February
21, 2003
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February
21, 2003 |
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Lab Scientists Create First
3-D Map of Protein Universe
Lab Scientists Create First 3-D Map
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This 3-D map of the protein universe shows the spacial distribution of the 500 most common protein folds as represented by spheres. The spheres reveal four distinct classes, three of which share a common area of origin while the fourth one is shown to be a late bloomer on the evolutionary flagpole. |
“Our map shows that protein folds are broadly grouped into four different classes that correspond to the four classes of protein structures defined by SCOP,” Kim says. “Some have argued that there are really only three classes of protein fold structures, but now we can mathematically prove there are four.”
Protein folds are recurring structural motifs, or “domains,” that underlie all protein architecture. Since architecture and function go hand in hand for proteins, determining what a protein’s structure looks like is a big step towards knowing what that protein does.
The 3-D map created by Kim and his colleagues is described in this week’s early edition of the Proceedings of the National Academy of Sciences. It shows the distribution in space of the 500 most common protein folds as represented by points that are spatially separated in proportion to their structural dissimilarities. The distribution of these points reveals a high level of organization in the fold structures of the protein universe and shows how these structures have evolved over time, growing increasingly larger and more complex.
“When the structure of a new protein is first solved, we can place it in the appropriate location on the map and immediately know who its neighbors are and its evolutionary history, which can help us predict what its function may be,” Kim says. “This map provides us with a conceptual framework to organize all protein structures and functions and have that information readily available in one place.”
With the completion of a “working draft” of the human genome, the big push now is to identify coding genes and the molecular and cellular functions of the proteins associated with them. The prevailing method for predicting the function of a newly discovered protein is to compare the sequence of its amino acids to the amino acid sequences of proteins whose functions have already been identified. A major problem with relying exclusively on this approach is that while proteins in different organisms may have similar structure and function, the sequences of their amino acids may be dramatically different.
“This is because protein structure and function are much more conserved through evolution than genetically based amino acid sequences,” Kim says.
Kim has been a leading advocate for grouping proteins into classes on the basis of their fold structures and using these structural similarities to help predict individual protein functions. While the protein universe may encompass as many as a trillion different kinds of proteins, most structural biologists agree there are probably only about 10,000 distinctly different types of folds.
“A smaller number of new protein folds are discovered each year despite the fact that the number of protein structures determined annually is increasing exponentially,” Kim says. “This and other observations strongly suggests that the total number of protein folds is dramatically smaller than the number of genes.”
The rationale behind this idea is that through the eons, proteins have selectively evolved into the architectural structures best suited to do their specific jobs. These structures essentially stay the same for proteins from all three kingdoms of life — bacteria, archaea and eukarya — even though the DNA sequences encoding for a specific type of protein can wildly vary from the genome of one organism to another, and sometimes even within the same organism.
In the map created by Kim and his colleagues, elongated groups of fold distributions approximately corresponding to the four SCOP structural classifications can be clearly seen. These classifications, which are based on secondary structural compositions and topology are the “alpha” helices, “beta” strands, and two mixes of helices and strands, one called “alpha plus beta” and the other “alpha slash beta.”
The Berkeley map reveals that the first three groups share a common area of origin, possibly corresponding to small primordial proteins, while the “alpha slash beta” class of proteins does not emerge until much later in time.
“It is conceivable that, of the primordial peptides, those containing fragments with high helix and/or strand propensity found their way to fold into small alpha, beta, and alpha plus beta structures,” Kim says. “The alpha slash beta fold structures do not appear until proteins of sufficient size rose through evolution and the formation of supersecondary structural units became possible.”
Since understanding the molecular functions of proteins is key to understanding cellular functions, the map developed by Kim and his colleagues holds promise for a number of areas of biology and biomedical research, including the design of more effective pharmaceutical drugs that have fewer side effects.
“This map can be used to help design a drug to act on a specific protein and to identify which other proteins with similar structures might also be affected by the drug,” Kim says.
For the next phase of this research, Kim and his colleagues plan to tap into the supercomputers at NERSC to add the rest of the some 20,000 — and counting — known protein structures to their map. They also plan to set up a website where researchers can submit for inclusion new protein structures they have solved.
Working with Kim on this protein universe mapping project were Jington Hou, Gregory Sims and Chao Zhang. The protein map was funded by grants through the National Science Foundation and the National Institutes of Health.
By Ron Kolb
Berkeley Lab has begun a major review of its small-value purchasing system, including the use of Procurement cards — or “P-cards.” Laboratory Director Charles Shank announced the need for major changes to the current procurement model in light of recent investigations of alleged financial misconduct at sister laboratories.
“We want to ensure good financial business practices, consistent with the highest expectations of the Department of Energy, the University of California, and the Congress,” said Shank. “This will mean significantly enhanced responsibility for fewer card holders, along with more effective controls.”
To develop the revamped system, Shank and Deputy Director for Operations Sally Benson have appointed a Task Force on Small Value Procurement, headed by Operations Deputy David McGraw. The group includes chief financial officer Bill Wasson, Human Resources head Randy Scott, acting deputy in Facilities Guy Bear, Sponsored Projects manager Jeff Weiner, Administrative Services head Anil More, Physical Biosciences administrator Ellen Ford, and Environment, Health and Safety business manager Carla Garbis. Significant contributions are also being made by all division business managers.
Over the next several weeks, the Laboratory is expected to seek the approval of both the DOE and UC Office of the President (UCOP) for a new P-card management system that will feature fewer P-card holders, clearer lines of accountability, expanded training, and tighter controls. UCOP, in conjunction with its three laboratories, has agreed to a new set of P-card principles that are being formalized in a new Standard Practice.
At present, the Laboratory has about 250 people using P-cards, accounting for approximately $17.6 million worth of purchases last year, which represents 8.6 percent of total procurement transaction dollars but 78.5 percent of the transaction volume.
Last April, a P-card review conducted by DOE-Oakland looked at 2,000 individual transactions. Although no fraud, abuse, waste or unallowable costs were found, many inconsistencies in documentation and training were identified. An action plan was implemented to enhance the process.
Task force lead McGraw said that, although the P-card system provides a convenient and cost-effective way to pay vendors and avoid unnecessary bureaucracy in acquiring goods and services, it has presented challenges in maintaining appropriate documentation and in managing such a distributed system.
He added that it will be important for the task force to come up with a retooled program that “is efficient, meets user needs, and provides effective stewardship of federal dollars.
“We are working the human resource issues that this change will bring. We need to make sure there is a clear policy with people’s roles and responsibilities defined,” McGraw said.
The task force will be looking at all aspects of the life cycle of small-value purchasing at the Laboratory.
By Lynn Yarris
“Since the earliest humans first noticed the stars above us, we have longed to understand the heavens,” said Raymond Orbach, director of DOE’s Office of Science, to begin his plenary address at the 2003 Annual Meeting of the American Association for the Advancement of Science (AAAS) last Friday, Feb. 14, in Denver. “We are privileged to live in an era where these fundamental questions can be addressed through experiment, theory, and computational simulations.”
In a lecture entitled “Genesis: Science and the Beginning of Time,” which ran just under an hour, Orbach, speaking before an audience estimated at nearly 1,000 AAAS attendees, discussed how modern science is beginning to understand the evolution of our universe. As part of his presentation, copies of “The History and Fate of the Universe” poster, developed by Berkeley Lab scientists (see story on page 5), were distributed to everyone in the audience.
“It has been a momentous ride from the primordial fireball to our world of today,” Orbach said. “As we learn more of the richness of our creation, there will surely be surprises ahead. Destiny will follow from the present composition of the universe — dark energy, dark matter, and ordinary matter will inexorably determine our fate.”
Throughout his talk, Orbach drew parallels between what has been learned through science and passages from the Bible, primarily the Book of Genesis. While the heavens may still in many ways be as mysterious to us as they were to those in Biblical times, he said, we have, in the last century, made substantial advancements in our understanding of our cosmic origins.
“In both astronomy and physics, the scientific focus is shifting from discovering what to understanding why,” Orbach said. “It has become apparent that many of the new frontiers for both fields lie at the astronomy-physics interface.”
Orbach proceeded to discuss eight individual epochs which “map the path” of the physical evolution of the universe from ten billionths of a trillionth of a trillionth of a trillionth of a second after the Big Bang, to the present, some 13.7 billion years later. He listed these epochs as the Superstring Era; the Grand Unified Theory Era; the Inflation Era; the Electroweak Era; the Particle Era; the Recombination Era; the Galaxy and Star Formation Era; and the Present Era.
The eight epochs, Orbach said, represent a relative time-scale of 61 orders of magnitude, a span over which occurred such momentous events as cosmic inflation, the origins of ordinary and dark matter, the birth of the first few elements, the formation of galaxies, the creation of the chemical elements as we now know them, and, the discovery of dark energy, which makes up most of the known energy in the universe today and drives the universe to an accelerated rate of expansion.
“Most of the universe is invisible to us and full of mystery,” Orbach said. “Our knowledge has evolved in discrete surprises. Thus, our very conception of the nature of our universe has changed, even over the time scale of decades.”
Many of modern science’s advances towards understanding the evolution of the universe have been led by Office of Science (SC) research programs in high energy and nuclear physics, Orbach said. These SC programs continue to be “strategically positioned to sharpen our understanding as we move forward,” he added. These programs will also, he said, “drive the development of many of the tools that will allow us to make progress in the decades to come.”
Prominent among the specific SC-backed efforts that Orbach cited as being key to advancing our understanding of our origins were the proposed SuperNova/Acceleration Probe (SNAP), which “will allow us to investigate the nature of dark energy,” and the Large Hadron Collider, now under construction at CERN, and the proposed International Linear Collider, which may “confirm that we live embedded in a higher dimensional universe or reveal new forces and particles that we cannot now imagine.”
Orbach also noted the value of the various neutrino, cosmic ray, and gravitational radiation observatories now online or in the works, the B Factory at SLAC, the Relativistic Heavy Ion Collider (RHIC) at Brookhaven, and the Tevatron at Fermilab.
“What we know is overwhelmed by what we don’t know,” Orbach said. “It is the essential optimism and, yes, fundamental arrogance of mankind that makes us believe we can discover the answers.”
Orbach’s AAAS plenary address can be read in its entirety at http://www.lbl.gov/today/2003/Feb/18-Tue/genesis-lecture1.pdf.
The months of federally-funded agencies operating on continuing resolution funds are over. Last Thursday the House and Senate passed an omnibus spending bill for FY 2003, which President Bush is expected to sign. The bill provided $20.9 billion for the U.S. Department of Energy, which is $8 million below Bush’s request but $920 million more than DOE received in FY02.
DOE’s Office of Science did reasonably well under the bill. It will be funded at $3.3 billion — about $73 million above last year’s spending levels and $26 million more than the administration sought. Also doing relatively well were DOE’s renewable and nuclear energy programs. Renewable energy funding will jump to $422 million, an increase of $26 million over last year’s appropriation and $15 million above the president’s request. Funding for nuclear energy will rise to $261.7 million, an increase of about $11 million over FY02 spending and about $12 million above the president’s request. The omnibus spending bill includes $460 million for DOE’s Yucca Mountain nuclear waste repository program, $85 million more than it received in FY02 but $130 million less than the budget request. DOE’s environmental cleanup programs, including defense and non-defense environmental management and uranium facilities maintenance, will get $7.44 billion, a slight decrease from the budget request and $310 million higher than last year’s levels. Funding for energy conservation will go down from $912.8 million to $897.6 million, about $4 million less than the administration’s request.
With FY 2003 finally dispensed with, Capitol Hill turned its attention to President Bush’s proposed budget for federal R&D spending in FY 2004. It was not a good start for the administration. Representatives of the administration, led by Office of Science and Technology Policy (OSTP) Director John Marburger, met with members of the House Science Committee last week to make their case and received critical reviews from Republicans and Democrats alike. While there was support from committee members for some proposals, such as the National Nanotechnology Initiative, there was sharp concern expressed over others, such as the virtual elimination of the Advanced Technology Program and the Manufacturing Extension Program.
There was especially sharp criticism of the proposed flat funding for DOE’s Office of Science. Said committee chairman Sherwood Boehlert (R-NY), “I understand that this is a very tight budget, but I think we should be able to invest more in basic research, particularly in the Energy Department’s Office of Science.” Marburger argued that DOE’s budget would boost funding for science programs by $55 million to $3.3 billion, including increased support for physical science research and nearly tripling the investment in new centers for nanoscale science research by “rolling off” money from the phasing down of the construction of the Spallation Neutron Source at Oak Ridge National Laboratory. — Lynn Yarris
“Today at Berkeley Lab,” the new daily e-newsletter delivering information to all employees via computers and video screens, has in its first three weeks generated a variety of comments and questions from interested readers. Below is an attempt to address the most frequently asked inquiries.
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Q: My computer doesn’t read html coding. Can you provide a text-only version of Today at Berkeley Lab?
A: Because it is a daily publication and thus labor intensive, additional conversion to a second delivery format is unfeasible. However, we hope non-html users will click on the “Today…” URL at the top of each issue, which allows users to read it using a web browser. Some users may wish to look for another way to access mail (for example, Netscape Messenger Express can access mail via the web at http://www.lbl.gov/mail). Users of Unix-Linux should be able to access the full publication by clicking on the “non-html” link, which opens up the Unix html browser. Bookmarking the URL in your browser will make it easy to access each day. More questions? The Computer Help Desk (X4357) is a good place to start.
The html format provides a professional richness and perspective that would be missing from text-only versions. Hence the decision to develop an html-based product. A majority of employees at Berkeley Lab use mail clients that can “see” html.
Q: Can I unsubscribe?
A: No. All Berkeley Lab employees with postal addresses in the lbl.gov domain are automatically signed up for the service. The required delivery to everyone stems from the newsletter’s use as a communications tool that carries mandated all-employee announcements and notices — including many of the items previously distributed as “Level One” e-mails.
Q: If I don’t have a computer or an electronic postal address, how can I see Today at Berkeley Lab?
A: Two ways. You may look up the video monitors displaying Today at Berkeley Lab on a scrolling screen, which are located in Buildings: 50 (lobby), 54 (coffee bar), 62, 84, 6 (ALS), 90, and 937 (downtown). Building 77 will have an active screen soon, and passengers waiting for the bus at Building 65 can see the program inside the kiosk. Or if you are not near one of the monitors, ask your supervisor to print out and post each day’s edition on an easily accessible bulletin board.
About 430 employees throughout the Laboratory do not have e-mail.
Q: How do I get my event or activity listed in Today at Berkeley Lab?
A: Click on the “Today …” link of the newsletter to submit items or send an e-mail to Today@lbl.gov. You can also bring the information to Building 65, the Public Affairs Department, where the Communications Office puts together the content for the newsletter.
Q: Some news stories that are hyperlinked to a complete story on the source media’s website require online registration to access them. How can I read these without registering?
A: Unfortunately, online registration is a prerequisite these days with many of the leading media outlets, such as the New York Times, the Los Angeles Times, and the Chicago Tribune. It takes only a few moments — one time — for you to get direct access to future stories on those websites. Today at Berkeley Lab will attempt, when possible, to link to versions that do not require preregistration. When a story is only available at one of those outlets, the e-newsletter will provide the link for those who wish to register and continue reading.
Q: Is Currents going to go away now that Today at Berkeley Lab has come?
A: No. Currents, the Laboratory’s longtime periodical, published biweekly throughout the year, will continue, albeit with a somewhat altered mission. While the new newsletter will focus on breaking news and events, Currents will concentrate more on features and on the news behind the news. We hope both communications tools will be complementary in their roles to keep all employees fully informed about the essential elements of this vital community.
The Communications Department is completing a program assessment process, one that included several employee focus groups both at the Laboratory and offsite. Much of the content of future publications will be directed by the responses given in these forums and through surveys. The Department appreciates the candid input provided by focus group participants.
Q: Isn’t this just extra e-mail that will result in additional storage costs on our IMAP accounts?
A: Not if you are diligent about cleaning out your files. Today at Berkeley Lab’s 12 kilobytes of information isn’t much more than the size of many Microsoft Word documents. Unless you wish to save past issues for any reason (an archive is maintained on the Laboratory web site), just make sure you delete each one, then empty your trash regularly before the monthly IMAP sweep of accounts. The storage size of the newsletter shouldn’t require any change in your normal file management habits.
Q: What if I see a video screen that’s not working?
A: Please report the problem by writing an e-mail to mailto:kiosk@lbl.gov. Technicians will attend to it right away and get the program back on line.
The inauguration of a daily electronic news service for Berkeley Lab has created an opportunity for the Laboratory’s long-time reliable information source, Currents, to reassess its contents. Now not having to be burdened with the constraints of time – Today at Berkeley Lab will handle that – Currents is free to evolve into something else. But what?
It is clear from the consensus of viewpoints gathered in a recent series of employee communications focus groups that people still want to receive and read Currents, and the present biweekly schedule seems about right. It is also clear that the "Flea Market" is an essential on most everyone’s must-read list and shouldn’t change.
But the rest is open. And the Communications Department would like to know what you, the readers, would consider most helpful and interesting as the content for Currents. Is it more science you want to know about? Or people in the news? How about management priorities? Or service programs?
Drop us a line and let us know how you feel. Send your suggestions and comments via e-mail to Monica Friedlander, editor of Currents. If your idea is incorporated into the “new” Currents, we’ll treat you to a drink at the coffee bar and put your picture in the newspaper.
All comments need to be received by March 14.
By Dan Krotz
Combine three Nobel laureates with one of the world’s brightest x-ray sources and you’re bound to get something big — or, in this case, exceedingly small. Using Berkeley Lab’s Advanced Light Source (ALS), a highly decorated team of University of Texas Southwestern Medical Center and Howard Hughes Medical Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream.
 New treatments may someday become available for those battling high cholesterol levels thanks to discoveries by scientists such as Keith Henderson (right) who helped unravel the structure of the protein thatensnares LDL. |
Knowing the structure of the protein, a cellular receptor that ensnares cholesterol-laden low-density lipoprotein (LDL), will help researchers understand how LDL receptor mutations promote dangerously high cholesterol levels in some people. And this knowledge could someday lead to treatments that target these diseases. But it all starts with the protein’s structure, and this starts with a process in which the protein is crystallized and then analyzed using light rays brighter than the sun.
“We were able to see the structure of the LDL receptor’s extracellular domain, and from this we can deduce its function,” said Keith Henderson, a physicist in Berkeley Lab’s Physical Biosciences division who helped the research team select a protein crystal most likely to yield its structural secrets. Only then could the ALS help elucidate how the LDL receptor capturescholesterol, pulls it inside a cell where it is released and metabolized, and cycles back to the cell surface to grab more cholesterol.
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Such success requires painstaking preparation. First, the LDL receptor must be crystallized in just the right way, so it best diffracts x-rays. This involves a process called crystal screening, in which a slew of promising protein crystals are evaluated to determine which has the best diffraction characteristics. In this case, the University of Texas Southwestern Medical Center team sent Henderson 60 crystals, which he evaluated using an ALS beamline that can be tuned to resonate at several frequencies.
This important step enables the beamline to be trained on an element that is specially introduced into each protein crystal. This element, a so-called anomalous scatterer, allows the collection of several data sets, each representing a unique diffraction pattern obtained as the beamline is tuned to various wavelengths around the element’s x-ray absorption edge. These data sets are combined to produce an electron density map of the crystal. It’s an elegant way to image complex proteins, provided the element is successfully embedded into the crystal — which is where Henderson’s work comes in.
“Out of the 60 crystals, we found a clear candidate, meaning we knew the anomalous scatterer had stuck and its diffraction quality was promising,” Henderson said.
Then it was back to the lab, where the team spent more than a year refining the crystal’s properties, carefully zeroing in on a specimen good enough to reveal its molecular framework under x-ray diffraction analysis.
Finally, once the crystal was perfected, the team determined the LDL receptor’s structure using data collected during the commissioning of ALS beamline 8.2.1. This beamline, part of the sector 8 superbend beamlines funded by the Howard Hughes Medical Institute, is powered by a superconducting magnet that produces photons which are nearly twice as bright at 1 angstrom as photons produced by standard bend magnets. Because the average length of a protein bond is about 1.5 angstroms, or 1.5 hundred-millionth of a centimeter, these super-bright photons are excellent sources of x-rays capable of probing the intricacies of protein molecules.
Together, the carefully selected protein crystal and the state-of-the-art beamline yielded a complete data set that was poured into powerful computer reconstruction programs. The result is the first image of the LDL receptor in three dimensions.
“It’s further confirmation that the Advanced Light Source is a world class facility,” Henderson said, adding that the six-year study also lends credence to time-consuming research that isn’t guaranteed to pan out. “It’s high-risk, high-reward science.”
The payoff is a better understanding of the molecular breakdowns that lead to high cholesterol. Normally, the portion of the LDL receptor that protrudes from a cell wall, called the extracellular domain, binds with LDL in the liver, pulls its cholesterol cargo inside the cell, and metabolizes it to replenish hormones, the cell membrane, and vitamin D. But in some people, the receptor’s extracellular domain is somehow hobbled, allowing cholesterol to accumulate in the bloodstream and contributing to life-threatening diseases such as atherosclerosis.
A common cause of this breakdown is familial hypercholesterolemia, a hereditary disease that affects about one in 500 people. Researchers have found more than 900 LDL receptor mutations in people with the disease, but they didn’t know how these mutations disrupt the receptor’s function. Now, with the blueprint of the LDL receptor in hand, they understand how mutations lead to structural changes, and how structural changes lead to high cholesterol.
“Without the receptor’s structure, we’re left with only biochemical evidence that something is wrong — high cholesterol caused by a mutation — but we’re not sure how,” Henderson said. “We’re now using the receptor’s form to learn its function.”
And with this knowledge, researchers can pursue a pharmaceutical remedy to familial hypercholesterolemia, Henderson said. The image also adds to the illustrious careers of three University of Texas Southwestern Medical Center researchers. Senior author Johann Deisenhofer, who is also a Howard Hughes Medical Institute investigator, received the 1988 Nobel Prize in chemistry for research using x-ray crystallography to reveal the three-dimensional structure of protein in cell membranes. And in 1985, Michael Brown and Joseph Goldstein shared the Nobel Prize in physiology or medicine for discoveries concerning cholesterol metabolism. The study, “Structure of the LDL receptor extracellular domain at endosomal pH,” appears in the Dec. 20, 2002 issue of Science.
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, msfriedlander@lbl.gov
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
FLEA MARKET / CALENDAR: 486-5771
fleamarket@lbl.gov /currents_calendar@lbl.gov
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DOE's Office of Science and all the national laboratories were well-represented at the exhibition for this year's annual AAAS meeting.
Shown here are Berkeley Lab science writer Paul Preuss (left), who helped staff the SC exhibit, and Berkeley Lab chemist Dale Perry, who as a newly elected AAAS fellow was at the meeting to be honored at a special forum.
The 2003 Annual Meeting of the American Association for
the Advancement of Science (AAAS) was held last Friday, Feb. 14, in Denver.
For more, see story on Page 1.
On Monday, Feb. 17, while the nation’s Eastern Seaboard congealed in a record-breaking storm that hinted, if only symbolically, at climatic crises to come, climate-modeler Inez Fung and oceanographer Jim Bishop of the Earth Sciences Division represented Berkeley Lab at an important AAAS symposium on understanding and managing the global carbon cycle.
Fung’s overview emphasized the essential role of “turnover time” in assessing how much carbon the terrestrial biosphere can store, and for how long. Deforestation, for example, happens in more than one way and with more than one set of consequences.
Citing data collected by Australian colleagues, Fung said that in a forest fire, “everything comes out right now.” Conversely, logging delays the return of carbon to the atmosphere, storing carbon in lumber. She noted that deforestation of the continental U.S. was reversed in the 20th century, and in recent decades the residence time of carbon in the country’s biosphere has lengthened, partly as a result of fire suppression.
“The question is not how much carbon can you stuff into the biosphere but how long can you keep it there,” Fung said. Yet while the country provides a more efficient carbon sink than before, the improvement can’t compensate for the 30 percent increase of carbon dioxide in the atmosphere since the beginning of the industrial revolution — most of that coming in the last half century.
 Carbon stored in trees is released into the atmosphere immediately when they burn. |
One of the questions Fung found most interesting was from an audience member who wanted to know what would happen to atmospheric carbon dioxide if all fossil fuel emissions were to stop immediately. Fung replied that it would be reduced only very slowly. As the carbon content of the atmosphere and the ocean approached equilibrium, the rate of decrease would slow even more.
Jim Bishop described his unique method of gathering the data that makes climate modeling possible, with robotic Carbon Explorer SOLO floats equipped by his group at Berkeley Lab. Launched at Ocean Station PAPA in the North Pacific, two Carbon Explorers were the first instruments ever to catch “on tape” a terrestrial dust storm fertilizing the ocean with wind-borne iron. Later, in the Southern Ocean, four floats tracked an artificial iron fertilization experiment (SOFeX) and continued measuring particulate carbon right through the Antarctic winter.
Three of the four SOFeX floats are still reporting from the far south after a year at sea. Meanwhile, as recently as Feb. 12, another two Carbon Explorers were launched in the North Pacific at Ocean Station PAPA from the Canadian Coast Guard vessel John P. Tully. These robotic floats are equipped with more sophisticated detectors that can track the sedimentation rate of particles fertilized by airborne nutrients; by measuring salinity, the relative contributions of windblown dust and freshwater run-off can be compared.
Of the well-received symposium, Bishop said, “I was glad to be able to reinforce the evidence that these little robots are capable of answering many of the questions we have about carbon in the ocean — and without breaking the bank to do it.”
Fung underscored the public policy aspect of the AAAS talks: “There’s rarely any new science presented, but going to AAAS is a necessary thing for scientists to do, in order to get out the broader educational message.” — Paul Preuss
Earlier this week Berkeley Lab rolled out Brightmail, a commercial service that uses a combination of advanced technologies and human analysis to identify junk e-mail, or SPAM.
The words “[SUSPECTED SPAM]” are now inserted in the message line of emails containing characteristics of spam. Brightmail automatically scans every message sent to an “@lbl.gov” e-mail address. Those that match the selection criteria for spam are labeled, or tagged, but not deleted.
Users can set up their system to handle these intruders in various ways. You can call out these messages for review and disposal by setting up your email preferences to either sort by subject or filter them into one folder.
To learn more about Brightmail and find out how to get the most out of this service, visit the Brightmail FAQ page on the Lab’s Computer Infrastructure Support website at http://www.lbl.gov/ITSD/CIS/citg/email/brightmail/faq.html.
By Lynn Yarris
What time did the universe begin? When did the first star appear? How long will the universe last? A colorful, graphically rich chart that illustrates and summarizes what is now known about the history and fate of the universe has been developed by scientists with Berkeley Lab’s Physics Division in collaboration with the Contemporary Physics Education Project (CPEP). More than 11,000 copies of this chart are being distributed this month through the Physics Teacher magazine to high school science teachers across the nation for field-testing with their students.
“I congratulate the physicists at Lawrence Berkeley National Laboratory who collaborated to produce this thoughtful, thorough and very engaging educational resource,” said Raymond Orbach, Director of the U.S. Department of Energy’s Office of Science, which oversees and funds DOE’s national laboratories. “The ‘History and Fate of the Universe’ poster is a wonderful example of the contributions that researchers at our national laboratories can make to science education for America’s teachers and students alike.”
“The History and Fate of the Universe” chart was first proposed about three years ago by Berkeley Lab physicists George Smoot and Michael Barnett.
“The hardest part in doing a chart like this is deciding what to include and what to exclude; the more we included the more we had to cut out,” says Smoot, who is best known for his pivotal role in the discovery of radiation ripples in the infant universe that grew into the galaxies of stars we see today.
“With field-testing, we’ll have a better idea of what works and what doesn’t work on the chart,” says Barnett who has played key roles in the development of three other charts which serve as guides to discoveries in particle physics, nuclear physics, and fusion energy and have been highly popular with teachers and students alike.
With the help of Berkeley Lab colleagues Eric Linder and Saul Perlmutter, plus Lincoln Sanders who designed the graphics and a number of other volunteers from around the world, Smoot and Barnett were able to pack plenty of information into the History and Fate of the Universe chart, covering a broad range of cosmological topics.
The centerpiece is an evolutionary timeline that takes viewers from 10-44 seconds, when the universe was much smaller than a proton, to the current era, about 14 billion years later, when the visible universe contains 4 x 1011 billion galaxies. Side panels provide short discussions on the birth, inflation and expansion of the universe, the cosmic microwave background, redshifts of distant supernovas, dark energy, dark matter, and what appears to be the ultimate fate of the universe based on what is now known.
“The History and Fate of the Universe” chart can be viewed on the Internet at http://universeadventure.org/. This website will be providing supplemental material including a glossary of terms, and an article to accompany the chart’s publication written by Lawrence M. Krauss, the award-winning Ambrose Swasey Professor of Physics and Professor of Astronomy at Case Western Reserve University in Ohio. Krauss is the author of the national best-seller The Physics of Star Trek and several other well-received books on astrophysics and cosmology.
“New observations of the ground, in the air, and in space, combined with exciting new theoretical insights have, over the past decade or two, literally revolutionized our picture of the universe in which live,” writes Krauss. “Ideas that were essentially pure speculation 20 years ago now rest firmly on the bedrock of experiment. At the same time, many new questions have arisen and some once firmly held notions about the future of the universe have been displaced.”
Development of “The History and Fate of the Universe” chart was funded by the U.S. Department of Energy and the National Science Foundation. Teachers wishing to participate in the field-testing of the chart may visit CPEP’s website at http://cpepweb.org/fieldtest.
Nomination Deadline: March 10
The Runaround …the annual picnic …holiday parties …softball, plus ballroom dancing, archery, the Mac Users Group, the Crafts Fair. Each of these activities enriches your experience as part of the Berkeley Lab community. But none of these activities would be possible without the support of the Employees Activities Association (EAA).
Through March 10, the EAA is accepting nominations for three positions on its Advisory Panel: a recreational representative, a cultural representative and a member at large. Serving on the EAA Panel offers employees an opportunity to have an impact on the success of its current clubs and events, as well as a chance to suggest and be involved in the development of new groups and activities.
The EAA Advisory Panel has five members elected by Laboratory employees to two and three-year terms. The heads of the Human Resources Department and the Work Force Diversity Office serve as ex-officio members. The Advisory Panel and the activities coordinator in the Human Resources Department provide guidance and leadership to EAA activities.
If you are interested, send an e-mail to mailto:eaacoordinator@lbl.gov. Include your name, mailstop, current position and division, the position you would like to be considered for, and a brief statement of 100 words or less about yourself (committees or panels you have served on, why you are interested in serving on the panel, etc.). The submission deadline is Monday, March 10.
For a complete list of clubs, upcoming events, and information about the Employee Activities Association, see http://www.lbl.gov/Workplace/HumanResources/EAA/. For other questions send e-mail to mailto:eaacoordinator@lbl.gov.
The EAA is an employee-administered association that is recognized and supported by the Laboratory to promote and support Laboratory-wide institutional, recreational, cultural, educational, and social activities for the benefit of all employees.
Dr. Peter Lichty, Berkeley Lab’s director of Health Services, has been named group leader for a new integrated Health and Safety function in the Environment, Health and Safety Division. In this role, Lichty will oversee all medical, industrial hygiene, occupational safety and other operations functions under EH&S Director David McGraw. Assisting Lichty as deputy will be Paul Blodgett, group leader for Industrial Hygiene. Don Van Acker will continue as group leader of Occupational Safety in the new group.
Raymond and Beverly Sackler Lecture, UC Berkeley
Riccardo Giaconni of Johns Hopkins University will be the featured speaker for this special lecture, to be held on campus on Tuesday, March 11 at 5:45 p.m. in 1 Pimental Hall.
The speaker will focus on the scientific and technological developments in the study of celestial sources in their x-ray light. This powerful tool allows for sophisticated observations and techniques for discovery of new aspects of the universe.
Bay Area Dates: March 3-6
Current and former U.S. Department of Energy workers and contractors interested in filing claims for medical assistance for illnesses due to radiation, silica or beryllium exposure at work will have an opportunity next month to get their questions answered.
A joint DOE–U.S. Department of Labor (DOL) Traveling Resource Center will return to two locations in the San Francisco Bay Area during the week of March 3. Representatives will be on hand to assist individuals with claims under the Energy Employees Occupational Illness Compensation Program Act. The Resource Center will return in May at a location and date to be determined.
Workers who need help filling out claim forms can schedule appointments at the Traveling Resource Center by calling toll-free, (866) 697-0841, or dropping in during office hours (8:30 a.m. to 6 p.m.) at one of the following locations: March 3-6 at the Four Points Hotel by Sheraton, 5115 Hopyard Road, Pleasanton; and March 5-6 at the Woodfin Suite Hotel, 5800 Shellmound Street, Emeryville.
The Act became effective on July 31, 2001 and provides two different types of assistance. Eligibility and benefits differ in each program. The DOL administers the program that provides a lump sum of up to $150,000 and payment of future medical expenses to current and former DOE employees and DOE contractor employees who suffer from specific diseases — radiogenic cancers, beryllium disease and chronic silicosis. Qualified survivors of covered employees, including adult children, are also eligible for benefits.
The DOE program helps DOE contractor employees apply for state workers’ compensation benefits provided that an independent physician’s panel determines that the worker sustained an illness caused by exposure to a toxic substance at a DOE facility. Benefits for successful claimants vary from state to state, but are generally a portion of lost wages plus reimbursement of medical costs.
Several facilities in this area have been designated by DOE as locations for prospective worker claims: Berkeley Lab, Lawrence Livermore and Sandia National Laboratories, and the Stanford Linear Accelerator Center. Additionally, 17 beryllium vendor facilities were recently added to the covered facilities list. These include City Tool and Die Manufacturing in Santa Clara, C.L. Hann Industries in San Jose, EDM Exotics in Hayward, Electrofusion and Poltech Precision in Fremont, Hafer Tool in Oakland, Hexcel Products in Berkeley, Jerry Carroll Machining in San Carlos, Pleasanton Tool and Manufacturing, Robin Materials in Mountain View, Ron Witherspoon, Inc., in Campbell, and Tapemation in Scotts Valley.
UC’s Office of the President programs has announced that the University of California has finalized an agreement with World Savings to make available a variety of home financing products to all University employees in California and New Mexico. In addition to standard secondary market loan products, World Savings has its own internal portfolio variable rate loan product that provides a wide range of options regarding repayment. World Savings has committed to offer the following home loan discounts to UC faculty and staff:
For more information call World Savings’ exclusive UC toll free number, 1-866-UC-LOAN8 (1-866-825-6268).
This program replaces a previous one between UC and North American Mortgage Company.
‘98 MAZDA 626 LX, 95K mi, mt, ac, all pwr, alarm, am/fm/cd, tilt whl, cruise, sliding sunrf, alloy wheels, exc cond, clean, recent 93K mi major service, $6,300/bo, (925) 422-6013 day, 595-1755 eve
‘94 TOYOTA PASEO Coupe 2D, 5 spd, teal, 82K mi, ac, airbag, cd/radio, exc cond, $4,800, Sven, X4053, 548-4484
‘94 MAZDA MPV, roof rack, fully loaded, taupe, am/fm/ cass, good family vehicle, $5,250, Mona, 704-0538.
‘91 VW JETTA, 92K mi, sunrf, runs very well, good mileage, new tires & brakes, cd/radio, $2,500, Greg, 527-4757
‘90 MAZDA MIATA convertible, blue w/ blk int, 58K mi, 5 spd, exc cond, great commute car, $4,800/ bo, Cathy, X6995, (707) 864-9451
‘87 VW JETTA, 4 dr, man trans, runs great, reg thru 1/04, $1200/bo, Maya, X4493
BERKELEY HILLS, perf for visiting scholars, by wk/ mo, quiet furn suite, sleeps up to 3 in 2 bdrm/1 bth, eleg & spacious, bay views, dsl/cable, microwv, walk to UCB, Denyse, 848-1830, dchew1@mindspring.com
BERKELEY, resid community of UC scientists, Lab personnel & grad students, Hearst near University & San Pablo, close to pub trans & bike path, studio townhouses w/ decks, hardwd floors, skylights, dw, ac, intercom, sec, $895 unit avail 6-7/03, longer term avail, Alan, 666-1150, editeur@earthlink.net
CENTRAL BERKELEY, nice furn rms, kitchen, laundry, TV, DSL, hardwd floors, linens, dishes, walk to pub trans/shops, $950/ mo incl util, $350/wk, Jin or Paul, 845-5959, jin. young@ juno.com, Paul X7363 (REPEAT)
KENSINGTON, 1 yr new white stucco 1 bdrm cottage with old world charm, lge liv rm, morning sun, bay view from terrace, spanish tile entry, high ceilings, vintage light fixtures, oak flrs, tile bath, bdrm w/ 2 closets, w&d, storage, galley kitchen, priv setting w/ birds & deer, avail now, yr lease pref but neg, $1,350/mo, Gawain, 527-9000, 206-8855, mailto:kessner@hotmail.com
KENSINGTON furn 3 bdrm house avail for visiting scholar, view, patio, very quiet, $1500/mo, Ruth, 526-2007, 526-6730
MORAGA furn modern 2 bdrm/1 bth townhouse w/ carport in beautiful setting, 20 min from campus, avail 3/1, $1,750/mo, Anna, 914-2842, annaib@uclink. berkeley.edu
NORTH BERKELEY, avail Sundays thru Tursdays, quiet room w/ deck, view of GG bridge in brwn shingle home, priv bth, street parking, 1 block to Solano Ave/pub trans, $62/night or $270/five nights, cont breakfast incl, 524-4171, mjbarrett11@ aol.com
NORTH BERKELEY, perf for vis scholars, by wk/mo, furn lge sunny 1 bdrm apt, walk to campus & shuttle, many amenities, priv garden, gated carport, avail after 8/1, Geoff, gfchew@ mindspring.com, 848-1830
SOUTH BERKELEY, avail now, bright & sunny, very quiet, 2 bdrm upstairs apt in duplex, Grant near Stuart, recent upgrad, newer appliances, w&d hookup, large priv deck, close to BART, Berkeley Bowl, park & pub trans, no smoking/ pets, mo-mo or lease, $1,400/mo + dep, Hisao, X4342, 843-8933 eves
VISITING SCHOLAR seeks 1 bdrm apt in Berkeley/Albany/El Cerritto, hrdwd flrs, w/d hkup, part furn, needed 3/03, Choi, X5553, dkchoi@moak.chonbuk.ac.kr
VISITING SCIENTIST seeks room near Lab or pub trans, start 3/14/ for 30 days, non-smoking/ drinking, no guests, very quiet, $400-500 range, Tom, X7022, adzergatch@ mtu-net.ru
VISITING SCIENTIST, female, seeks 1 bdrm apt to share or house sitting arrangement, near public trans, 6 mos or longer, Guy, X4703
17" VIEWSONIC E773 CRT monitor in very good cond, barely used, max res 1280x1024 @ 66Hz, $60, George, X7252, 234-5250
BABY & TODDLER ITEMS, evenflow crib, evenflow infant car seat, greco stroller, greco toddler car seat & toys, all in exc cond, prices neg, Negest, 205-4883
DOUBLE BED, antique tiger oak, c. 1910, carved tall headboard, roll top footboard, new matt avail, $1,000; antique 5-drawer oak dresser, $700, Ken, X7739, 482-3331
GATEWAY COMPUTER, 433 MHz Celeron processor, 192 MB memory, 15” monitor, DVD player, surround sound speakers, Windows millennium OS, multifunctn keyboard w/ mouse, Epson Stylus 440 Inkjet printer, add’l software & acc incl, $300/bo, Mary, 638-1451 lv msg
HEALTHWAY AIR FILTER 10100, enhanced media filtration, 12"x12"x22", 17#, eggplant, filters down to 0.15 microns, cleans 150 sq ft 6x per hr, used about 1 yr, $100/bo, Harvard, X5742, 526-5347
IPAQ H3850, new in box, 64k color, 64MB RAM, Li-Ion polymer battery, cradle, ac adapter, software cd, $300, Matt, X6347, (925) 689-3611
POWER MAC 5400/120, 15" monitor all-in-one, G3 400Mhz upgraded, 1.6G HD, 134M RAM, $170; ext drives Zip100, $10, and Jaz1G, $15, Nobuo, X5662
RHODE GEAR LIMO BIKE SEAT, brand new, incl Blackburn EX-1 rack, $80; Kenmore electric dryer, purchased new 1 year ago, exc cond, 5 temps, moisture sensing, wrinkle guard, quiet pack, lge cap, $250, Tom, X5319
SOFA & LOVESEAT, tan, exc cond, $200/bo; white lge capacity w&d, $200/ bo, Harsh, X5575, (925) 210-1883
WALL SHELF DESK, 2, white, $20/ea or b/o, Al, X5906, (925) 672-2716
SWING SET, Sears T-shaped set, Al, X5906, (925) 672-2716
TWO CATS: a 4-yr-old inside cat w/ white hair, 2 diff color eyes, deaf; and a black 1 yr old; both are spayed females, Michael, X4780, (925) 930-0672
PARIS, FRANCE, near Eiffel Tower, furn eleg, sunny 2 bdrm apt, avail year round by wk/mo, Geoff, 848-1830
SOUTH LAKE TAHOE, spacious chalet in Tyrol area, close to Heavenly, fully furn, peek of the lake from front porch, sleeps 8+, sunny deck, pool & spa in club house, close to casinos/attractions, $155/ night, Angela, X7712, Pat/Maria, 724-9450
SPRING BREAK tickets to Rosarito for sale starting at $229, package incl 4 nights at a hotel, 3 all you can eat meals daily, and access to all the parties w/ thousands of spring-breakers from colleges around the country, space limited, Tony, X2672, 220-1003
TAHOE KEYS at S. Lake Tahoe, 3 bdrm house, 2-1/2 ba, fenced yard, quiet, sunny, skiing nearby, prvt dock, great view, $195/night, 2 night min, Bob, (925) 376-2211
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:fleamarket@ lbl.gov), 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 7 issue is Thursday, Feb. 27.
No, you’re not imagining it. Something peculiar happened to Currents — and no, it’s not an accident. The Flea Market has moved to the inside, some of the front page news stories are jumping to the back for easier reading, and yes, the calendars are gone.
Since most readers have much easier access now to the daily calendars of events via Today at Berkeley Lab, running them here would be redundant, as well as less current than the daily postings in the e-newsletter.
The Communications Department hopes that the new format and the combined reach of these two publications will better serve Lab community. But we welcome your feedback and will take your comments into consideration.
Please send your comments to Currents editor Monica Friedlander at msfriedlander@lbl.gov. Thank you.
|
Date |
Course |
|
Time |
Building |
||
|
3/4 |
EHS 60 |
Ergonomics for Computer Users |
10:30 – 12:00 |
51-201 |
||
|
3/5 |
EHS 256 |
Lockout/Tagout |
1:00 – 2:30 |
51-201 |
||
|
3/5 |
EHS 210 |
Hoist Safety |
3:00 – 4:30 |
51-201 |
||
|
3/6 |
EHS 116 |
First Aid Safety |
9:00 – 12:00 |
48-109 |
||
|
3/10 |
EHS 535 |
Hot Work Permit Training |
11:00 – 12:00 |
51-201 |
||
|
3/11 |
EHS 10 |
Introduction to ES&H at LBNL* |
8:00 – 10:15 |
50-Aud |
||
|
3/12 |
EHS 135 |
Earthquake/Wildland Fire Safety |
10:30 – 12:00 |
48-109 |
||
|
3/12 |
EHS 125 |
Infant/Child CPR |
6:00 – 8:00 |
48-109 |
||
|
3/13 |
EHS 123 |
Adult Cardio-Pulmonary Resuscitation |
9:00 – 11:00 |
48-109 |
||
|
3/18 |
EHS 275 |
Confined Space Hazards |
8:30 – 11:00 |
51-201 |
||
|
3/18 |
EHS 274 |
Confined Space-Retraining |
11:00 – 12:00 |
51-201 |
||
|
3/18 |
EHS 330 |
Lead Hazards Awareness |
1:00 – 2:00 |
51-201 |
||
|
3/19 |
EHS 280 |
Laser Safety |
9:00 – 12:00 |
51-201 |
||
|
3/19 |
EHS 154 |
Building Emergency Team Training |
1:00 – 3:00 |
48-109 |
||
|
3/19 |
EHS 60 |
Ergonomics for Computer Users |
1:30 – 3:00 |
51-201 |
||
|
3/20 |
EHS 530 |
Fire Extinguisher |
9:00 – 11:00 |
48-109 |
||
|
3/20 |
EHS 20 |
ES&H for Supervisors |
9:00 – 11:00 |
51-201 |
||
|
3/25 |
EHS 604 |
Hazardous Waste Generator |
9:30 – 11:00 |
51-201 |
||
|
3/25 |
EHS 622 |
Radioactive & Mixed Waste Generator |
11:00 – 12:00 |
51-201 |
||
|
Biosafety/Bloodborne Pathogen |
1:30 – 2:45 |
51-201 |
||||
|
3/26 |
EHS 260 |
Basic Electric Hazard Awareness |
1:00 – 2:30 |
51-201 |
||
|
3/27 |
EHS 400 |
Radiation Protection-Fundamentals |
9:00 – 12:00 |
51-201 |
||
|
3/28 |
EHS 432 |
Radiation Protection-Lab Safety |
8:00 – 12:30 |
51-201 |
||
* Includes EHS 392/405, followed by the orientation.
To enroll, contact Valarie Espinoza-Ross at VMEspinoza-Ross@lbl.gov or enroll via the web at https://hris.lbl.gov/self_service/training/. Preregistration is required for all courses except EHS 10. For a full, updated schedule, see http://www-ia1.lbl.gov/schedule/.
Berkeley Lab Director Charles Shank and University Auditor Patrick Reed have issued the following joint statement for Laboratory employees, reaffirming their interest in receiving information about any suspected improprieties and explaining the avenues available for reporting such concerns.
The University of California, of which the Laboratory is a proud and integral part, is committed to fostering an environment in which employees and others with concerns about possible improprieties can come forward with confidence that their concerns will receive appropriate attention and without fear of retaliation.
With this communication we want to reaffirm the interest of both the University of California Office of the President and Berkeley Laboratory in receiving information about any suspected improprieties and inform you of avenues available to make a report.
Since August 1997, the Laboratory has engaged an independent service called EthicsLine to provide callers with a means of providing anonymous information about suspected improprieties. In the next few weeks this anonymous hotline service will be enhanced utilizing case numbers so that: (1) anonymous callers have a mechanism to make inquiries about the status of their complaints and receive feedback, and (2) investigators have a mechanism for letting anonymous callers know when additional information is critical to determining the facts of the matter at hand, without compromising the anonymity of the caller. The independent service provider will report callers’ concerns to both UC, through the University Auditor’s Office, and to appropriate Laboratory officials. Independent, anonymous hotlines with similar capabilities have been established at our sister laboratories.
The EthicsLine telephone number, 1-800-999-9057, is posted on Laboratory bulletin boards and was communicated via a Level-1 email in August 2002. This number will remain unchanged. The EthicsLine number and other contact numbers available for reporting suspected improper activities follow:
If you would like to learn more about University polices
for reporting and investigating allegations and protection from retaliation,
see http://www.ucop.edu/ucophome/coordrev/policy/10-04-02.html.
