A breakfast discussion on “Getting Ready for the Rebound” held yesterday by the San Diego Venture Group might have been more aptly billed as “Waiting for the Rebound: A Tragicomedy in Two Acts.” But then again, with San Diego News Network CEO Neil Senturia serving as moderator, there really can only be one act.

The irrepressible Senturia was in his element (which is to say he was on stage) as he delivered one-liners while leading a panel of local experts through a conversation about the rebound that ranged from the venture capital outlook in San Diego to Wall Street ethics and the overall U.S. economy.

So, for example, as UC San Diego Economist Allan Timmermann talked about government spending and the prospects of inflation, Senturia interjected, “Inflation is what allows you to live in a more expensive neighborhood without moving.” And when Mission Ventures managing partner Leo Spiegel talked about the strength of character he looks for in startup entrepreneurs, saying, “I want to see that they went to the wall,” Senturia quipped, “You mean the wailing wall.”

As the only economist on the panel, Timmermann was an obvious target for such Senturian gibes as, “If you put 10 economists in a room, you get 11 opinions.” But a riposte from the UCSD economist got one of the biggest laughs when Senturia indignantly denounced the outrageous pay and bonus demands of disgraced Wall Street executives, the corruption of Bernie Madoff, the alleged corruption of hedge fund manager Raj Rajaratnam—and demanded the panelists explain what has happened to American ethics. Timmermann answered, “It’s only when the tide retreats that you see who’s swimming naked.” The audience roared.

But seriously folks, the conversation about preparing for a rebound led to a number of interesting points and observations:

—The outlook for venture-backed companies is clearly improving, according to Mission Ventures’ Spiegel. Following what he describes as a “brutal” period last winter, in which a third of the employees were laid off across Mission Ventures’ 30 portfolio companies, Spiegel says two of those ventures are now responding to buyout offers and a third is …Next Page »

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The San Diego Supercomputer Center at U.C. San Diego today named UCSD astrophysicist Michael L. Norman as interim director. Norman replaces Fran Berman, a specialist in grid computing (and San Diego Xconomist), who has served as the center’s director since 2001. Berman plans to join the Rensselaer Polytechnic Institute as vice president of research, effective Aug. 1. Norman, a UCSD distinguished professor of physics, was appointed as the center’s chief scientific officer a year ago. The university says it plans to name a permanent director at a later date.

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What recourse does an entrepreneur have when there is no venture capital for a start-up with a truly promising invention? At San Diego’s Biological Dynamics, 27-year-old founder Raj Krishnan’s solution is to win entrepreneur and student competitions—and so far he has won 13 awards, nine of them this year, including most recently a $40,000 first prize in the UC San Diego Entrepreneur Challenge, where the judges were impressed with his presentation skills. “We went to the competitions because venture capital is extremely hard to find now, and we have been fortunate. It enables us now to protect our IP and pay bills,” Krishnan says.

Raj Krishnan talks eagerly about the prospects of someday making a cancer diagnosis no more troubling to a patient than telling someone they have caught a common cold. And the bioengineering Ph.D. student at UC San Diego says he may have found a way to make that happen. Krishnan’s team of fellow UCSD students and professor Michael J. Heller believe they have found a simple and cost-effective way of detecting cancer at its outset.

Nowadays finding a cancer at an early stage usually means it can be cured. But there hasn’t been any method of detecting cancer in its earliest stages. Symptoms usually aren’t apparent until the cancer has reached a late stage of growth.

As cancer cells begin to grow, an increased amount of DNA circulates in the blood. Krishnan says this increase in “cell-free” DNA is believed to be of cancerous origin. In the 1970s, scientists noted that people with tumors have a lot of free DNA in their blood, but serious studies have only been done lately. “There still hasn’t been an easy method to isolate the DNA without degrading it,” says Krishnan. “Ours is the first that doesn’t do that, and it’s a very clear and very easy separation.”

Michael Heller and Raj Krishnan

Krishnan’s research efforts have been directed at creating technology to identify abnormal amounts of cell-free high molecular weight DNA in the blood. High molecular weight DNA is widely considered a good secondary biomarker for almost every type of cancer, but separating nanoparticles of DNA that circulate in extremely small amounts has been problematic, to say the least. This DNA is thought to be of 5-50 nanometers in size, which means it is smaller than the wavelength of light. “It’s very difficult to find in blood. The analogy of needle in the haystack has been used, but I’d say it’s more like looking for a needle on the whole farm,” says UCSD’s Heller, a professor of bioengineering. Krishnan discovered it can be done by generating an electric field through a microelectrode array.

Until recently, using AC (alternating current) electric field techniques to separate nanoparticles such as DNA from blood would have been considered impossible because of …Next Page »

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A biotechnology company aiming to revolutionize early-stage cancer screening last night won the UC San Diego Entrepreneur Challenge. Biological Dynamics, led by bioengineering PhD student and CEO Raj Krishnan and his fellow graduate students David Charlot and Roy Lefkowitz, took home the $40,000 first prize.

Biological Dynamics has developed a screening tool that identifies secondary cancer biomarkers such as free circulating DNA from unnatural cell death. Krishnan’s technology helps to detect signs of early stage tumors with a cost-effective blood test that takes less than 30 minutes and shows signs of almost every cancer type, according to the already much-awarded team.

Medical device company Tritonics, which has a solution to treat clogging in implanted catheters, came in second. Third prize was given to Radiofast, which is creating new integrated circuits technology for medical and security imaging.

In addition, the best entries in five categories got $2,000 each. They were Biological Dynamics (Biotech/Life Sciences), Radiofast (Hi-Tech/IT), Profile UST (CleanTech), The Nicholas Conor Institute (Social Entrepreneurship), and Cyrotrace Solutions (Undergraduate).

The UC San Diego Entrepreneur Challenge is a student-run competition now in its third year. Each of the 70 competing teams had to have at least one active company team member who is a UCSD or affiliate student or recent graduate.

Last fall, teams had to present their business concept, and during the winter quarter they went head-to-head in an executive summary competition. The spring quarter culminated Monday night with business plan presentations.

Judges for the final round included Mary Ann Beyster, president of the Foundation for Enterprise Development; biotech entrepreneur, venture investor, and Xconomist Larry Bock; SDSU College of Business dean Gail Naughton; Connect CEO Duane Roth; Mission Ventures managing partner Leo Spiegel; and UCSD’s Rady School of Management’s founding dean Robert Sullivan.

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Expectations were high at UC San Diego yesterday as the city’s academic, business, and political leaders gathered to announce the formation of SD-CAB, the San Diego Center for Algae Biotechnology.

Steve Kay, UCSD’s dean of biological sciences and SD-CAB’s founding director, told the audience the single point of the center was to position San Diego as “the leader in the new algae economy.” Such hyperbole aside, the underlying idea for the consortium of academic and industry researchers was basically how Kay described it in January, when I first learned about SD-CAB. Since then, organizers have added the Salk Institute and San Diego State University to the consortium, which intends to make San Diego a nationally recognized center for the kind of innovative solutions needed to make algae biofuels production commercially viable.

One difference that was evident yesterday, though, is that expectations have soared beyond making San Diego what UCSD Chancellor Marye Anne Fox calls “a big green cluster” for algae biotechnology research. Some speakers talked about making San Diego a “green Houston” of the biofuels industry. ”Maybe someday, if the history of algae is ever written, this will be remembered as the day when it all started,” Jim Waring, chairman of Cleantech San Diego, told me before the press conference began.

Joining in the exuberance, Stephen Mayfield, an expert in the genetics of algae at The Scripps Research Institute, told the audience that algae-based biofuels, which includes gasoline, jet fuel, and diesel, “will be under $2 a gallon” in the next five to 10 years. Who knows if Mayfield is right? But with his enthusiasm and scientific credentials, Mayfield had people listening raptly. In addition to serving as SD-CAB’s co-founder and associate director, Mayfield also is a scientific adviser and co-founder of Sapphire Energy, the algae biofuels startup funded in part by Bill Gates’ Cascade Investment fund.

And perhaps there is cause to celebrate. Biofuels Digest says venture capital firms invested $175.9 million in to develop algae-based biofuels throughout the United States last year, and $100-million of that went to Sapphire Energy. Panelists at the press conference also cited a San Diego regional economic study that found every $100 million of venture capital funding applied …Next Page »

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President Obama announced today the members of the President’s Council of Advisors on Science and Technology, in remarks made at the National Academy of Sciences in Washington DC. Some members were announced previously, but this is the first time the full council was presented publicly. Obama cited the distinguished council’s “diversity of experience and views,” and said the members would advise him on “national strategies to nurture and sustain a culture of scientific innovation.” You can see the full list here.

Xconomy’s cities of Boston, Seattle, and San Diego are all represented prominently on the advisory council. Here’s a quick rundown:

Council members with strong ties to the Northwest include Craig Mundie, chief research and strategy officer at Microsoft; and Christine Cassel, president and CEO of the American Board of Internal Medicine, who was previously dean of the School of Medicine and vice president for medical affairs at Oregon Health & Science University. (Another presidential advisor with ties to Oregon—though she’s not on this council—is Jane Lubchenco, a professor at Oregon State University, who was confirmed by the U.S. Senate last month as under secretary of commerce for oceans and atmosphere, and the ninth administrator of the National Oceanic and Atmospheric Administration.)

Not to be outdone, the Boston area contributes luminaries John Holdren (co-chair), director of the Office for Science and Technology Policy and former director of the Program on Science, Technology, and Public Policy at Harvard University’s Kennedy School of Government; Eric Lander (co-chair), director of the Broad Institute of MIT and Harvard; Ernest J. Moniz, director of the Laboratory for Energy and the Environment at MIT; Daniel Schrag, professor of geology and professor of environmental science and engineering at Harvard; and Shirley Ann Jackson, president of Rensselaer Polytechnic Institute, former chair of the U.S. Nuclear Regulatory Commission, past president of the American Association for the Advancement of Science, and the first African-American woman to earn a doctorate from MIT.

And San Diego has Mario Molina, professor of chemistry and biochemistry at the University of California, San Diego, and the Center for Atmospheric Sciences at the Scripps Institution of Oceanography. Molina is a Nobel Laureate in Chemistry, and is also the director of the Mario Molina Center for Energy and Environment in Mexico City.

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UC San Diego says it has established a center for next-generation digital media with a gift from IBM (NYSE: IBM)—a high-performance IBM System z mainframe computer. In a statement, UCSD says IBM made the center possible through a shared university research award that includes the z mainframe, valued at about $2.2 million. The center, which will be housed at the San Diego Supercomputer Center, is dedicated to inventing the next generation of virtual worlds, multiple player online games, and high-fidelity digital cinema. UCSD says the center initially will focus on new production platforms for digital cinema through existing relationships with Hollywood studios.

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California’s jobless data for January is set for release Friday, but there’s little reason to expect much improvement since December, when the statewide unemployment rate hit 9.3 percent, with more than 1.73 million California residents out of work. In San Diego County, overall unemployment was at 7.4 percent in December, with 117,000 people jobless.

For the tech sector job market specifically, Xconomy’s layoff trackers offer another barometer of a generally grim situation (You can find our San Diego layoff tracker here). Greg and Wade provided another perspective last month by talking to some of the MBA students at MIT’s Sloan School of Management in Cambridge, MA, during their annual “tech trek” to meet with companies in Silicon Valley, as well as Seattle and Boston.

But I sensed more anxiety—or maybe it was less confidence—when I dropped in at UC San Diego Friday for an annual job fair organized by students at the Jacobs School of Engineering.

“Everyone’s worried about the economy,” says Dat Kieu, a third-year undergraduate studying mechanical engineering. He was looking for an internship or part-time job.

UCSD says its Disciplines of Engineering Career Fair (DECaF) is the only annual, student-managed, multidisciplinary career fair on campus. and this year 71 companies participated. A public relations coordinator, eager to convey the idea that companies are hiring, even provided a survey (with 30 of the 71 companies responding) that shows 40 percent of the companies attending the fair say they plan to hire the same number of full-time positions in 2009 as they hired in 2008—although 33 percent say they plan to hire fewer entry-level engineers. The same survey shows 53 percent expect to place the same number of engineering interns this year, with 23 percent planning to recruit fewer interns in 2009.

“It’s an interesting hiring climate,” says Qualcomm recruiter Vince Walker. “We’re not going full throttle, but we’re still bringing people on board.” Yet Walker and other recruiters told me the tough job market enables them to be far more selective.

Bob Balderas, a recruiter for New Jersey-based BD Biosciences, which employs about 400 in San Diego, says the company plans to start …Next Page »

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Bill Weihl, Google’s green energy czar, says the computer you’re likely using now is a bit like a toaster. It takes in energy and produces heat. A typical network server is more energy-efficient, but Weihl says it’s usually loaded with cheap parts and still wastes a third of the power it consumes, which emanates as heat. That’s not really hot enough to toast bread, and probably not enough to bring a teapot to boil. But a key issue for the industry is that it takes as much electricity to cool a typical data center as it takes to run the servers inside it.

So it was no minor accomplishment for Google to recently cut its energy use roughly in half, which is what Weihl told a conference in San Diego yesterday afternoon. You could even say it makes Google a green giant in the Valley (ho, ho, ho). It’s also worth noting that Weihl says engineers at the Mountain View, CA, technology colossus achieved the reduction by rejecting industry “best practices” and designing their own servers and data centers.

The two-day symposium on “Greening the Internet Economy” in itself represents a growing recognition by the ICT industry (Information and Communications Technology) that the computer and everything it’s connected to consumes enormous amounts of power. Also noteworthy is the fact that the California Public Utilities Commission co-sponsored the conference with U.C. San Diego, because of the role the agency has played in recent years in promoting renewable energy and curbing global warming. Weihl, a former computer science professor at the Massachusetts Institute of Technology and former CTO of Akamai Technologies, got top billing as keynote speaker on the opening day.

Weihl says Google has committed itself to being carbon neutral by reducing power use, relying on renewable energy and investing in projects that cut greenhouse gas emissions. It’s seen by many as a noble goal, but going green also impacts Google’s bottom line. For the past seven years, Google has been designing its own servers because it saves money over the long run. Weihl says the company spends between $20 and $100 more for each server it buys, depending on size. But he says the extra cost pays for itself in reduced energy costs within six to 12 months.

The Internet search engine giant also designs and builds its own data centers, using evaporative cooling to keep its systems running. Citing figures from the Environmental Protection Agency, Weihl says the typical enterprise data center has a power usage effectiveness, or PUE, of 2. That means a facility consumes twice as much power as the computer equipment inside it. Weihl says Google has reduced its PUE to 1.2.

“Overall, through the efficiency work that we’ve done by …Next Page »

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The San Diego region is undertaking a broad initiative to accelerate development of algae-to-biofuels technology by establishing a new organization, the San Diego Center for Algae-based Biofuels, or SD-CAB. The center is being organized by a consortium of academic and industry researchers and represents a regional effort to make sustainable algae-based biofuel production a reality in the next 5 to 10 years, says Steve Kay, dean of Biological Sciences at UC San Diego.

Kay says the center is currently virtual, with initial funding for SD-CAB coming from what he described as “a corporate affiliates program.” He didn’t elaborate, but such an effort might attract financial support, for example,from a big oil company. In any case, I recently counted at least nine companies in the San Diego area that are working to develop algae-based substitutes for conventional petroleum products. Most of them are early-stage startups, but the list includes SAIC (NYSE: SAI) and privately held General Atomics. Both are major government contractors accustomed to managing collaborative research programs, and both recently got grants from the Defense Advanced Research Project Agency to develop technologies that use algae to make jet fuel.

The collaborative effort behind the new center emerged from a non-profit membership organization called Cleantech San Diego, which was formed in late 2007 by the city of San Diego and local economic development groups.

Lisa Bicker, Cleantech San Diego’s CEO, told me last week she helped organize an initial meeting of scientists and industry officials last July—just to talk about who’s doing what …Next Page »

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DARPA, the Pentagon’s R&D funding agency, yesterday awarded a $19.5 million contract to privately held General Atomics of San Diego to make jet fuel from algae and cellulosic feedstocks. Work on developing JP-8 grade biofuel will be done at General Atomics and UC San Diego’s Scripps Institution of Oceanography, Arizona State University, Blue Sun Biodiesel of Golden, CO, Martek Biosciences in Boulder, CO, Texas A&M, UOP of Des Plains, IL, Hawaii Bio Energy, Honolulu, the University of North Dakota’s Energy and Environment Research Center and Utah State.

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The new five-story building that doubles the size of the San Diego Supercomputer Center is more than just concrete, steel, and glass. As Fran Berman, SDSC director (and an Xconomist) said yesterday, the new building also represents the next generation in supercomputing—and she wants to ensure that San Diego’s emerging companies feel like they’re part of the family.

Berman ostensibly was hosting a dedication ceremony for the SDSC’s $44 million expansion. But the event included breakfast for more than 100 local technology executives, venture capital partners, and others to explain how supercomputing is crunching massive amounts of data to analyze Medicare fraud, cancer cells, earthquakes, and climate change.

Such research may not necessarily be useful to the venture community, but biotech and information technology startups increasingly need such capabilities, especially in digital storage and data mining, and to analyze complex models and simulations.

Today “SDSC sees its role as a partner and pathfinder with the research and education community to harness the power of cyberinfrastructure to adderess science and society’s most critical problems,” Berman said.

The supercomputer center, which was founded on the UCSD campus 23 years ago, now boasts that it has more archival storage capacity than any other academic institution in the world, about 25 petabytes (25 thousand trillion bytes). That’s about 1,000 times the digital plain-text equivalent of the printed collection in the Library of Congress.

The new building also houses some of the first optical networking equipment to be connected to the TeraGrid, a next-generation Internet for scientific research funded by the National Science Foundation.

“I have a number of models where we could work with industry,” said Ron Hawkins, SDSC’s director of industry relations.

The center could conduct sponsored research to address specific questions a company may have, Hawkins said. SDSC researchers also can do “high-end consulting” on corporate projects, or the center can simply offer access to its computational resources.

As one industry consultant noted, however, the programming required to solve complex problems on high-performance computers can be extremely expensive.

“Parallel processing is a specialized field, so, yes, it requires specialized expertise,” Hawkins acknowledged. “But the computing world and the IT world is going to parallel processing, so it’s only appropriate for us to work with industry to bring them along.”

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Updated, Oct. 8, 5 am PST: Roger Tsien was not only on the short list for the Nobel Prize in chemistry—he won it! See below for more details:

Was it me, or did researchers’ heads whip around yesterday as I walked through Roger Tsien’s biochemistry laboratory at U.C. San Diego?

If there was an atmosphere of excitement and anticipation in Tsien’s lab, it’s not necessarily because Xconomy has arrived in San Diego. (We launched the San Diego site Monday). Tsien had never heard of Xconomy, and he studied my business card—which consisted of “Xconomy.com” handwritten on the back of another business card—with an expression of…apprehension.

A more likely explanation for all the electricity in the air is that my friend David Pendlebury, who handicaps the Nobel prizes for Thomson Reuters Scientific, put the 56-year-old Tsien on his short list for this year’s Nobel Prize in chemistry.

Pendlebury, who bases his predictions on scientific citations of “high-impact papers,” also put Harvard’s Charles M. Lieber and Carnegie Mellon’s Krzysztof Matyjaszewski on his short list. The announcement in Stockholm by the Royal Swedish Academy of Sciences is scheduled for today.

Tsien, who was funny and self-deprecating, explained how his research led to the development of “fluorescent proteins” that have become a valuable new tool used in labs around the world for studying cellular activity.

A variety of fluorescent proteins and similar tools that Tsien and his colleagues developed now allow academic researchers to study changes in cellular acidity, calcium, oxidation reduction, and cyclic AMP, among other things.

But after developing a new technique and demonstrating one or two new applications in molecular biology, Tsien says he often moves on to other uncharted realms. He compared himself to John C. Fremont, the frontier pathfinder “who finds the pass but who is not the homesteading type.”

At another moment, he fatalistically compared his illustrious career to Woody Allen’s, saying, “I’m doomed to be this sort of comedic guy who just makes tools.”

Yet Tsien’s work led to the creation of San Diego’s Aurora Biosciences Corp., which developed new technologies for ultra-high screening of molecules as potential drug candidates. (Seed funding for Tsien’s startup came from Avalon Ventures, a San Diego venture firm headed by Kevin Kinsella.)

Tsien said his early investors “asked me if I was interested in being CEO, and it took me about two milliseconds to say no.” He has no interest in managing a business, and says, “It’s completely not within my talents.”

The value of his work was demonstrated, though, when Vertex Pharmaceuticals acquired Aurora in 2001 for more than $500 million. Tsien said his screening techniques also are used by San Diego’s Invitrogen, which supplies products and services to laboratories, and Senomyx, a San Diego biotech developing taste receptor technologies to discover novel flavors, and taste enhancers and modulators.

All of this might lead to a Nobel Prize for Tsien, or perhaps not. But a Woody Allen quote comes to mind.
“I don’t want to achieve immortality through my work,” he said. “I want to achieve it through not dying.”

Update, Oct. 8: The Nobel Prize committee today announced that Tsien will share the chemistry prize equally with fellow Americans Martin Chalfie of Columbia University and Osamu Shimomura, who is with the Marine Biological Laboratory in Woods Hole, MA, and Boston University Medical School.

The prize carries with it a cash award of 10 million Swedish kronor, just over $1.4 million, which will be shared equally by the winners.

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Irwin Jacobs is the chairman and founder of Qualcomm, the San Diego-based giant in digital wireless communications. With sales of more than $10 billion a year, Qualcomm now has a market valuation of roughly $66 billion—more than McDonald’s.

Yet Jacobs, who will celebrate his 75th birthday later this month, seemed remarkably unpretentious for a wireless industry tycoon when he appeared at a recent UC San Diego event. He was the main attraction at the Oct. 1 kickoff for UCSD’s 3rd Annual Entrepreneur Challenge. The yearlong challenge is run by UCSD students, and combines a series of campus-wide entrepreneurial competitions, educational workshops and social events.

Jacobs, who moved to San Diego from MIT almost 50 years ago, still comes across like a professor of electrical engineering, which is how he began his career, and makes self-deprecating comments about his New England accent.

“I still say pahrk the cahr in the gahrage,” Jacobs said to the amusement of more than 300 UCSD students and others.

The San Diego billionaire also arrived by himself and mingled with students before and after the evening event. Another sign of Jacobs’ sensibility was his willingness to tell his life story, which he no doubt has recounted many times before.

What came through his talk, though, was his inherent curiosity and ability to learn deeply about new subjects. He told one anecdote about learning everything he could about the military specifications that were holding up a government contract, to the point where he identified conflicting standards among various specs cited by government program managers.

His advice to entrepreneurs in the audience included:

—In creating a technology business, “you have a technology side, a financial side and a sales and marketing side, and you really have to make sure that you have all three of those in alignment before you go forward.”

—”As you become more successful, you have to keep running fast. If you develop a good product, you can’t just sit on it — other people will run right by you.”

—”One of the key items of course is to have a lot of persistence. Whatever your (cost) estimates are, you’re going to be off at least by a factor of two.”

Jacobs compared managing an executive team to managing his engineering graduate students, saying, “you kind of have to explain to senior executives what it is you want them to do and then let them go off and do their own thing.”

At the same time, Jacobs says it becomes necessary as a startup expands to develop processes for accounting, project management, purchasing, and other business tasks. But even that seemed comparable to university life for Jacobs.

“It reminded me of working on committees at a university” he said. “The main difference is that you can make a decision when you’re in business.”

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If it seems as if San Diego sprang to sudden prominence as a global capital for innovation, at least part of the explanation can be found atop the oceanside bluff known as Torrey Pines Mesa.

This perch has one of the most prestigious zip codes in the world, 92037, used by the Burnham Institute for Medical Research, The Scripps Research Institute, and The Salk Institute for Biological Studies. Across the street from the Salk is the University of California, San Diego, with its own zip code, 92093. Just down the road are General Atomics and the San Diego headquarters of SAIC, Science Applications International Corp., both government contractors that operate as R&D conglomerates.

Torrey Pines Mesa also may be the most stunningly scenic vista in a city renowned for its Mediterranean-like views of coastal cliffs and beaches, sun-splashed bays, and urban skyline.

The mesa encompasses a 2,000-acre wildlands park, with trails that drop 300 feet through deep ravines to the Pacific Ocean. Coastal fog and rain occasionally sweep through the partly wooded bluff, which is usually bathed in sunshine. The zip code includes the Torrey Pines Golf Course, which hosted the U.S. Open earlier this year, and parts of fabled La Jolla, the affluent seaside resort. As it turns, 92037 also includes the latest office for Xconomy, on North Torrey Pines Road.

Leading researchers who relocate to San Diego often cite the combined allure of this scenic landscape and scientific firepower as a major reason for making the move.

It was part of the reason why K. Barry Sharpless, who shared the 2001 Nobel Prize in chemistry, moved to San Diego from MIT 17 years ago. Sharpless told me years ago he particularly enjoyed the ocean swim from La Jolla shores to La Jolla Cove, a roundtrip distance of roughly 2 miles.

Ron Evans, a professor in the gene expression lab at Salk (and a San Diego Xconomist), described the research institute where he works as “an architectural masterpiece” designed by Louis Kahn on a bluff selected personally by Jonas Salk, best known for his development of a killed-virus polio vaccine.

“It was meant to be symbolic of the movement of Americans from East to West,” Evans told me last week. “This is the last West Coast outpost overlooking the Pacific, constructed by Salk at the peak of his fame. Not only does it have magnificent views of the ocean and cliffs, but it is an uncluttered landscape. One never gets tired of that.”

Still, the emergence of Torrey Pines Mesa as a scientific powerhouse did not happen by chance, says Mary Walshok, a UCSD Associate Vice Chancellor and sociologist who has studied Silicon Valley and other technology clusters.

San Diego has a 100-year history of courting the U.S. Navy and relying on the military for its economic development, Walshok says. The Navy and Marine Corps continue to maintain major military bases in the region today.

Yet Walshok credits John J. Hopkins, president of General Dynamics Corp. …Next Page »

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It’s a curious thing, when a major public research university commissions an independent study to assess its economic impact, especially when we’re talking about an individual school in the University of California system. In this case, the University of California, San Diego, hired a consulting firm in San Francisco to remind the public just how big and important it really is.

The study, released by university officials yesterday, dutifully reported that UCSD contributes more than $7.2 billion a year to the California economy. The full report is available here.

When asked why the university launched the study, UC San Diego Chancellor Marye Anne Fox told reporters who gathered for the announcement that it was intended for campus planning purposes and was commissioned “about a year ago.” That was roughly the same time when allegations of academic misconduct were flying at the Preuss School, a tuition-free charter school on UCSD’s campus for poor and minority students.

The turmoil at the Preuss school erupted as a statewide furor over undisclosed pay for UC administrators was finally subsiding, a controversy that included UCSD’s Fox.

But none of that was dredged up again at the press event.

Fox explained that UCSD paid $130,000 for a report that was more independent and provided a more detailed analysis than UCSD had obtained from previous internal studies. Whatever the rationalization, the 98-page study by CBRE Consultants yielded insights on the economic ripple effects of UCSD’s role as a hotbed for new technologies.

The study reported that UCSD faculty and alumni have started at least 193 companies, a conservative estimate, and that 67 remain “independent and operational” in the state today. Those companies now generate more than $10 billion in annual sales, with Qualcomm accounting for $8.8 billion of the total. The San Diego wireless giant was founded by former UCSD engineering professor Irwin Jacobs.

Using economic multipliers, the study found that startups coming out of UCSD have created 129,570 jobs and generate more than $37 billion a year in direct and indirect spending and personal income.

UCSD alumnus Steven R. Hart, co-founder of San Diego-based satellite and digital-communications firm ViaSat (NASDAQ: VSAT), may have provided the most succinct commentary, though. In light of the financial crisis that has been dominating the news, Hart said, “I can’t help but think about the type of entrepreneurialism that goes on around a university and the type of innovation that takes place in the financial sector. We’re not thinking of new ways to leverage debt and develop new types of mortgage-backed securities.”

Hart, a mathematician, explained afterward that the innovation in and around universities is instead focused primarily on advances in new technologies and products, from satellite transmitters and terminals to molecular biology.

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Wireless pioneer and UC San Diego professor emeritus Andrew Viterbi received a National Medal of Science from President Bush in a White House ceremony Monday, in part for work that later became known as “the Viterbi algorithm.”

That might sound like a sequel to “The Bourne Ultimatum,” but the algorithm is actually used in virtually every cell phone today. Also known as the “maximum-likelihood algorithm for convolutional coding,” it is used to suppress radio interference and efficiently decode digital transmission sequences.

Viterbi also made important contributions to CDMA, the wireless technology shorthand for Code Division Multiple Access, which served as the foundation for San Diego-based Qualcomm and transformed the theory and practice of digital communications.

Viterbi is one of the founders of Linkabit, one of San Diego’s early startups and a co-founder of Qualcomm. One of Viterbi’s co-founders in both companies was Irwin Jacobs, who took home a National Medal of Science of his own in 1994.

Viterbi received his bachelor’s and master’s degrees from MIT, and his Ph.D. in digital communications from the University of Southern California. In 2004, Andrew and Erna Viterbi committed $52 million to USC’s engineering school, which was renamed in their honor. He is currently a professor emeritus at UCSD’s Jacobs School of Engineering and heads the Viterbi Group, a San Diego technical advisory and investment business.

President Bush told the recipients who gathered in the White House East Room that the setting was  appropriate for a ceremony honoring innovators for extending the frontiers of knowledge, because ”Thomas Jefferson reportedly used this room as a place to lay out his fossils.” A White House transcript of the event is here.

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