It seems doubtful that the U.S. Navy has ever gotten as much media attention for offshore cruising between San Diego and Port Hueneme as the decommissioned destroyer Paul H. Foster received last week.

The Spruance-class destroyer, which has been refitted to serve in various ways as an ocean-going test platform, arrived at the naval base near Oxnard, CA, about 185 miles north of San Diego, Thursday morning after a 17-hour transit powered by a fuel blend that included algae-derived biofuel. It was the Navy’s largest alternative fuel trial.

The overnight sojourn was intended as a demonstration of the Navy’s plan to expand the use of “drop-in” biofuels that would require no changes to Navy engines, ships, supply infrastructure, or fueling piers. The only difference is that the biofuel was derived from algae, or “green crude,” instead of conventional fuels made from petroleum-based crude. (A pretty good account of the demonstration is here.)

San Francisco-based Solazyme provided the algae-based biofuel, which can be produced in its U.S.-based facility in a few days, according to Stephanie Tabor, a spokeswoman for the company. “We use standard industrial fermentation equipment to efficiently scale and accelerate microalgae’s natural oil production time to a few days,” Tabor says in an e-mail this afternoon. Solazyme’s technology is flexible, she says, “and can utilize a wide variety of renewable plant-based sugars, such as sugarcane-based sucrose, dextrose, and sugars from other sustainable biomass sources including cellulosics.”

As we reported last year, the Navy has decided for reasons of energy security, naval strategy, and environmental stewardship to develop and certify alternative fuels that can be used instead of standard-issue ship and aircraft fuels.  Navy Secretary Ray Mabus has announced a goal of conducting a test exercise next year with a “Great Green Fleet”—a 13-ship carrier battle group powered either by nuclear energy or 50-50 blends of biofuels, based on press reports.

The Foster took on about 20,000 gallons of diesel biofuel that Solazyme delivered to the Defense Fuel Supply Point at Naval Base Point Loma. It was blended 50-50 with a standard naval marine diesel known as F-76 (a NATO specification), and used in gas-turbine engines aboard the Foster that are equivalent to engines in U.S. destroyers and cruisers around the world.

“For our program with the Defense Logistics Agency,” Tabor says, “we are supplying the U.S. Navy with renewable F-76 diesel fuel and renewable JP-5 jet fuel for testing and certification.”

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The corporate controller at San Diego’s Sapphire Energy was killed earlier this week when an out-of-control sport-utility vehicle swerved into a bike path while he was bicycling home from work. A close friend told The San Diego Union-Tribune that Poway, CA-resident Nick Venuto, 40, was an avid bicyclist and married father of two. Venuto was pedaling home from work on a bike path along State Route 56 Tuesday evening when he was struck by a Ford Escape driven by 27-year-old Sheena Saranita after she lost control of her vehicle. Another bicylist, Baron Herdelin-Doherty also was hit, and was taken to Scripps Memorial Hospital in critical condition.

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San Diego algae biofuels developer Sapphire Energy said today it has signed a multi-year agreement with the Linde Group of Munich, Germany, to co-develop a low-cost system for supplying carbon dioxide to commercial-scale, open-pond, algae-to-fuel cultivation systems. Linde, the leading commercial supplier of carbon dioxide in the United States, agreed to deliver carbon dioxide to Sapphire’s commercial demonstration facility near Columbus, NM, and to work with Sapphire to reduce the costs associated with re-purposing manmade carbon dioxide for commercial-scale open pond algae cultivation.

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On this St. Patrick’s Day, it seems only appropriate to lead our roundup of biotech news with an item from San Diego’s Sapphire Energy, the algal biofuels startup using biotech tools to develop emerald-green crude. We’ve got the rest of the life sciences news too, as well as a hearty “Top o’ the morning” to you.

—San Diego biofuels startup Sapphire Energy signed a strategic partnership with Monsanto, the agricultural chemical specialist based in St. Louis, MO. Sapphire Energy said it is already in the business of identifying valuable traits for the use of algae in commercial agriculture, and plans to share information with Monsanto on stress tolerance, yield enhancement, and other traits.

—Genomatica, the San Diego sustainable chemicals company, forged a strategic partnership with the U.K.’s Tate & Lyle. Genomatica plans to use a Tate & Lyle high-fructose corn syrup plant in Decatur, IL, to make commercial-scale quantities of “Bio BDO,” an intermediate chemical also known as 1,4-butanediol that is used to make spandex, running shoes, automotive plastics, and other consumer products.

—San Diego’s Amylin Pharmaceuticals and Takeda Pharmaceutical of Japan said they suspended a mid-stage clinical trial of an obesity drug candidate that combines two synthetic hormones. The drug companies said they want to investigate new antibody-related laboratory findings from a previous obesity trial involving metreleptin, one of the synthetic hormones.

—I talked with James Fowler, a professor of medical genetics and political science at UC San Diego about his research into social networks and Connected, the book he wrote with co-author Nicholas Christakis of Harvard. Since the book was published, Fowler said he’s done some work for 23andMe, the personal genomics company based in Mountain View, CA. “They realized that in order to provide information about genetics that you need to know something about the social environment as well,” Fowler said.

—The San Diego-based Polaris Group said it is expanding its leadership in conjunction with the advance of the company’s lead cancer drug candidate into late-stage clinical trials. Polaris named former Arena Pharmaceuticals CFO Robert E. Hoffman as its chief financial officer as it moves forward into trials of ADI-PEG 20, a drug developed to treat hepatocellular carcinoma.

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Foreign competition is rising, and U.S. consumers haven’t departed from their penny-pinching mentality of The Great Recession, and behind this double whammy the cleantech industry is feeling the squeeze. That’s one of the big impressions I came away with after polling a crop of cleantech experts from Xconomy’s network of advisors and op-ed contributors for their predictions for 2011. But take heart; there’s plenty of room for optimism, especially in the fields of energy efficiency and monitoring, where the U.S. may be leading the way to a greener future that’s much more achievable—at least in the short term—than through any form of alternative energy.

One sub-theme was pretty overwhelming among the responses I received: the actual materials manufacturing side of cleantech (i.e. the production of components for generating solar and wind energy, efficient batteries, and LED chips) is struggling, but energy-focused software and services are rising to the occasion. A number of Xconomists and contributors have pointed out that the U.S. cleantech manufacturing base is weakening due to competition from countries like China, which offer cheaper production and strong government incentives (or mandates) for adopting the new technology.

“It’s a rapidly commoditizing good,” Ray Demeo, VP of worldwide sales at Marlborough, MA-based Coolcentric, says of solar equipment. “The price that China can produce the product at is lower than U.S. manufacturers.”

Additionally, consumers and investors are nervous about spending upfront on things like efficient appliances, electric vehicles, or solar power, to get cleaner sources of energy into their homes (or cars), and would rather find ways to save. Makes enough sense. That’s actually the silver lining for the cleantech space, though, several experts say.

“The fundamental business proposition is we will go in and evaluate some aspect of your energy utilization and we will cut your cost—-I won’t be surprised to see those kinds of business models continue to thrive,” says Tom Ranken, president and CEO of the Washington Clean Technology Alliance. “Ten to 15 years from now, people might be slapping themselves upside the head saying, ‘how did I miss that?’”

Here’s a roundup of some specific predictions we gathered from our network of cities:

—Stephen Mayfield, director of the San Diego Center for Algae Biotechnology and a professor in UC San Diego’s Department of Molecular Biology, said we can expect to see a slew of biofuels advances this year:

• The first synthetic algal genome.
• The first significant scale-up of

… Next Page »

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San Diego’s life sciences news began to slow down over the past week, but there was still plenty of items to round up. Happy holidays from Xconomy.

—San Diego’s emerging algal biofuels industry got encouragement from the U.S. Navy, which said it will need 336 million gallons of advanced biofuels a year, beginning in 2020, to meet a goal set by Secretary of the Navy Ray Mabus. The Navy secretary wants to use alternative energy sources to provide 50 percent of the energy for all its war-fighting ships, planes, vehicles and shore installations in less than 10 years.  That’s good news for San Diego-based General Atomics, a private defense contractor developing algal biofuels for the Pentagon.

—San Diego-based Lpath said it has granted Pfizer an exclusive option for a worldwide license to develop and commercialize its lead monoclonal antibody drug candidate, iSONEP, as a possible treatment for wet age-related macular degeneration and other disorders of the eye. Under the agreement, Pfizer will provide Lpath with an upfront option payment of $14 million and share the cost of planned early stage clinical trials. If Pfizer exercises additional options, Lpath could receive as much as $497.5 million and sales-based royalties.

—Shares of San Diego’s Arena Pharmaceuticals (NASDAQ: ARNA) fell 24 cents, or almost 12 percent, yesterday after the biopharmaceutical company said it will likely be the end of 2011 before the company will resubmit the new drug application for its weight loss drug, lorcaserin. Arena, which closed at $1.80 a share in heavy trading, said it’s now planning new studies of the drug’s potential cancer risks after meeting this week with the Food and Drug Administration. “The meeting discussions reinforce our position that we have a path forward to seek FDA approval of lorcaserin,” Arena CEO Jack Lief says in a statement from the company.

—Reva Medical, a San Diego maker of absorbable stents, is scheduled to begin trading today on the Australian Securities Exchange after the medical device company raised almost $85 million in its initial public offering.

—Santa Clara, CA-based Affymetrix (NASDAQ: AFFX) said a federal judge dismissed a patent infringement lawsuit that San Diego-based Illumina (NASDAQ: ILMN) had filed against it.

—San Diego diagnostic product maker Gen-Probe (NASDAQ: GPRO), paid $53 million to acquire GTI Diagnostics of Waukesha, WI. Gen-Probe said GTI’s technology will expand its product offerings with diagnostics focused on transplantation.

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After reading Andy Pollack’s reportage on biotechnology for years in the New York Times, I finally got a chance to meet him a couple of weeks ago in San Diego, at a briefing to update reporters and VIPs on the $300-million partnership that Synthetic Genomics and ExxonMobil formed to develop algae biofuels.

Today Pollack published an overview on algal biofuels that features two San Diego algae biofuels startups—Synthetic Genomics and Sapphire Energy—and mentions the concerns raised in some quarters about growing genetically engineered algae in open ponds. The concerns about genetically engineered algae are similar in nature to the concerns raised about growing any genetically modified organism (GMO) in an open environment.

While genetically modified crops are grown throughout the United States, many environmental groups—particularly in Europe—remain opposed to agricultural production of genetically engineered plants. In the case of genetically engineered algae, Synthetic Genomics’ founding CEO J. Craig Venter says in the Times article that “suicide genes” could be inserted that would kill the algae if they escaped from the lab or fuel production facility.

But the Times article left me with a sinking feeling that I had gotten some important information wrong in a story I posted last October, “Two Things I Learned During My Tour of Sapphire Energy.”

One of the things I learned—or thought I learned—last year was that San Diego-based Sapphire Energy wasn’t genetically engineering its algae. The algal biofuels startup, which has funding from Bill Gates, Arch Venture Partners, and others, was using high-throughput screening to test thousands of different species of algae daily—and thereby identify which species are ideally suited for producing natural oils that can be used to make gasoline and other fuels.

In an e-mail to Sapphire spokesman Tim Zenk, I said I wanted to set the record straight, and I felt like my headline should have said, “Two Things I Learned During My Tour of Sapphire—One of Which is Wrong…”

But in his reply, Zenk assures me that … Next Page »

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Sometimes in this job, the stuff you hear just seems too good to be true. Like when the mayor of San Diego invites members of an audience to suggest a slogan more exciting than the one he came up with: “When you think of pond scum, think of San Diego.”

It’s not often that the mayor of a major city serves up an opportunity to respond to something like that.

Yet that’s pretty much what San Diego Mayor Jerry Sanders did in public remarks last week at an event that Synthetic Genomics organized to mark the first anniversary of its partnership with the oil giant ExxonMobil (NYSE: XOM). The San Diego startup is getting at least half of the $600 million that ExxonMobil is spending to develop algae that could someplace replace crude oil as a refinery raw material for the production of diesel, gasoline, and jet fuel.

There are thousands of different types of algae, so the task of identifying—or genetically engineering—the ideal algal species for making biofuels still represents a huge scientific challenge. Still, if all goes as planned, our next generation of transportation fuels could someday come from ordinary pond scum.

So it was a proud mayor who stepped to the microphone following a few introductory comments by J. Craig Venter, the human genome pioneer who is Synthetic Genomics’ CEO and co-founder.

Mayor Jerry Sanders

“Our region, the San Diego region, has been able to gain stature as a hub for biofuels,” Mayor Sanders said. “We have more than 20 companies right now working on alternative fuels—including fuels made from used cooking oil, plant-based fuels, and then the micro-algae research being done right here. Between our first-rate research universities—UCSD and San Diego State University—and all of the research institutions up here on Torrey Pines Mesa, we believe that San Diego will soon be synonymous with alternative energy and biofuels.”

The mayor then went on to make a little joke—which now must seem like a soft pitch down the middle of the strike zone to wordsmiths everywhere.

“Now we’re still working on our slogan, after our initial efforts failed to generate excitement,” Sanders said. “So if anyone can think of something more exciting than, ‘When you think of pond scum, think of San Diego,’ we’d appreciate some help on that.”

Amid the polite laughter that ensued, an idea was born. Let’s ask the gentle readers of Xconomy to take up the offer that hizzoner so generously extended!

But first a little background.

As a popular convention and tourist destination, San Diego has promoted itself since … Next Page »

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[Corrected 7/19/10, 1:05 pm. See below.] Some 13,000 developers of geographic information systems (GIS) gathered at the San Diego Convention Center last week as ESRI, the Redlands, CA-based GIS software developer, moved to address the market for mobile and other users. We’ve got that and the rest of our BizTech News all mapped out for you.

—Verenium (NASDAQ: VRNM), the Cambridge, MA-based company formed in the 2006 merger of San Diego-based Diversa and Cambridge-based Celunol, decided to sell its cellulosic biofuels business for $98.3 million to BP. The global energy giant at the center of the oil spill crisis in the Gulf of Mexico gets Verenium’s San Diego-based R&D sites, as well as its demonstration-scale facility and pilot plant in Jennings, LA.

—J. Craig Venter, the human genome pioneer and founding CEO of San Diego’s Synthetic Genomics, said the algal biofuels company is growing its algae in saltwater at its new greenhouse near the company’s La Jolla headquarters. In remarks that might have been aimed at the corn ethanol industry, Venter said his algae biofuels company should not be diverting resources from agriculture. “Fuel cannot compete with agriculture if this is going to be successful,” he said.

—Japan’s Sony Corp. named one of its European executives, Phil Molyneux, as the new president and chief operating officer of Sony Electronics in San Diego, the North American headquarters for the company’s consumer electronics business. Sony Electronics’ current president and COO, Stan Glasgow, is moving to a newly created position—senior advisor of  entrepreneurship and innovation—at Sony Corp. of America.

—[Corrected to refer to open-API software, instead of open-source software.] Free and open-API software was a prevailing theme last week at the 2010 ESRI International User Conference. ESRI, the private developer of geographic information systems based in Redlands, CA, demonstrated some of the map-making tools available at its recently launched … Next Page »

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San Diego’s Synthetic Genomics and Texas-based ExxonMobil celebrated the first anniversary of their strategic alliance today with the official opening of a greenhouse for growing and testing algae that could someday replace crude oil in the production of diesel and other fuels.

On this day last year, ExxonMobil announced plans to spend at least $600 million to develop next-generation transportation fuels from algae—a renewable resource—with $300 million directed to Synthetic Genomics, a five-year-old startup that has assembled an all-star roster of biologists. The founders include CEO J. Craig Venter, the human genome pioneer, Nobel Laureate Hamilton O. Smith, and Juan Enriquez of Boston’s Excel Venture Management.

The greenhouse, near Synthetic Genomics’ headquarters atop San Diego’s Torrey Pines Mesa represents the next step in a 1,000-mile journey to algae-based fuel production, figuratively speaking. The greenhouse is intended to serve as a facility bathed in real sunlight (instead of indoor laboratory lighting), where scientists can work to identify—or genetically engineer—the particular algae that is best-suited to serve as a biological feedstock in the existing fuel production infrastructure. The next major milestone in the program would be establishing an outdoor test facility, a step the partners would likely announce about this time next year.

“I like to think of this greenhouse as sort of a halfway house,” Venter told a small crowd of dignitaries and journalists who gathered for the event under an intense Southern California sun. “Most of what you hear in algae research happens in the research laboratory. But things don’t always translate well out from the laboratory bench to the scale that we need here, of literally billions of gallons of fuel if this is going to have any impact at all on shifting the CO2 levels or coming up with alternate sources of energy.”

Growing algae in the greenhouse requires only sunlight, “which we have in abundance here today,” and carbon dioxide, Venter said. Synthetic Genomics scientists are working with various types of both cyanobacteria (also known as blue-green algae) and eukaryotes. Promising batches begin in small glass flasks and are transferred in steps to larger containers, including 8-liter and 100-liter plastic bags (also known as photobioreactors) that hang on racks in the greenhouse. Algae also are grown in oval, raceway-like ponds stirred by paddlewheels.

One surprising detail that Venter disclosed: All the algae under cultivation in Synthetic Genomics’ greenhouse are grown in saltwater taken from the Pacific Ocean, off the end of a pier near La Jolla. Algae thrives in both fresh water and saltwater, but Venter says he does not want to develop a process that takes agricultural resources by using fresh water. “Fuel cannot compete … Next Page »

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San Diego’s quest to become a hub for the development of algae-based biofuels got a boost today, with the San Diego Center for Algae Biotechnology (SD-CAB), saying it’s getting the lion’s share of a three-year, $9 million federal Department of Energy grant awarded today.

In addition to the $9 million in federal funds, a consortium of seven companies—including San Diego-based Sapphire Energy, General Atomics, and Sempra Energy—are providing $3 million to finance R&D slated to begin this summer. Funding for the consortium has been structured in a way that is similar to the National Alliance for Advanced Biofuels and Bioproducts (NAABB), which I profiled in May when Jose Olivares, the group’s executive director, came through San Diego. The San Diego-based consortium had also sought funding under the DOE program, and the funding announced today was in some respects a political consolation prize for the San Diego contingent.

About two-thirds of the cash will fund research underway at SD-CAB, which includes UC San Diego and the Scripps Institution of Oceanography, according to Stephen Mayfield, a UCSD professor of biology who leads the San Diego algae biotech center. DOE funding also is going to UC Davis, the University of Nebraska, and Rutgers University to identify ways to protect algae crops, improve nutrient recycling, and for developing new genetic tools to improve algal fuel production.

Mayfield says protecting algal crops from predators ranks as one of the key problems that must be addressed as companies like Sapphire Energy move to commercialize methods of producing gasoline, jet fuels, and diesel from algae. “The reason it’s still basic research is because there is no one in the country who works on algal pathology,” says Mayfield, who also is a co-founder and scientific advisor at Sapphire. Algae fall prey to a variety of predators, Mayfield says, including primitive fungi known as chytrids, and microscopic filter feeders like rotofers and Daphnia (water fleas).

The announcement of the DOE award was made today by Cathy Zoi, the Assistant Secretary for Energy Efficiency and Renewable Energy. Life Technologies, Chevron, Praxair, and W.R. Grace contributed part of the $3 million in financing, joined the industrial consortium of supporters, along with Sapphire Energy, General Atomics and Sempra Energy.

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It was just over a year ago that some of San Diego’s biggest life sciences research institutions announced the formation of SD-CAB, the San Diego Center for Algae Biotechnology, amid some outsized calls to make San Diego the top of the mountain in biofuels development. Since then, we’ve continued to see occasional flurries of activity, including startup financings, industry partnerships, and development plans.

At another level, though, a lot of hard work remains to make algal biofuels a reality. An all-day symposium held last month at the Salk Institute highlighted some of the basic R&D that still needs to get done. A two-day Algae World Summit that begins today at the Del Mar Hilton is more of the same, with sessions on “real world” experiences in growing algae, “meeting the challenges” of growing algae in industrial quantities, and practical considerations in project development.

Jose Olivares outlined some of these technical issues for me when he came through San Diego a few weeks ago. Olivares, who was a deputy biosciences leader at the Los Alamos National Laboratory, is now executive director of, the National Alliance for Advanced Biofuels and Bioproducts (NAABB), a consortium of industry, academic, and government researchers. Locally, the alliance includes UC San Diego, as wells as some scientists from HR BioPetroleum and Kai BioEnergy.

Basically, what Olivares told me is that while it is scientifically possible to make gasoline, diesel, and jet fuel from algae, a host of complex engineering and production problems must be solved before algal biofuels production can become an economically viable industry.

“Our mission is to cover innovative technologies that can be brought to bear on any and all parts of algal biofuels production,” Olivares said. Officially, the NAABB’s mission is to lay the technical foundations for a scalable, responsible, and affordable renewable biofuels industry. “We can bring basic scientific principles to prove that the technologies work, and if they don’t work, to establish under what conditions they don’t work,” Olivares said.

As a national alliance, Olivares said the NAABB is focusing its … Next Page »

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San Diego’s Synthetic Genomics, which said last year it’s getting at least $300 million from ExxonMobil to develop algae-based biofuels, has named James Flatt as its new chief technology officer, effective May 19. Flatt previously served as the senior vice president of research at Mascoma Biosciences, a cellulosic ethanol developer that moved last fall from Boston to Lebanon, NH.

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A rising star of the Boston-area venture capital scene is in Seattle today. He’s David Berry, a partner with Flagship Ventures, and he’s speaking on a panel tonight that will tackle a question on every young company’s mind, when it comes to financing: to VC or not to VC? The event is organized by the MIT Enterprise Forum, and the other speakers will include Jonathan Sposato from Picnik (a bootstrapped startup recently acquired by Google); Mark Ashida from OVP Venture Partners; Michael Butler from Cascadia Capital; and moderator Chase Franklin from Daptiv (the former CEO of Qpass).

Berry’s background is quite different from the other panelists—and from most VCs. He graduated in 2005 with an MD-PhD from Harvard and MIT, where he studied bioengineering under professors Ram Sasisekharan and Robert Langer. Flagship Ventures stole him away from an academic career to work on building new companies and developing technologies in energy and therapeutics. He has since co-founded LS9, a Silicon Valley-based synthetic biology firm developing new fuels and chemicals, and Joule Unlimited (formerly Joule Biotechnologies), a Cambridge, MA-based startup that’s using genome engineering to create other types of clean fuels. (Given the strong interest in biofuels and renewable chemicals in the Northwest, Berry has plenty of connections out here.)

When it comes to advising entrepreneurs, Berry is frank about the alternatives to venture money. “It’s unusual for a VC to say venture capital is not always the best choice,” Berry told me by phone yesterday. “But with venture capital firms folding, you have to know where your money is coming from. While money is fungible, long-term money isn’t.”

Here are a few edited highlights from my chat with Berry:

—On his general advice to entrepreneurs:

“At some point you do need capital. There are ways where you can get government grants and so forth. In certain areas you can get some revenues to offset capital needs. As [entrepreneurs] think about where they want to go, the real question is who are the best partners to have along the way, to build the company. That means someone who’s not only trusted around the board table or as an advisor, but someone who will challenge you and push back and make sure you’re thinking strategically in the best way possible.

“From our end [Flagship], we invest in the beginning of a company—the two most important assets are its people and its IP. We care about having the best people around the table, entrepreneurial people who want to solve big problems. Also, people who have a very interesting approach to that—differentiated technologies that are IP protected, and that have some degree of validation.”

—On alternatives to VC in energy and biotech:

“Venture has played a bit of a mainstay role as of late. In energy, there are sovereigns and private wealth holders which have played significant roles—Temasek, and Masdar has been quite active … Next Page »

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NextCAT, a Detroit-based developer of catalysts for biodiesel production, announced today that it has signed an option agreement to produce technology developed at the National Biofuels Energy Laboratory at Wayne State University. NextCat says its catalyst technology can take biomass not currently in the food stream, such as algae and recycled cooking oil, and convert it into fuel. Charles Salley, NextCAT’s interim CEO, said in a prepared statement that with the option agreement, pilot-scale testing can begin this year. NextCAT is housed at TechTown, a Detroit business incubator, and has received funding from the Michigan Pre-Seed Capital Fund.

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There are many differences between this new world of online media and the old world of ink-on-paper that I used to inhabit. So many, in fact, that sometimes I feel like the earthling in the blockbuster “Avatar” who must take archery lessons and learn how to live in an alien culture.

One of the most important differences, though, is that Web-based technologies make it possible nowadays to measure exactly how many people view every story we publish. This can be a humbling experience, and it tends to upend some of those old-world media sensibilities that decreed by front-page fiat that certain stories—like lima beans—are important for readers to digest, whether they like them or not.

So, with the end of 2009 drawing near, I can share some of the stories that attracted the most traffic over the past year at Xconomy San Diego site. I have listed them below, ranked according to popularity, so think of them in a way as Xconomy’s “People’s Choice Awards.” It’s a mixed bag, for sure, which suggests perhaps that we’re appealing to a diverse audience with a variety of interests in our coverage of what we like to call “the exponential economy.” Which is a way of saying, you know, when the facts speak for themselves, what else can an editor to do but interpret and analyze?

—The Untold Story of SAIC, Network Solutions, and the Rise of the Web

This story was No. 1by a long shot. SAIC, the defense contractor that specializes in IT integration, research, and engineering projects, has maintained a low profile since it was founded in San Diego in 1969. So the story behind SAIC’s 1995 acquisition of Network Solutions Inc., which held exclusive rights to register Internet domain names was not widely known. Looking back, former SAIC executive Mike Daniels told me: “Nobody really understood that NSI basically had an exclusive contract to sell dot-com, dot-net, and dot-org to every human being on the planet…”

—San Diego’s Stem Cell Startup Reports Hair-Regrowth Results

The bald truth is many people are yearning for information about new biomedical innovations with the potential to redress an age-old inequity—some people have hair and some don’t. San Diego-based Histogen, which was founded to develop a variety of medical therapies that use stem cells, reported in February that results of an overseas study of its ReGenica treatment for hair growth were encouraging. But a patent infringement lawsuit filed by SkinMedica, a Carlsbad, CA-rival, triggered a funding crisis and forced Histogen to lay off its entire workforce.

—Arena Eagerly Awaits Answer to $1Billion Question: Does it Have a Big Time Obesity Drug?

Sometimes readers show more interest of the story published in advance of a big news announcement than in the announcement itself. That may have been the case with San Diego’s Arena Pharmaceuticals (NASDAQ: ARNA) in reporting the final results of a clinical trial for its experimental weight-loss pill, lorcaserin. The subsequent results were encouraging enough for Arena to file a new drug application earlier this week with the Food and Drug Administration.

—San Diego Biofuels Industry Gains Steam With R&D Consortium

As a journalist, it’s always great to get the big scoop before the rest of the pack.In the case of the formation of the San Diego Center for Algae Biotechnology, I broke this story about four months before the official announcement. Steve Kay, the dean of Biological Sciences at UC San Diego, told me in January that SD-CAB was being organized as a consortium of academic and industry researchers, and represented a regional effort to establish a sustainable algae biofuels industry here in the next five to 10 years. When the formation of SD-CAB was officially announced on April 28, Cleantech San Diego chairman Jim Waring said, “Maybe someday, if the history of algae is ever written, this will be remembered as the day when it all started.”

—La Jolla Pharmaceutical Stock Crashes After Drug Fails in Pivotal Clinical Trial

Luke’s breaking news story about the failed clinical trial of Riquent, a drug developed by San Diego’s La Jolla Pharmaceutical, noted that the announcement wiped out almost 90 percent of the San Diego-based company’s stock value. It also marked the beginning of a series of Xconomy stories that chronicled the layoffs, liquidation plan, and eventual merger of La Jolla Pharmaceutical with Adamis Pharmaceuticals of Del Mar, CA, earlier this month.

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Covering the life sciences in San Diego is never dull, and the news flow last year provided plenty of drama. What follows are some highlights from the past year:

— Embattled tools company Sequenom (NASDAQ: SQNM) scuttled the debut of a non-invasive prenatal Down syndrome test amid a data-mishandling scandal. CEO Harry Stylli was fired along with four other employees. Two others, including CFO Paul Hawran, resigned. The future of the diagnostic test is now in doubt and in November the company, which was being investigated by the SEC and FBI, said it was taking steps to conserve cash to improve its odds of survival.

—Dissident shareholders billionaire Carl Icahn and Eastbourne Capital won two of five board seats in a proxy fight that centered on San Diego-based Amylin Pharmaceuticals’ (NASDAQ: AMLN) strategic management of its strong-selling diabetes drug exenatide (Byetta). Months after its partial victory, Eastbourne sold its entire Amylin stake—after Eastbourne founder Rick Barry voiced some frustration over Amylin’s slow pace of change. Since then, the company struck an important deal to co-develop weight-loss drugs with Japan’s Takeda Pharmaceuticals.

—The spread of swine flu provided a fleeting business opportunity to companies working on diagnostic equipment or novel vaccines. Quidel (NASDAQ: QDEL) reported a surge in sales driven by purchases of its rapid flu test and Life Technologies (NASDAQ: LIFE) saw a bump in revenue from sales to public health laboratories of equipment and reagents for swine flu testing. Funding from the Navy enabled Vical (NASDAQ: VICL) to conduct pre-clinical studies of an experimental swine flu vaccine, but the company has not received the added support needed to conduct a human test.

—San Diego’s emergence as a center for algae-based biofuels came into view during the Algae Biomass Summit in October. Two of the most closely watched algae biofuels companies are here: Sapphire Energy, which is backed by billionaire Bill Gates, and Synthetic Genomics, whose partner, ExxonMobil, announced plans in July to invest $600 million investment in algae-derived biofuels. They and other start-ups are taking advantage of the rich pool of biotechnology talent here. Still, there is no denying it’s early days, and the technology needs to prove itself.

—Biotechs Arena Pharmaceuticals (NASDAQ: ARNA) and Orexigen Therapeutics (NASDAQ: OREX) continued their race for the next blockbuster obesity drug. The companies have released clinical trial results showing … Next Page »

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Here are my top 10 innovations that are coming to the forefront in 2010. Of course, none of these would be possible without the economic engine that is embodied by the USA Science & Engineering Festival, which is creating the innovative minds of the future.

1) High-tech treatment of nuclear waste, a technology that solves the key bottleneck to new nuclear growth and old nuclear cleanup. Example: stealth company Kurion of New York, NY.

2) Coal to Liquid Technologies are the culmination of decades of innovative processes now ready for widespread commercialization. That makes abundant U.S. coal a clean fuel. Example: Accelergy of Houston, TX.

3) LEDs for clean water. Using ultraviolet light emitting diodes (LEDs), which operate at 265nm—the optimum wavelength for germicidal disinfection—represents a breakthrough in water purification. Example: CrystalIS of Green Island, NY.

4) Nanotechnology is transforming cancer treatment by using precise targeting of out-of-control cells, which limits the harsh side-effects of poisoning people with chemotherapy and burning them with radiation. Example: Cerulean Pharma of Cambridge, MA.

5) Rapid Vaccine discovery. Quickly evolving antigens need quickly evolving vaccines. Example: Genocea Biosciences of Cambridge, MA.

6) Wireless TV & Video at 60GHz cuts the cords and the messy morass of connecting wires to create higher quality in-room wireless video area networks. Example: SiBeam of Sunnyvale, CA, with offices in San Diego, Tokyo and Seoul.

7) Efficient data centers at light-speed. By integrating high-performance optics directly with silicon-based electronics, it is possible to bring “fiber to the chip” connectivity to market. Example: Luxtera of Carlsbad, CA.

8) Touch-screens so cheap they’re disposable. Nanostructured materials offer display devices and components with enhanced performance at a lower manufacturing cost. Example: Cambrios of Sunnyvale, CA.

9) Powerless Memory, using the magnetism of electron spin. Technology innovation makes it feasible to store information in magnetic material integrated with silicon circuitry to deliver the speed of SRAM with the non-volatility of Flash. Example: Everspin Technologies of Chandler, AZ.

10) Bio-algae produced fuels. Using the tools of modern biotechnology to identify and optimize strains of algae for the production of biological oils as a substitute for petroleum-based crude oil. Example: Sapphire Energy of San Diego.

[Editor's Note: As the decade comes to an end, we've asked Xconomists and other technology leaders around the country to identify the top innovations they've seen in their fields the past 10 years, or predict the top disruptive technologies that will impact the next decade.]

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Cyber Monday’s online shopping trends provided much of the electronic grist for our Xconomy news mill last week. Get your news here while it’s hot.

—The Department of Energy awarded San Diego’s Sapphire Energy a $50 million grant and the Department of Agriculture provided the company with $54.5 million in federal loan guarantees for construction of an algae biofuel refinery in Southern New Mexico. Sapphire plans to begin construction of the pre-commercial demonstration plant late next year in Columbus, near Las Cruces.

—Internet guru Larry Smarr is encouraging the widespread use of sensors to monitor energy use in buildings. Smarr, director of the California Institute for Telecommunications and Information Technology, told a UCSD forum on green innovation last week, “If you can’t measure it, you can’t manage it.”

—Stylefeeder is an online shopping website with a proprietary recommendation engine that makes personalized product suggestions for users. Because Stylefeeder’s customized learning program is based on shoppers’ preferences and actual purchases, the Cambridge, MA, company is gradually assembling insights into online shopping preferences in different parts of the country. For example Stylefeeder found San Diego shoppers are losing their fervor for Hurley, Volcom, and Kenneth Cole. But they’re excited about Puma, Oakley, and Charlotte Russe.

—Michael Robertson, who sold San Diego-based Gizmo5 to Google a few weeks ago, says the online world has changed since he founded MP3.com and sold it eight years ago to Vivendi for $372 million. “If you’re one of the big guys like eBay, Facebook, or MP3.com, you get that network effect going,” Robertson told me. “But if you’re an also-ran, you have to be more strategic. If you’re not that leader, it’s a totally different business dynamic. You have to source the business opportunities, chase the partners, and work for every deal.”

—Noah Auerhahn and Jeff Nobbs moved to San Diego last year to re-launch an online shopping portal called Extrabux, based on the business plan that won a campus-wide $25,000 business plan competition at USC. Extrabux got a boost from a segment about Cyber Monday online shopping tricks on the ABC-TV news show Good Morning America that prompted 83,000 hits in one day, including 63,000 unique visitors.

—Based on information provided by aspiring technology entrepreneurs and company founders who enroll in the Founder Institute’s business incubator and mentoring program, Seattle ranks highest and San Diego lowest in likelihood for entrepreneurial success. The Seattle program begins today. The San Diego program, which began in November, has enrolled 22 students and has scheduled its graduation for Feb. 23.

—Connect, the San Diego non-profit group that supports technology and entrepreneurship, gave its 2009 William W. Otterson Award to the Predator, the unmanned surveillance aircraft developed for the military by San Diego-based General Atomics. The Otterson award is based on technologies or product developed in San Diego that have demonstrated a significan positive impact on society or on quality of life.

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San Diego’s tech sector got some money and glory during a week that was overshadowed by news from two life science conferences: TEDMED and the annual Biocom Investor Conference. Get your tech news now while it’s still hot.

—To stay connected with open-source development for smart phones, San Diego’s Qualcomm created a subsidiary, the Qualcomm Innovation Center, that is focused on making sure the chipmaker’s technology works smoothly with Android, Symbian, and other open-source wireless platforms. Qualcomm (NASDAQ: QCOM) also joined the Symbian Foundation and is supporting the open source systems used by Nokia and others.

—One of the big selling points for algae-based fuels is that algae absorbs a lot of carbon dioxide before it gets harvested and turned into biofuels. Yet San Diego-based Sapphire Energy and other algae biofuel companies say they are having a hard time getting enough carbon dioxide at an affordable price to support their research and development efforts.

—Federal stimulus funds will help cover almost half the cost of a new $60 million wireless communications system that San Diego Gas & Electric is developing as part of its smart grid program. The $28.1 million grant is part of $3.4 billion to be allocated nationwide.

—Carlsbad CA-based Verdezyne, which is applying advanced biotechnology tools to the development of industrial chemicals and biofuels, raised nearly $3 million of a planned $15.2 million round of venture capital.

—JMI Equity, the venture firm based in San Diego and Baltimore, led a $5 million investment in Axeda, the Waltham, MA-based startup that makes a cloud-based system for wireless tracking of company assets. Axeda also raised $4 million in venture debt from MMV Financial of Toronto.

—TechAmerica San Diego, the local chapter of the industry group previously known as the AeA, issued nine awards at its 16th annual high tech awards luncheon. The group named winners in nine categories: MadCap Software (Software); InterKnowlogy (Internet); Verari Systems (Hardware); Quake Global (Communications); SeaBotix Inc. (Defense); Peregrine Semiconductor (Integrated Circuits); OneRecovery (Medical Device) IPS Group (Cleantech); Legend Films (Emerging Growth).

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