.

“Ray Orbach is a widely respected physicist,” said Berkeley Lab Director Charles Shank. “He will bring a unique combination of both scientist and leader to the job, following his great success as chancellor at UC Riverside. Ray will contribute an important science perspective to the Department of Energy and to our representatives in Washington.”

An internationally-known theoretical physicist and a professor at Riverside, Orbach, 67, was appointed chancellor in March 1992. He joined UCR following a 29-year career at UCLA.

Orbach’s research focused on solid-state physics, particularly in the field of fractal studies. He received his bachelor’s degree from the California Institute of Technology and a Ph.D. from UC Berkeley. He was named a full professor at UCLA in 1966 following a postdoctoral fellowship at Oxford University and a position as assistant professor at Harvard.

“This is an extraordinary opportunity to help my country achieve at the highest scientific levels,” said Orbach. “I am committed with all of my heart to this aggressive program furthering the nation’s scientific endeavors.”

Orbach’s honors include Sloan, Guggenheim and National Science Foundation fellowships and visiting professorships in France, the Netherlands and Israel. 

Upon Senate confirmation, Orbach will replace interim director James F. Decker, who has served since Jan. 20. During the confirmation period, Orbach will continue as chancellor, although much of the day-to-day operations will be vested with Executive Vice Chancellor David H. Warren. UC President Richard C. Atkinson plans to appoint Warren acting chancellor to serve until a permanent chancellor is seated.

Livermore Director to Step Down in 2002

C. Bruce Tarter, the director of the Lawrence Livermore National Laboratory, announced on Dec. 7 his intention to leave his post as lab director next year, seven years after having been named to that position.

“Exactly seven years ago, I began my official tenure as lab director,” he said. “We’ve accomplished a great deal during this time, and the laboratory is in excellent shape. I believe that today’s anniversary is an appropriate time to start the transition to my successor.”

Livermore Lab’s accomplishments during Tarter’s tenure include the current construction of the National Ignition Facility, the development of Livermore as a principal institution in the nation’s Stockpile Stewardship Program, the Human Genome Project, and the partnership with the semiconductor industry on extreme ultraviolet technology. Under Tarter’s guidance, the laboratory has focused on nonproliferation, arms control and international security.

“The country owes a great deal to Bruce Tarter,” said DOE Secretary Spencer Abraham. “For more than 30 years, Dr. Tarter has worked to make Lawrence Livermore National Laboratory one of the nation’s leading research institutions, first as a scientist and then as a manager.”

A theoretical physicist, Tarter spent most of his career (since 1967) at Livermore. He received his bachelor’s in physics from the Massachusetts Institute of Technology and a Ph.D from Cornell University. Prior to his selection as director of LLNL, Tarter served as deputy director and acting director.

UC President Richard C. Atkinson called the announcement “a decision I have accepted with regret,” and said he will immediately appoint a committee to begin the search for Tarter’s  successor. — Monica Friedlande

New APS Fellows

Six Berkeley Lab physicists have been elected Fellows of the American Physical Society — an honor confirred on less than 1 percent of the APS membership. They are:

Ali Belkacem of Chemical Sciences for contributions “to the study of charge changing mechanisms involving high energy, relativistic, highly charged ions leading to the discovery of new atomic processes involving the negative energy continuum.”

Ashok Gadgil of EETD for his “work modeling air and pollutant transport inside buildings, analyzing energy issues in developing countries, and developing UV Waterworks.” 

Carl Haber of the Physics Division for the application of silicon strip detectors to hadron collider experiments, “thereby opening new paths to B-hadron physics and permitting efficient identification of b-quark jets.”

Wim Pieter Leemans of AFRD “for pioneering experiments on the interaction of relativistic electron beams, lasers and plasmas, including femtosecond x-ray generation using Thomson scattering, plasma lens focusing, laser-plasma accelerators and advanced diagnostic techniques.”

Natalie Ann Roe of the Physics Division for “her leadership in the design and construction of the BaBar silicon vertex detector, and her studies of BB mixing, oscillations, and CP violation in B meson decays.”

Howard Henry Wieman of Nuclear Science “for the development of the time projection chamber into an essential tool for the study of relativistic heavy ion collisions.”

Solved: The Elegant Architecture
of a Cell-Membrane Water Channel

By Paul Preuss

Biophysicist Bing Jap has led a team from the Life Sciences Division in determining the structure of one of the basic members of the cell-membrane water-channel family, a protein called aquaporin 1 (AQP1). The structure — solved to a resolution of 2.2 angstroms (22 billionths of a meter) — reveals the elegantly simple means by which AQP1 can transport water through the cell membrane at a high rate while effectively blocking everything else, even individual protons, the nuclei of hydrogen atoms.

The team’s first accomplishment was the difficult and painstaking crystallization of the membrane protein, whose crystal structure was then solved from x-ray diffraction at Beamline 5.0.2 of the Advanced Light Source. Their report appeared this week in Nature.

In almost all cells, from bacteria to those found in a variety of human tissues, pores embedded in cell membranes transport water rapidly into or out of the cell. Body temperature, digestion, reproduction, fluid pressure in the eye, and water conservation in the kidney are only a few of the processes in humans that depend on the proper functioning of cellular water channels.

“Membrane proteins are a very large class of proteins; some 30 percent of the genes in the human genome code for them. But they are notoriously difficult to crystallize, and only a few structures have been solved at very high resolution,” Jap says.

Electron-microscope crystallography can use very small crystals, and the structure of AQP1 had previously been solved to a resolution of about 4 angsrtoms using this technique. At that resolution it was impossible to see individual water molecules, however, so vital features were left out or mistakenly characterized.

Jap and his colleagues crystallized AQP1, closely similar to that in human and other cells, from bovine red blood cells. They liberated enough protein from “gallons of blood” to make .2-millimeter crystals, suitable for x-ray crystallography at the ALS

“AQP1 is interesting because it is so specific for water,” says Jap. “The key question was how it achieves this specificity. Theorists had come up with lots of ideas, but before we saw the structure in high resolution, nobody knew how it was accomplished.”

Architecturally, AQP1 is an assembly of four units, each with three major structural features: each has an entrance, or “vestibule,” on the outside of the cell envelope, which is connected to a similar vestibule inside the cell by a long, narrow pore.

“The secret of AQP1’s specificity is two-fold: it selects for size and for chemical nature,” Jap says. “There is a very narrow constriction in the pore, which admits no molecule bigger than water. To keep out molecules smaller than water there is also a chemical filter, formed by the specific orientation and distribution of the amino acid residues lining the pore.” Molecules attempting to enter the channel are bound to water molecules that are stripped away in the pore; charged species are therefore left with net electrical charge. “The filter strongly rejects charged molecules or ions, even as small as single protons,” Jap explains.

The unique distribution of amino acid residues along the pore wall also accounts for the channel’s ability to move water quickly, explains Peter Wa-lian, a member of the team that solved the structure. “It’s a schizophrenic environment, half hydrophilic and half hydrophobic” — half water-loving and half water-fearing. “Water molecules readily get in because of the hydrophilic sites, but the hydrophobic regions prevent them from binding too frequently.”

Thus water and only water flows freely in and out of the cell through AQP1’s pores, the direction of flow depending only on the change in relative pressure inside and outside the cell. “It’s a beautiful mechanism,” Walian remarks. “It’s remarkable that nobody thought of it before now.”

“This is what structural biology is for,” Jap says. “It shows us how extremely simple nature’s solutions can be.”

“Structural basis of water specific transport through AQP1 water channel,” by Haixin Sui, Bong-Gyoon Han, John K. Lee, Peter Walian, and Bing K. Jap, appeared in the Dec. 20, 2001 issue of Nature. 

In Memoriam: Gil Shapiro

Gil Shapiro (center) is pictured at the Bevatron in 1963 with Nobel laureate Owen Chamberlain (left) and Carson Jeffries, members of the Polarized Proton Target team.

Gilbert “Gil” Shapiro, a veteran of Berkeley Lab’s Physics Division for more than 40 years, as well as a popular UC Berkeley professor and author of an acclaimed book on serendipitous scientific discoveries, has died. He passed away in his home on Dec. 5, succumbing to a battle with cancer that lasted more than two years. He was 67 years old.

“We’ll all miss Gil very much,” said Jim Siegrist, director of the Physics Division. “He was a great colleague who worked well with the students and postdocs.”

Shapiro was born in Phi-ladelphia on March 17, 1934, the son of a pharmacist father. For his thirteenth birthday his parents gave him a membership in the Franklin Institute, which in 1947 was one of the few places in town with a television set.

“It was great because I could go there and watch baseball games,” he once said. He became sufficiently interested in the Institute’s science exhibits to attend Central High School, Philadelphia’s science academy. There he won a National Science Foundation scholarship that enabled him to attend the University of Pennsylvania, where he earned his B.S. in physics.

Shapiro earned his Ph.D. in phys-ics from the University of Columbia. While there he met Harriet Lerman, a student at nearby Hunter College, whom he married in 1958. Shapiro joined the scientific staff of this laboratory in 1961 and became a faculty member two years later.

At the Lab, Shapiro was part of the renowned Segre-Chamberlain Group (named for its Nobel laureate leaders Emilio Segre and Owen Chamberlain) where, among other things, he helped develop the first polarized targets for use in high-energy physics experiments. He would contribute to a number of significant projects, including the Time Projection Chamber.

“Gil was not flamboyant, but he would quietly understand what was going on and find the solutions that would enable us to do the experiments,” said long-time collaborator and fellow Segre-Chamberlain group member Herb Steiner. “Gil did not know how to say no. He was always willing to pitch in to get the job done. He had a deep interest in physics and was a fine mentor to our students.”

In the 1970’s he joined Steiner, Chamberlain and others to explore various aspects of the interactions of high-energy nuclei at the Lab’s now defunct Bevatron. More recently, he was part of an LBNL-SLAC collaboration that tested the Standard Model through a high-sensitivity study of electroweak interactions. In another collaboration with Hank Crawford of the Nuclear Science Division, he investigated the feasibility of using neutrinos to map subsurface densities.

In addition to his research, Shapiro was perhaps best known on campus for his lecture formally known as “A Descriptive Introduction to Physics” but which he called “Physics for Football Players.” These lectures led to his writing a popular textbook, Physics without Math. The success of this book led to a second book entitled A Skeleton in the Darkroom, which described the element of chance behind of a number of famous scientific discoveries.

Shapiro is survived by his wife Harriet Shapiro, three children (James Shapiro, Dinah Shapiro and Susan Gross), and two grandchildren.

In keeping with Shapiro’s wishes, no services were held for him. Contributions may be sent to the U.C. Regents, the Gilbert Shapiro Fund, and mailed to the Department of Physics, University of California, Berkeley, 366 LeConte Hall #7300, Berkeley, CA 94720. — Lynn Yarris

Thanks for Sharing

Still time to donate to SHARES

A total of $77,768 was donated by 194 Lab employees to assist various nonprofit agencies and organizations as part of Berkeley Lab’s annual SHARES community giving campaign.

“The generosity of our employees demonstrates a real commitment to our neighbors and friends,” said Karen Ramorino, Operations HR center manager and one of this year’s SHARES coordinators. “The range of charitable organizations — especially those focused on science education — that received our charitable donations ensures that our giving will be felt throughout the community.”

Ramorino also reminded those who still wish to donate to SHARES that they may still submit donations to the Payroll Office until the end of tax year 2001. SHARES forms may be requested via e-mail from

Said Ramorino, “On behalf of all the agencies and programs that will benefit from these contributions, thanks to all who participated.” — Lisa Gonzales

Bulletin Board

Happy Holidays

Today is the last work day before the Lab officially shuts down for the holiday break, which lasts through Jan. 1, 2002. Keep in mind that the shutdown offers a significant opportunity for energy cost savings, provided employees shut down lights and equipment while away from the Lab.

A minimum work force will continue to function, including staff in Plant Operations and Maintenance, safety personnel (Fire Department, Environmental Protection, Radiation Assessment), and staff in animal care and the Mail Room. All employees who work during the shutdown period must have advance approval by their division director. 

The Currents staff wishes everyone a very happy holiday.

Fidelity is Back with Planning Sessions for Retirement Investment

Fidelity Investments is returning to Berkeley Lab to advise employees how to plan for their retirement and make the most out of their long-term investments.

The 45-minute personal sessions with a Fidelity Investments representative will be offered on Jan. 9, Feb. 13, and March 13, and will be held in the conference room in Bldg. 65A.

Appointments can be arranged by calling the Fidelity Central Reservation System at 1-800-642-7131.

Employee Activities Association Seeks Nominations

The deadline for submitting nominations for the Employee Activities Association Advisory Panel has been extended to Friday, Jan. 11. Three positions are open, subject to labwide election: a representative for the recreation group, one for the cultural group, and a member at large.

The EAA is an employee-administered group that is recognized and supported by the Laboratory to promote labwide recreational, cultural, educational, and social activities. Guidance and leadership of EAA activities are provided by the Activities Advisory Panel and the activities coordinator in the Human Resources Department.

To place your name in nomination, e-mail eaacoordinator@ with your name, mail stop, and current position and division, and include a brief statement (100 words or less) about yourself, committees you have served on, and why you are interested in serving.

Rate Increase for UPS and FedEx

Effective Jan. 7, both the United Parcel Service and Federal Express will increase their rates. UPS will have an average increase of 3.5 percent for its ground service and 4 percent for overnight and two-day express service. Its residential surcharge will increase by 5 cents to $1.10.

FedEx rates will go up by an average of 3.5 percent for air and ground shipments. FedEx is maintaining its 1.25 percent fuel surcharge on ground deliveries and its variable surcharge on air shipments, expected to be 2 percent in December. The increase also includes a residential surcharge of $1.35 per package in FedEx ground, a 5 cent increase. The FedEx Home delivery surcharge to residences will increase 5 cents to $1.10.

Shuttle Bus Change of Schedule Today

Please note the following schedule changes to the Lab shuttle bus service for Friday, Dec. 21, the last work day before the holiday shutdown.

  • The last offsite bus will depart Building 65 at 6:10 p.m.
  • The last onsite bus will depart at 6:10 p.m.
  • The last Strawberry bus will depart the Hearst Mining Circle at the regularly scheduled time of 5:40 p.m.

The last Rockridge bus will depart Building 65 at the regularly scheduled time of 6:10 p.m., and the Building 937 express bus will also operate on the regular schedule.

No bus service will be offered during the holiday break, Dec. 24 through Jan. 1, 2002. Regular service will resume on Jan. 2. For more information contact Tammy Brown at X4165.

Course on Unix Security on Jan. 2

Unix system administrators and programmers are encouraged to attend a free, full-day course on security in Unix systems on Tuesday, Jan. 22, 2002. Sponsored by the Lab’s Computer Protection Program, the course will cover:

  • Security-related vulnerabilities
  • Physical security
  • File protection
  • System and network protection
  • Account security
  • Logging
  • Special security needs in different flavors of Unix
  • Useful tools (ssh, sudo, tcpdump, Tripwire, Crack, Fix-Modes, etc.)

The course will be held in the 943-238 conference room of the Oakland Scientific Facility (19th Street BART station) from 9 a.m. to 5 p.m. The instructors will be Jim Mellander and Gene Schultz. Space is limited to 65 attendees, and registration will be accepted on a first-come, first served basis. To register, send e-mail to and

Higher Tax Deduction Next Year for Commuter Incentive Program

The Benefits Office has announced that effective Jan. 1, the Commuter Incentive Program (CIP) tax-deferred deduction limit will increase from $65 to $100 per month. This program makes it possible for employees to use a pre-tax payroll deduction for public transportation expenses such transit passes and vanpooling costs. All employees on Lab payroll are eligible for this incentive except graduate student research assistants, student assistants and guests. The $100 pretax deduction will apply to all federal and state income tax laws.

Everyone currently enrolled in the CIP program will be automatically switched over to the new deduction limit. Employees interested in enrolling in the CIP may do so by contacting Maki Tabata at X7572 or by Jan. 12.

Two transportation packages are available to employees:

1. The Public Transit Option Package offers choices such as Bart tickets for $45; a 31-day AC Transit pass for $49; two half-monthly BART Plus tickets ($56 to $122 range); and four AC Transit ticket booklets (10 tickets each) at $46 per booklet. (For transit information, look up the BART and AC transit websites at and

Application forms for the Public Transit Option Package payroll deductions can be downloaded off the Site Access web site at or picked up from the office in Building 65 (lower level).

Once enrolled in the program, employees may pick up their BART/AC Transit tickets from the following locations:

  • the Berkeley Trip Office, 2033 Center Street
  • the Berkeley Trip Satellite Office, 2543 Channing Street
  • the Berkeley Tripmobile, which comes to the Lab cafeteria on the first Monday of every month.

2. A vanpool option is available to employees who commute at least 20 miles one way. Offered by Berkeley Lab in conjunction with Enterprise Vanpool, this program offers access to vehicles with various seating choices, a full insurance program, full maintenance, 24-hour roadside assistance, replacement vans, and a variety of lease options. Payment for the vanpool can be made through payroll deduction (pre- or post-tax.) For more information visit the Enterprise website at or contact Maki Tabata at X7572,


General Interest




For biweekly-paid employees without electronic deposit, 10 a.m. to 12 p.m., Bldg. 69-102


For monthly employees without electronic deposit, 10 a.m. to 12 p.m., Bldg. 69-102


Oakland Scientific Facility, Rm. 943-238, 9 a.m. - 5 p.m.


Starts at 8:00 a.m., Bldg. 50 auditorium


12 p.m., Bldg. 50 auditorium

Send us your announcements

Announcements for the General Calendar and Bulletin Board page may be sent to Seminar & Lectures items may be mailed to currents_ You may also fax items to X6641 or mail them to Bldg. 65B. The deadline for the Jan. 11 issue is 5 p.m. Monday, Jan. 7.

Seminars & Lectures


Historical Roots of Gauge Invariance
Speaker: J. D. Jackson, Physics Division
10:30 a.m., Bldg. 71, Room 264 (Albert Ghiorso Conference Room)
Refreshments at 10:20 a.m.

Genetics of Hypercholesterolemia and Atherosclerosis: Lessons from Mendelian Disorders of Lipid Metabolism
Speaker: Helen Hobbs, McDermott Center of Human Growth and Development, University of Texas Southwestern Medical Center
4:00 p.m., Bldg 66 auditorium

EH&S Classes – January 2002







EHS 116

First Aid

8:30 – 12:00



EHS 52

Back Safety

9:00 – 11:00



EHS 60

Ergo for Computer Users

1:00 – 2:30



EHS 10

Intro to EHS & Orientation to LBNL

8:00 – 10:15



EHS 205


8:00 – 12:00



EHS 135

Earthquake Safety

10:00 – 11:00



EHS 256


1:30 – 3:00



EHS 123

Adult CPR

8:30 – 12:00



EHS 210


10:30 – 12:00



EHS 154

Building ER Team

9:00 – 11:00



EHS 280

Laser Safety

1:00 – 4:00



EHS 400

Radiation Safety/Fundamentals

9:00 – 12:00



EHS 432

Radiation Protection/Lab Safety

8:00 – 12:00



EHS 260

Basic Electric Hazard

10:00 – 11:30



EHS 283

Ultra Violet User Safety

1:30 – 2:30



EHS 275

Confined Space Hazards

9:00 – 11:30



EHS 530

Fire Extinguisher

10:00 – 11:30



EHS 274

Confined Space Retraining

1:00 – 2:00



EHS 60

Ergo for Computer Users

1:00 – 2:30



EHS 210


10:30 – 12:00



EHS 61

Ergonomics Evaluator

1:00 – 3:30



EHS 348

Chemical Hygiene

9:00 – 12:00



EHS 231

Compressed Gas

1:30 – 4:00



EHS 277

Confined Space/Permit Writer

9:00 – 10:00



EHS 330

Lead Hazards Awareness

10:00 – 11:00



EHS 735/

Biosafety/Bloodborne Pathogen

1:30 – 2:45



EHS 730

Medical/Biohazardous Waste

2:45 – 3:30



EHS 604

Hazardous Waste Generator

9:30 – 11:00



EHS 622

Radioactive/Mixed Waste Generator

11:00 – 12:00


To enroll, contact Valarie Espinoza at or enroll via the web at Preregistration is required for all courses except EHS 10. For a full, updated schedule, see

Counter-Terrorist Expert to Speak at Berkeley Lab

January 10 • Noon
Building 50 auditorium

One of the nation’s top counter-terrorism specialists, whose 29 years of work with the FBI included heading task forces involved in the infamous Ted Kaczynski UNABOM case and the hunt for fugitive Eric Rudolph in North Carolina, will tell Berkeley Lab employees “How to Catch Terrorists” in a special talk on Jan. 10.

Terry Turchie, recently named head of the Security Awareness For Employees (SAFE) program at Lawrence Livermore National Laboratory, will discuss his extensive experience in investigating both domestic and international terrorists in a noontime presentation in the Building 50 auditorium.

Attendees will also meet Bill Cleveland, new senior counter-intelligence officer for Berkeley Lab and Turchie’s predecessor for eight years at Livermore.

Turchie’s last assignment at FBI headquarters in Washington, D.C., was as deputy assistant director of the counter-terrorism division. His duties included overall managerial responsibility for FBI’s efforts to pursue international terrorists and to coordinate crisis management planning for events such as the 2001 presidential inauguration and the 2002 Winter Olympic Games. Turchie also was responsible for the FBI’s Domestic and International Terrorism programs, its weapons of mass destruction (WMD) efforts, the National Domestic Preparedness Office, and the National Infrastructure Protection Center.

From March 1999 to May 2000, Turchie was assigned to the FBI’s San Francisco field division office, where he managed all of the bureau’s foreign counterintelligence, counter-terrorism, and criminal cases in Northern California.

As a FBI supervisory special agent from 1988 to 1994, Turchie supervised FBI foreign counterintelligence efforts to neutralize hostile intelligence collection targeted at companies and U.S. government agencies in Silicon Valley. In 1990 he received the CIA’s Outstanding Intelligence Collector’s Award for his work as supervisor of an FBI squad that dismantled a nationwide hostile intelligence service’s illegal network. Turchie also supervised the FBI’s nationwide Foreign Counterintelligence Program, directed at the KGB’s Line X (Scientific and Technology Branch).

In his talk here next month, Turchie will provide employees with a better feel for terrorism, insight on how past experience can influence the present and future, and measures people can take to protect themselves and their families.

Flea Market

Autos / Supplies

‘95 VW JETTA GL, 29K mi, black, 5-spd, 4 dr, ac, sunrf, pwr steer/ locks, dual airbags, alarm, am/fm/ cass, prem sound, $9,750/bo, Steve, X6966, 204-9494

‘95 CADILLAC SEVILLE STS, exc cond, 71K miles, fully-trans warranty, 4.6L V-8, silver ext, lt grey leather int w/ wood trim, Bose prem sound w/ cd, prem wheels, heated seats, ac, all pwr, tilt, cruise, 4-wheel ABS, dual air bags, all records/maint, manual, $15,500/bo (below Blue Book), Wayne, X7685, (925) 837-2409

‘95 BMW 325 IS, black on black, 77K mi, at, sport pkg, ac, sunrf, am/fm/cass/cd, dual pwr leather seats/pwr air bags, prem wheels, recently serviced, new brakes, extra clean, well cared for in & out, $17,900/bo, June, X2916, Rich (650) 867-8828

‘93 TOYOTA TERCEL, 61K mi, 2 dr, blue, ac, am/fm/cass, man trans, exc cond, 1 owner, $4,000, Hugh/Airdri, 243-1675

‘93 TOYOTA PICK-UP, 2 wd, 5 spd, 60K mi, clean, $6,000, Aurora, 799-2323

‘91 MITSUBISHI 3000GT sportscar, racing red, 110K mi, runs great, ac, leather, a/t, pwr steer, smart/safe tires w/ sensors, constant full care, exc cond, $7,000, Jose, X4206, (925) 254-7656

‘89 PORSCHE 944, 76K mi, great engine & tranny, needs cosmetic & elec work, fun car, great fixer-upper, $4,000, Dan, 845-5822

‘87 CHEVROLET CAPRICE, 4 dr sedan, 5L V8, 80K mi, 1 owner, maint records avail, running gear in good shape, $1,500, Jim, X4507, 658-2683


ALBANY, short-term rental avail starting 12/18, studio cottage, priv bth w/ tub, kitchen, w&d in main house, priv ent, lots of storage space, fully furn, nice/secluded yard w/ fruit trees, lge deck, quiet resid neighbrhd, Talbot at Gilman, walking dist to BART, $800/mo + $800 dep + util, PhD/ postdoc/professional pref, Paola, 326-9315 cell, paolamoretto@

BERKELEY B&B, close to shuttle, 1 garden cottage rm & 1 lge rm avail now, 1 person per rm, $950/ mo or $325/wk, 2 wks min, Hellen, 527-3252, Rachel, X6262

BERKELEY, 2 furn rooms avail Jan 1 in comfortable 6 bdrm/   2 bth ‘House of Scholars’, 1425 Ward St. at Sacramento, incl house phone, w/d, common liv rm, kitchen, house computer w/ DSL access, bike storage, off-str parking, housecleaning, 2 mo min stay, $720/mo + 15% util , Rafael, 486-8153 eve, 782-4481 day, 

EMERYVILLE house avail end of Jan, 15 min drive from campus,             2 bdrm, din/liv rm, carport, some pets ok, non-smokers only, $1,500/mo, Clelia, 486-1925, 

NORTH BERKELEY, 3 bdrm/1 bth house on beautiful quiet street in Berkeley hills, panoramic views, great light, front & back yards, lge liv rm, lge kitchen w/ dining nook, firplc w/ wood pile, arched portico, close to 2 bus lines & paths, ~$2,800/mo, Steve, X2430, 525-3253

Housing Wanted

GRAD STUDENT from Germany seeks housing, 2/15 -9/20, Catholic & uncomplicated, single rm near shuttle or pub trans, priv bth & laundry, use of utinsils & small things, $550/mo, stadler@

LBNL EMPLOYEE looking for 1 bdrm/studio for long-term rent in Oakland/Berkeley/Albany, Steve, X6966

VISITING ACADEMIC COUPLE seek 1-bdrm apt from mid-Jan to early April, pref close to campus, email Keith at k.barnham@

VISITING FULBRIGHT scholar & spouse looking for housing 1/15 - 5/12, rent up to $800/mo, Barbara, X5958

Misc Items for Sale

AQUARIUM, 6-gal w/ accessories, perfect cond, $90, Tennessee, X5013

DISHWASHER, Bosch SHU33 DLX, built-in, white ext, stainless int, adj racks, super quiet, used twice, pd $650, asking $500, Ken, X7739

FREEZER: 16.1 cu ft upright, white, Wards HMG 4538-0, $135; kneeling chair, ergonomic, $35; white wood cabinet, 25"x11"x 30", $35; TV tray/table set, $20; Fisher stereo & speakers, digital tuning, dual cass, $50; Brother elec typewriter, $25; Patton compact heater, $20; Proctor-Silex wide slot toaster, $9, Ron, X4410, 276-8079

FUTON SOFA/BED, natural color, pine, 2 covers, $90, Sue, X4628, 215-0873

GAS STOVE, 4 burner, 2 yrs old, pd $700, ask $325, Art, 527-1060

KENMORE ELECTRIC DRYER, exc cond, $75; 16.5" Ford 8-lug rims & tires, set of 4, great shape, $50, Angelic or Kris, X4079, 276-6756

LATHE/MILL combo, Maximat 7, $1,000/bo, Tracy, X7668, 733-6101

LITTLE TYKES SPORTS CAR BED, twin size, blue, incl mattress board, exc cond, paid $270, asking $150/bo, Steve or Kris, (925) 256-9725

MAC G3 POWERBOOK, barely used, purchased 10/00, incl lots of software (Photoshop, Illustrator, Macromedia, Flash, Dream-weaver, Appleworks 6), bubblejet printer, zip, accessories, orig manuals, receipts, AppleCare 3-yr serv plan, pd $3,500, ask $2,000 for all; Sony camcorder, DCR-TRV6, digital, never used, purchased 10/00, incl ext serv plan (Circuit City), carrying case, accessories, manuals, orig receipts, pd $2,500, ask $1,000 for all, Christina, 643-0572, 559-8777


NANNY, f/t for 3-mo-old twins, 4-5 days per week, beg 2/1, north Berkeley/El Cerrito area, pref English speaker, possibly also German or Mandarin, Ulli or Jingly, X5347, 527 6643

VEHICLE & LAPTOP computer donation for the Flying Samaritans, a group of volunteer physicians, nurses, dentists and others who run a free clinic in Baja California, Mexico; need car, van or pickup truck to transport staff and patients (no smog check necessary) and a laptop to track medical histories; all donations are tax deductible, Drew Kemp, X5789, 524-7165 eve


SOUTH LAKE TAHOE, spacious chalet in Tyrol area, close to Heavenly, fully furn, peek of the lake from the front porch, sleeps 8+, sunny deck, pool & spa in club house, close to casinos & other attractions, $150/day + $75 one-time cleaning fee, Angela, X7712, Pat/Maria, 724-9450


ROOFING material, FREE, you pick up, Angelic or Kris, X4079, 276-6756

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 number. Ads must be submitted in writing via e-mail (, fax (X6641), or delivered/mailed to Bldg. 65B.

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

The deadline for the Jan. 11, 2002  issue is Thursday, Jan. 3.