Contrary to what you might expect, the pace of tech news out of San Diego didn’t slow down much before the Thanksgiving Holiday. We still managed to round it all up, though, and our briefing begins here.

—As director of the UC system’s California Institute for Telecommunications and Information Technology (CalIT2), Larry Smarr is an Internet pioneer who frequently offers his perspective on the future of IT technologies. Lately, however, Smarr has been providing a glimpse at the future of “quantified health” and digitally enabled genomic medicine. In a Q&A with Smarr, he told me he found he had one chemical marker (out of 60 that he regularly tracks) that was five times higher than the recommended upper limit—triggering a kind of detective story that illustrates the potential revolution in health IT and wireless health.

—In the U.S. Navy’s largest demonstration of alternative fuels, a decommissioned Navy destroyer refitted as a kind of ocean-going test facility completed a 17-hour transit from San Diego to Port Hueneme. The Spruance-class destroyer used a 50-50 mixture of standard Navy diesel fuel and algae-based diesel produced by San Francisco-based Solazyme.

—Mellmo, the four-year-old startup based in Solana Beach, CA, has been moving into overseas markets in Europe and Asia with Roambi, its Web-based business intelligence graphics service. Mellmo co-founder Quinton Alsbury also talked with me about Roambi Flow, a new service that enables corporate customers to wrap text around their Roambi graphics to produce magazine-quality reports for the iPad.

—The case of the 2010 murder of San Diego angel investor and retired life sciences executive John G. Watson came to a close when a San Diego jury convicted Kent Thomas Keigwin of first-degree murder, attempted grand theft of personal property, burglary, and forgery. The prosecutor argued that Keigwin, who was working as a financial advisor, used Watson’s personal information to transfer some $8.9 million from Watson’s accounts.

—San Diego-based Next Autoworks, which was once known as V Vehicle, withdrew its … Next Page »

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There are two kinds of people: Those who already own an iPhone 4S, and those who don’t but have seen Apple’s Siri ads and wish they did. Siri, of course, is the voice-operated personal assistant that can read your text messages, schedule appointments, check on the weather, make waffles, and babysit your toddler (just kidding about those last two). It’s the coolest feature of the latest Apple smartphone, which went on sale last week. Virtually overnight, it has brought state-of-the-art artificial intelligence technology into the consumer mainstream.

Well, it turns out that there’s more where that came from. The same Silicon Valley defense project that gave birth to Siri—called CALO, for Cognitive Assistant that Learns and Organizes (more on this below)—has another, lesser-known spinoff, a Palo Alto news personalization startup called Trapit. The company’s web-based service uses AI to organize the welter of new content that appears online every day into tailored collections called “traps.” And while the technology is still a bit raw, there’s a chance that it could have the same kind of impact in the world of Web search and online news that Siri is beginning to have on mobile interfaces.

I’ve been playing with TrapIt for about three months now. It hasn’t become a part of my daily news-browsing routine, but I can definitely see that happening if the startup continues to refine the interface, improve its search algorithms, and make the site more tablet-friendly. (Trapit took the lid off its service in June, but it remains in closed beta testing, which means you have to request an invitation to get an account. The wait was short when I registered. The company says it’s going to open the beta version of its service to the whole public later this fall.)

The first thing to try when you go to Trapit is either to browse one of the existing, featured traps—which are often related to breaking news, such as yesterday’s killing of Muammar Qaddafi—or start one of your own by entering a phrase or keyword into the “Discover” bar. After a short wait, you’ll be presented with recent news stories and blog posts on your topic, culled from across the Web.

At first the selection may seem pretty random. The neat part is that as you peruse various articles, which pop up in lightbox-style windows, Trapit observes what you’re reading, how long you spend with each article, and what you’re sharing with others. It uses these cues and others to beef up its profile of your personal tastes, so that over time it’s able to surface more articles that fit your interests and fewer that don’t.

You can also train Trapit manually by clicking on the thumbs-up or thumbs-down buttons—and the more you do this, the faster the software will learn your preferences. As you create traps on new topics and train your existing traps, you can end up with a whole gallery of mini-magazines, exclusively tuned to the mix of subjects that you, and you alone, are passionate about. It’s a pretty unique service—the closest comparison I can think of is Google Alerts, which are like standing search queries with the results e-mailed to your inbox every day. But Trapit is more like regular Web surfing. It’s just that you’re surfing the Web you want.

Trapit’s AI-driven approach goes completely counter to the dominant trend in news curation today, which emphasizes the power of social networking and collaborative filtering. News aggregation apps like Flipboard, Pulse, AOL’s Editions, CNN’s Zite, Yahoo’s Livestand, and Google’s forthcoming Propeller platform may seem to provide personalized news feeds, but … Next Page »

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It was a full and busy week for life sciences news in San Diego, with interesting advances in wireless health and a variety of deals. I’m planning at least one more report from the Wireless Health 2011 Conference, but in the meantime, here’s everything else.

North Carolina Gov. Beverly Burdue said yesterday that San Diego-based Sequenom (NASDAQ: SQNM) plans to build an $18.7 million molecular diagnostics clinical laboratory in the Research Triangle Park. Tar Heels state officials offered the diagnostics company as much as $2.3 million in incentives if Sequenom can meet certain hiring and investment goals. Sequenom, which currently has more than 280 employees in San Diego, would nearly double in size, as the North Carolina lab is expected to create 242 jobs over the next five years. Sequenom has been working to commercialize its noninvasive test for Down syndrome, which identifies a fetal marker for the condition that circulates in the maternal bloodstream.

—The Wireless Health 2011 Conference, a scientific and technical symposium, continues through today at the Hilton La Jolla Torrey Pines. In a keynote presentation earlier this week, Qualcomm (NASDAQ: QCOM) CEO Paul Jacobs demonstrated a mobile app developed by San Francisco-based AliveCor that turns an iPhone into an electrocardiograph device. “The future is already here,” Jacobs said, quoting the sci-fi writer William Gibson. “It’s just not very equally distributed.” AliveCor raised $3 million in first round venture funding earlier this year from Qualcomm Ventures, Burrill & Co., and the Oklahoma Life Sciences Fund.

—The price of shares in San Diego-based Illumina plunged by 32 percent after the company posted disappointing third quarter sales of $235 million, about $40 million short of expectations. Illumina, the market leader in high-speed gene sequencing instruments, also withdrew its 2011 sales forecast “due to the many market uncertainties.” Illumina’s stock, which had been trading around $40 a share, fell to $27.08 on the news last week. Illumina (NASDAQ: ILMN) shares closed yesterday at $26.04.

—I sat down with the chairman and CEO of PatientSafe Solutions, Jim Sweeney, who talked about the wireless healthcare company’s PatientTouch device, a souped-up Apple iPod Touch that’s been extensively modified to help … Next Page »

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What was the biggest life sciences news over the past week? It might be that five San Diego companies landed financing deals, grants, and payments. Here are our highlights.

—The U.S. Food and Drug Administration outlined a new strategic initiative intended to address industry criticism that the agency has been thwarting life sciences innovation through its bureaucratic reviews and overall unpredictability. “The number of new products in the development pipeline is not where we’d like it to be,” FDA commissioner Margaret Hamburg told reporters last week in releasing a 40-page overview. “Timelines are long, costs are high, and rates of failure are distressingly high.”

—Mountain View, CA’s Complete Genomics said it has agreed to generate the whole genome sequences of 1,000 healthy senior citizens for a study underway at the Scripps Health system in San Diego. The trial dubbed as the Wellderly Study is enrolling people from 80 through 108 years old who are without long-term health complications. Scripps cardiologist Eric Topol, who is overseeing the Wellderly Study, wants to identify factors that have enabled them to live such long, healthy lives.

—It’s clear that the kind of fast and inexpensive genome sequencing to be used in Scripps Wellderly Study is provoking widespread attention. Xconomy is convening an Oct. 24 conference in San Francisco on the implication of fast and cheap genome sequencing and the role computing will play in this big story over the coming decade. In San Diego, Biocom has organized an Oct. 26 event to discuss how life sciences organizations can take advantage of advances in fast and cheap sequencing.

—Cyberonics (NASDAQ: CYBX) said it’s making an investment in ImThera Medical that could eventually total as much as $12 million if ImThera meets certain milestones. ImThera, which initially got $4 million in funding, has been developing an implantable neurostimulation device for treating obstructive sleep apnea. Cyberonics makes a neurostimulation device used to … Next Page »

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The Pentagon’s Defense Advance Research Projects Agency (DARPA) has awarded a $6.8 million contract to San Diego’s Aethlon Medical to develop a medical device that could be used to reduce the incidence of sepsis, a potentially fatal bloodstream infection.

In a statement today, Aethlon says sepsis often the cause of death in combat-injured soldiers.

Aethlon says it will use its adaptive dialysis-like affinity platform technology as the basis for a blood purification system capable of filtering multiple sepsis-enabling particles from circulation. Developing such technology falls under the auspices of DARPA’s Dialysis-Like Therapeutics program, and is intended to dramatically reduce sepsis-induced morbidity and mortality.

Aethlon says it plans to incorporate a new blood pump strategy to reduce or eliminate the systemic administration of anticoagulants normally required during dialysis and other extracorporeal device therapies.

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As one who’s spent a lifetime chasing the quest of a practical, sustainable bioeconomy – I have sympathy for biofuel skeptics. Let’s face it; petroleum is an incumbent that has no match in political or economic strength. But it is hard to deny the convergence of historical and technological trends that suggest a sustainable biofuel might soon be feasible. I have had the privilege of spending the last year in an effort called Sustainable Aviation Fuels Northwest and learned much from over forty stakeholders in the project. Let me offer four observations that give me some optimism about the viability of next generation biofuels.

Historical Shifts

Serious support for biofuels is very recent. The chemurgy movement (the early 20th century emphasis on biofuels and bioproducts from agriculture) never gained broad political traction. The Energy Security Act of 1980 mentioned biofuels but funding and interest fizzled quickly. It was not until the Farm Bill of 2002 there was an energy title, and serious support began. The last decade’s rapid ascent of Biofuels 1.0 (that being corn-based ethanol and soy-based diesel) was unprecedented. While hindsight suggests energy efficiency, environmental and economic impact could have been better managed, the creation of B1.0 didn’t include those requirements. The spark that ignited growth was the diversification and creation of new markets for a surplus of agricultural commodities while also reducing oil imports and boosting rural economic development. It was a supply-side push.

The biofuels industry emerging today (let’s call it B2.0) has learned from this brief history. First, it is now the consumers (not the producers) of the fuel looking for diversity – they seek a reliably sourced portfolio of biofeedstocks – not one silver bullet. Second, unlike ethanol and biodiesel, these new biofuels are distillates or ‘drop-in’ fuels meaning they can be blended and are compatible with petroleum’s infrastructure of refineries, pipelines, and storage. Third, these consumers are demanding global accepted standards for sustainability. Very pragmatic, in exchange for their backing of these new biofuels, they want assurance the supply chains are net energy positive, that carbon and other greenhouse gas emissions are significantly reduced, and they contribute to the environmental, economic, and social health of the region from which they are sourced and used.

Creating a viable B2.0 industry is also attracting talent, perhaps like never before. Biologists who pioneered the human genome like Craig Venter, George Church, even Lee Hood of the Institute for Systems Biology and David Baker of the University of Washington—all noted life science rock stars—have been attracted to the allure and challenge of a sustainable biofuel. Coupled with legacy agricultural land grants, like Washington State University where biofuels never went out of style, the sector is rapidly advancing. Over the past year, among the 10 IPOs in the clean tech space, four are involved with biofuels (Codexis, Solazyme, Amyris, Gevo) and one more is expected, Qteros. A few of these are converting alcohol fuels to distillates, efficiently linking B1.0 to 2.0. Most have valuable co-products and multinational partners. Some might call it a tipping point.

Acknowledging Limits

Deserved or not, B1.0 can also be credited with popularizing the food versus fuel debate. I am pleased with this acknowledgment that our fields, forests, and waters have a finite (but growing) capacity to produce biomass. I am disappointed that the issues have been purposely shaped into a false choice.

Regardless of how or where it’s produced, biomass has five primary fates:

Food – eaten in human diets

Feed – grazed, fed, or consumed in animal diets

Fiber -used for textiles, paper, and other products

Fuel – consumed (usually combusted) for its energy content

Functionality – residing in the ecosystem necessary to cycle nutrients and energy

The allocation of biomass among the ’5F’ fates have been on-going for all of human existence, and always been determined by society. Many a study and book have been written about those cultures where choices were unwise, and history suggests success has only come with … Next Page »

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Sometimes what’s bad for companies is good for business. That’s the case for a number of Massachusetts security software firms. These days, the Boston area seems to have renewed its claim as an epicenter of cyber security activity.

In the wake of the recent, much-publicized cyber attack on RSA Security, a division of Hopkinton, MA-based EMC (NYSE: EMC), I thought it would be a good time to check on efforts to meet new cyber threats by some local security companies. RSA classified the attack on its system last week as an “advanced persistent threat”—a phrase used to describe a sophisticated effort to target software applications, sensitive data, or end users—but the firm was vague about exactly how it was hacked, what kinds of data were stolen, and what risks its customers face. (RSA said it is working closely with customers, but security expert Bruce Schneier wrote in a blog post that “the company has lost its customers’ trust.”)

This kind of advanced threat is a far cry from the corporate hacking of the past couple of decades. Companies used to be able to defend themselves from rogue hackers by deploying technologies around the perimeter of their network—such as firewalls and “deep packet inspection,” which detects things like viruses and worms as they enter the network. But advanced persistent threats are what defense and intelligence agencies are used to seeing from nation-states (from China to the Middle East to Eastern Europe) trying to hack into government databases—except now their targets include banks, insurance companies, tech firms (Google, Adobe, and others), and critical infrastructure like energy and chemical firms.

All is not lost yet. In addition to big companies like EMC/RSA (which also includes security technology from Network Intelligence), a number of smaller but established software companies are working on ways to combat the latest security threats. One of these companies is Fidelis Security Systems, a nine-year-old firm in Waltham, MA, that is giving corporations and government agencies the ability to continuously identify and analyze threats from within their networks, down to the level of applications, files, and individual sessions.

That’s apparently crucial for fighting advanced persistent threats, which can take the form of anything from malware embedded in a PDF file to tricking an employee into accessing a website and then exploiting a software bug. “When somebody decides to make you a target, they will persistently and, in a very targeted way, try to infiltrate your network,” says Fidelis CEO Peter George.

One big emerging trend is government agencies working together with corporations to try to thwart such attacks. This increased cooperation was evident at the RSA Conference in San Francisco last month, George says, where a number of forums and panels featured “three-star generals sitting side by side with business leaders.” The U.S. government, he says, is “working in collaboration with the biggest enterprises in the world to show them best practices, to show them how to fight advanced threats.”

All of this points to a major mindset shift when it comes to corporate data security. “Organizations should continue to act under the assumption that the attackers are already inside, rather than dedicate excessive time and resources to securing their perimeter,” says Adam Bosnian, executive vice president at Cyber-Ark Software, a Newton, MA-based security company that specializes in managing privileged users and protecting against insider threats, among other things.

Fidelis and Cyber-Ark are part of a thriving cluster of Boston-area security companies … Next Page »

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In case you haven’t noticed, heart disease remains a debilitating illness for millions. Cancer, despite some recent advances, has not been cured. Drug resistant strains of bacteria are spreading across the globe. There are still no effective treatments for Parkinson’s disease, amyotrophic lateral sclerosis, muscular dystrophy, and a huge number of other illnesses.

The number of new medicines being brought to market has been declining in recent years at a time when we desperately need new treatments. A recent analysis of drugs moving through FDA trials in 2003-2010 found that the overall success rate was only about 14 percent for primary indications, and a dismal 3 percent success rate for secondary indications. The number of new drugs launched annually has fallen 44 percent since 1997, according to CMR International.

A variety of reasons have been put forth to explain this deterioration, as described below. As a nation, we should be doing all that we can to encourage innovators to find effective treatments for these diseases. Developing medications to successfully treat human diseases is an expensive enterprise, so it makes sense to ask the question: where will the new medicines come from? What financial resources are available now to biomedical researchers to fund their work, and who’s going to pay for future drug development?

A good place to start to answer these questions is to have an understanding of where our present drugs have come from. Two recent studies illustrate nicely that modern medicines originate from a variety of sources, and help explain the expanding number of partnerships between industry and academia. Robert Kneller examined every drug approved by the FDA over the past 10 years, and determined for each one whether it originated with pharmaceutical companies, from biotechs, or sprang forth from the labs of academic investigators. His analysis showed that about half of all new drugs arise from pharmaceutical companies, while the other half arise from the efforts of biotech firms and academic investigators. In a separate study, other researchers identified which medicines resulted from public sector research over the past 40 years. Their analysis identified some 153 products that were discovered or co-discovered by 75 different academic institutions. These drugs accounted for some 13 percent of all FDA approvals over that period. Having roughly quantified where our drugs come from, let’s shift our focus to how this drug discovery work gets funded. What monetary sources are available to biomedical researchers in the public and private sectors? Here’s what my informal survey found:

Pharma and Biotechs Still Lead the Charge (Funding Level: $65.3 billion in 2009)

There is no doubt that pharma and biotech companies are the major source of new drug discoveries. However, both groups find themselves under significant fiscal pressures as a result of troubles in the financial markets, recent patent expirations, and their diminishing number of drug approvals in the past decade. Why have these numbers been declining? The primary problem faced by industry is the challenge of translating basic biological discoveries (e.g. genomic sequences; RNA interference; mutated genes) into functional drugs. Although scientists have determined the causes of many diseases over the past quarter century, they haven’t figured out yet how to fix many of them. Other urgent industry concerns include pricing pressures, reimbursement issues, regulatory hurdles, generic competition, and investor expectations. Big Pharma’s response to these challenges have varied: some companies responded by either maintaining or increasing their research and development commitments (e.g. Merck), while others took the opposite approach and slashed their research dollars (e.g. Pfizer, Glaxo).

Many Big Pharma companies have been slowly transforming themselves over the past few years to be more like biotechs. They have taken note of the fact that the success rate for getting biologics (e.g. recombinant growth factors, monoclonal antibodies) approved is twice that seen with their small molecule drugs. Generic competitors of their blockbuster small molecule drugs are continuing to poke enormous … Next Page »

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Last week’s Consumer Electronics Show dominated San Diego’s tech news last week. We have the highlights from the two dozen San Diego tech companies that attended the annual conference, along with the rest of the local biztech news.

—In one more sign that Wi-Fi is becoming increasingly important to the future of wireless network infrastructure, San Diego’s Qualcomm (NASDAQ: QCOM) said it’s buying San Jose-based chipmaker Atheros Communications (NASDAQ: ATHR) for roughly $3.1 billion. The acquisition, if finalized, is Qualcomm’s biggest ever—and expands the wireless giant’s reach into products that span cellular, home, smart grid, and sensor networks.

—Motorola split into two new companies—Motorola Solutions, which will remain in Motorola’s headquarters in Schaumburg, IL, and Motorola Mobility, which is moving, for now, to nearby Libertyville, IL. There’s no word yet on whether Motorola Mobility, now headed by former Qualcomm COO Sanjay Jha, will move its HQ to San Diego, the Bay Area, or Austin, TX, the three cities Jha said the company was considering late last year.

—The annual Consumer Electronics Show regained its appeal as more than 140,000 attendees flooded the halls of the Las Vegas Convention Center last week. The hottest electronics categories this year included smart phones, tablets, and TVs, and we saw the world of software apps moving from complex suites such as Microsoft Office to simpler “best of breed” apps available online at places like the Apple App Store.

—Sony Electronics, whose North American headquarters is in San Diego, led the charge in Web-enabled television with its lineup of sets powered … Next Page »

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When science fiction fans think about language translation, they have two main reference points. One is the Universal Translator, software built into the communicators used by Star Trek crews for simultaneous, two-way translation of alien languages. The other is the Babel fish from Douglas Adams’ The Hitchhiker’s Guide to the Galaxy, which did the same thing from its home in the listener’s auditory canal.

When AltaVista named its Web-based text translation service after the Babel fish in 1997, it was a bit of a stretch: the tool’s translations were often hilariously bad. For a while, in fact, it seemed that the predictions of the Star Trek writers—that the Universal Translator would be invented sometime around the year 2150—might be accurate.

But the once-infant field of machine translation has grown up quite a bit in the last half-decade. It’s been nourished by the same three trends that I wrote about on Monday in the first part of this week’s series about Google’s vision of “augmented humanity.” One is the gradual displacement of rules-based approaches to processing speech and language by statistical, data-driven approaches, which have proved far more effective. Another is the creation of a distributed cloud-computing infrastructure capable of holding the statistical models in active memory and crunching the numbers on a massive scale. Third, and just as important, has been the profusion of real-world data for the models to learn from.

In machine translation, just as in speech recognition, Google has unique assets in all three of these areas—assets that are allowing it to build a product-development lead that may become more and more difficult for competitors to surmount. Already, the search giant offers a “Google Translate” app that lets an Android user speak to his phone in one language and hear speech-synthesized translations in a range of languages almost instantly. In on-stage previews, Google has been showing off “conversation-mode” version of the app that does the same thing for two people. (Check out Google employees Hugo Barra and Kay Oberbeck carrying out a conversation in English and German in this section of a Google presentation in Berlin last September.)

While still experimental, the conversation app is eerily reminiscent of the fictional Universal Translator. Suddenly, the day seems much closer when anyone with an Internet-connected smartphone will be able to make their way through a foreign city without knowing a word of the local language.

In October, I met with Franz Josef Och, the head of Google’s machine translation research effort behind the Translate app, and learned quite a bit about how Google approaches translation. Och’s long-term vision is similar to that of Michael Cohen, who leads Google’s efforts in speech recognition. Cohen wants to eliminate the speech-text dichotomy as an impediment, so that it’s easier to communicate with and through our mobile devices; Och wants to take away the problem of language incomprehension. “The goal right from the beginning was to say, what can we do to break down the language barrier wherever it appears,” Och says.

This barrier is obviously higher for many Americans than it is for others, present company included—I’m functionally monolingual despite years of Russian, French, and Spanish classes. (“It’s always a shock to Americans,” Google CEO Eric Schmidt quipped during the Berlin presentation, but “people actually don’t all speak English.”) So a Babel fish in my ear—or in my phone, at any rate—would definitely count as a step toward the augmented existence Schmidt describes.

But in the big picture, Google’s machine translation work is really just a subset of its larger effort to make the world’s information “universally accessible and useful.” After all, quite a bit of this information is in languages other than those you or I may understand.

The Magic Is in the Data

Given the importance of language understanding in military affairs, from intelligence-gathering to communicating with local citizens in conflict zones, it isn’t surprising that Och, like Cohen, found his way to Google by way of the U.S. Defense Advanced Research Projects Agency (DARPA). The German native, who had done masters work in statistical machine translation at the University of Nuremberg and PhD work at the University of Aachen, spent the early 2000s doing DARPA-funded research at USC’s Information Sciences Institute. His work there focused on … Next Page »

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The U.S. military’s interest in developing algae biofuels dates back at least three years, when the Defense Advanced Research Projects Agency (DARPA) began to assess the technical capabilities needed to produce JP-8 grade jet fuel. By the end of 2008, DARPA awarded separate contracts to San Diego’s General Atomics and SAIC, now based in McLean, VA, to make jet fuel from algae and cellulosic feedstocks.

The extent of the Pentagon’s interest became more apparent last week at BIO’s Pacific Rim Summit in Honolulu, according to Biofuels Digest. Editor Jim Lane says the Department of Defense could prove to be the ultimate driver of advanced algae-based biofuels in the United States, “by stepping up as a buyer, and communicating buying signals to the makers of advanced biofuels and their financiers.”

That view was seconded in a weekend column by none other than Thomas L. Friedman of The New York Times, who wrote that Secretary of the Navy Ray Mabus (a former U.S. ambassador to Saudi Arabia) wants to create a “Great Green Fleet” by 2012—a 13-ship carrier battle group powered either by nuclear energy or 50-50 blends of biofuels. Navy aircraft assigned to the fleet would fly on a 50-50 blend of biofuel and conventional fuel.

Friedman adds: “Mabus has also set a goal for the Navy to use alternative energy sources to provide 50 percent of the energy for all its war-fighting ships, planes, vehicles and shore installations by 2020. If the Navy really uses its buying power when buying power, and setting building efficiency standards, it alone could expand the green energy market in a decisive way.”

To meet this goal in 2020, the Navy will need 336 million gallons of drop-in advanced biofuels every year.

Biofuels Digest quotes Chris Tindal, the Navy’s Deputy Director for Renewable Energy, telling the audience in Honolulu: “We need drop-in replacements—we don’t have the time to do engine reconfigurations, so we are working on a series of tests to ensure green strike group certification by 2012 and across our fleet. Which is why we conducted, this past Earth Day, a 1.2 Mach supersonic test of our F-18 Hornet, which we renamed the Green Hornet of course, using camelina-based jet fuel.”

Also quoted is Jason Pyle, founding CEO of San Diego’s Sapphire Energy: “In looking to agriculture to provide the answers, we saw that there are 375 million acres of water-based agriculture. 27 percent of world’s dietary energy comes from rice, and rice is the model system we aspire to.”

The confluence of these two forces, Navy business and algae-based biofuel development, can only enhance San Diego’s emergence as a center for biofuel development.

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Pulmatrix might have just the defense for soldiers against respiratory invaders. Now the Lexington, MA-based biotech firm has won a $5.7 million grant to advance its technology that originated at MIT and Harvard for defense purposes.

The Defense Advanced Research Projects Agency (DARPA), part of the U.S. Department of Defense, awarded the firm the grant to fund research for two years that is intended to lead to an inhaled dry-powder therapy, according to the company. The idea is to provide a soldier with one inhaled therapy that could treat and prevent multiple lung infections, including those brought on by natural pathogens or acts of biological warfare. The treatment could also be given to civilians, according to the company.

CEO Robert Connelly explained that this grant complements the work his firm is already doing to develop inhaled dry-powder therapies for reducing the effects of respiratory ailments such as asthma and chronic obstructive pulmonary disease (COPD). Yet this defense award calls for the firm’s therapy to be delivered with a small inhaler that a soldier would carry during a mission. First, though, the company needs to develop the powder formula for the inhaler, then develop the inhaler itself.

“If you put yourself in the shoes of a soldier who is [at war] somewhere around the world, it’s not known what weapon or what viruses that are specific to that locale are in the air,” Connelly said. “So off the bat what you get with our technology is a take-on-all-comers approach” to combating multiple inhaled pathogens.

Defense agencies have known of the startup for years. Founded in 2003 with technology from the labs of Bob Langer at MIT and David Edwards at Harvard University, the firm received some of its early support through $1.8 million in defense- and homeland security-related funding from the U.S. government’s Technical Support Working Group, according to Connelly.

The DARPA grant will support work of the company’s core technology that has already helped the firm raise $45 million in equity investments from … Next Page »

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OK, a flying Humvee doesn’t sound like a very green vehicle—but the U.S. Defense Advanced Research Projects Agency isn’t interested in green.

DARPA is interested in improving the safety and lethality of U.S. troops in dangerous environments. And it is willing to pay handsomely for it—to the tune of a five-year, $65 million research program to develop what it calls a “Transformer” vehicle that works like a Humvee on land, but can also fly.

No, this isn’t an Onion article. The goal is to be able to carry four troops and their gear (1,000 pounds) over a distance of 280 miles on one tank of fuel, by any combination of air and land, the agency says. The vehicle must be able to take off and land vertically—meaning it will fly like a cross between a helicopter and a plane (see drawing above). And, oh yeah, it has to be piloted by an average Marine Corps soldier without any flight experience. In other words, it needs to fly mostly by itself.

If it works—a big if, indeed—such a vehicle could swoop over obstacles or tough terrain, and potentially could help troops avoid ambushes and improvised explosive devices in roads. It could also be used for evacuation or rescue missions where it would be very useful to scan the situation from the air and then drop in at the right spot—in urban combat operations, say—while maintaining some mobility on the ground after landing. (You can read more details and speculation in this Popular Mechanics article.)

A key participant in the DARPA program is Woburn, MA-based Terrafugia. You might know it as the “flying car” company, though the firm much prefers the drier term “roadable aircraft.” Terrafugia was founded in 2006 by five MIT-educated pilots, and has been developing a light sport plane, called the Transition, that can be driven on roads and is slated for testing and production next year. The company declined to comment on its involvement in the DARPA program beyond the information in its press release this week. But it’s clear that Terrafugia’s expertise in combining flying and driving vehicles is valuable here.

Indeed, Terrafugia is “one of the few companies that has experience blending the disparate ground vehicle and aircraft requirements into a single functional concept,” says Stephen Waller, the program manager for the DARPA project, in an e-mail. “This is the primary challenge to successfully develop the Transformer vehicle.”

Terrafugia is one of several companies participating in the program—and a few have connections to the Boston area. Virginia-based aerospace firm Aurora Flight Sciences, which has a research and development office in Cambridge, MA, and technical consulting firm Metis Design, based in Cambridge, both have received small-business research grants to work on the project. For its part, Terrafugia is the largest subcontractor to AAI, a Maryland-based aerospace and defense company owned by Textron, a multi-industry conglomerate headquartered in Rhode Island. AAI is one of the two main contractors on the DARPA project; defense tech giant Lockheed Martin is the other (see drawing on left for Lockheed’s competing design concept).

Meanwhile, Carnegie Mellon University in Pittsburgh has been awarded $988,000 to develop an autonomous control system for the vehicle. Sanjiv Singh, a professor in CMU’s Robotics Institute, is leading that effort. And rocket engine company Pratt & Whitney Rocketdyne is working on the engine and propulsion technology for the … Next Page »

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Seattle-based supercomputing company Cray (NASDAQ: CRAY) has inked a contract deal with the University of Stuttgart, to deliver two supercomputers to the University’s High Performance Computing Center Stuttgart (HLRS). The multi-year, multi-phase contract is worth an estimated $60 million. The first phase of the contract will take place in 2011, during which the Cray XE6 supercomputer will go into production at the university. The second supercomputer, the next-generation Cascade, will be delivered to the university in 2013. Cray says the Cascade is made possible, in part, by the company’s participation in the Defense Advance Research Project Agency’s (DARPA) High Productivity Computer Systems program earlier this year.

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Last week, Waltham, MA-based defense contractor Raytheon (NYSE: RTN) unveiled its latest prototype “exoskeleton.” This is a powered robotic suit that a soldier or worker could strap on in the field to enable them to load heavy equipment faster, carry supplies or munitions using less energy, or—let’s face it—just look ultra-cool. Raytheon said in a statement that the new robotic suit is “lighter, stronger, and faster than its predecessor, yet it uses 50 percent less power.” The device is powered by high-pressure hydraulics and gives its wearer some degree of super strength.

In the demo, which took place at Raytheon’s Sarcos subsidiary in Salt Lake City, UT, an engineer wearing the suit (which includes arms and legs) punched through some boards, did pushups, and lifted weights with little effort. The news was reported fairly breathlessly by media outlets including CNET, Wired, Scientific American, and the L.A. Times. And I understand why—it’s a sexy technology that conjures up visions of “Iron Man” and mythical references to superhuman strength. Plus it’s far more accessible than all the top-secret stuff Raytheon does that is actually useful for the military—radar systems, cybersecurity, missile defense, and so forth.

But I wondered how much progress has really been made in exoskeletons—in the fundamental robotics, sensing, control, and energy technologies necessary to make a robot suit powerful, safe, and reliable to move around in. Raytheon declined to be interviewed for this story, but I did some digging around.

After all, I’ve been following the field since 2001, when I worked in the old Leg Lab at MIT, which was home to robots that could walk, run, hop, and keep their balance. Back then, the main problems with designing a robotic exoskeleton were how to make it powerful without being clunky, how to control it safely, and how to supply enough energy to it.

In 2002, I attended a private meeting of the U.S. Defense Advanced Research Projects Agency program on “exoskeletons for human performance augmentation” (from which I still sport a nifty backpack, though it doesn’t give me super strength). The program manager was Ephrahim Garcia, a professor at Cornell University, who later handed it off to engineer John Main. At the time, about a dozen universities and research groups were competing to build exoskeleton technologies for DARPA, and Sarcos had one of the designs that eventually won out. A couple years later, I visited Sarcos (which Raytheon acquired in 2007) and got a tour of the Utah lab and an early demo from its leader, Steve Jacobsen, for a photo essay in Technology Review.

My first impression from the demo last week was that not much has changed in the field in the past decade. That’s a bit surprising, since other kinds of robots—Predator aerial drones, PackBots, Roombas—have become increasingly sophisticated as they’ve been commercialized and deployed by the military. As it turns out, though, my first impression of the Raytheon device was not entirely correct.

“They’ve clearly demonstrated increases in strength,” says Hugh Herr, a professor who leads the biomechatronics group at the MIT Media Lab, which works on things like smart … Next Page »

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It’s hard to hear the term “wind power” without picturing the giant, bladed turbines that are currently used to generate this kind of renewable energy.

Ann Arbor, MI-based Accio Energy is trying to shake this up. The company is using fundamental physics to produce wind power without turbines—a transformation that could make wind energy more widespread and easier to deploy, says Jennifer Baird, who joined the company as CEO just last week. (Baird is no newcomer to Accio, though, having worked on a part-time basis at the company for a stint earlier this year.)

Accio‘s (pronounced ACK-ee-o) method hinges on flat panels that spray an electrically charged mist of water into a windy area. “That charged mist is a screen and the wind is pushing against that screen and doing work,” she says. Baird didn’t give too many details on how exactly it works, but essentially the device separates the charged water particles and creates an electric current that can be harvested. And the wind’s movement produces more energy than it takes to get the particles charged, Baird says.

While traditional turbines require significant planning, space, and maintenance to harvest wind energy, Accio says its technology can be easily scaled, since it all relies on the flat-panel units (check out this report for a picture of the devices). The “aerovoltaic” system can be expanded by linking additional panels together, to accommodate larger areas and generate more energy, Baird says.

The main challenge to the system is the water supply that’s required to create the charged mist. But Baird says that’s less of a burden than it might appear to be on the surface. “The really scarce resource is clean drinking water; [The Accio system] can use lots of other versions of water,” like unpurified or wastewater, she says,

Baird says this method of using fundamental physics to … Next Page »

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There were, surprisingly, quite a few Seattle-area technology deals this week, breaking the typically slow summer deals trend we’ve seen recently. In the last week we’ve seen a local supercomputing company nab a pretty hefty Department of Defense grant, a cleantech startup partner with the Environmental Protection Agency, and an info commerce company settle a nasty dispute with the Washington State Attorney General’s office. Take a look at the highlights:

—Seattle-based supercomputing company Cray (NASDAQ: CRAY), was part of a team that was awarded a $25 million U.S. Defense Advanced Research Projects Agency (DARPA) grant to further develop supercomputer technology. The four-year research project is being led by Nvidia (NASDAQ: NVDA), a graphics processing unit (GPU) developer, and includes Oak Ridge National Laboratory and six U.S. universities. The objective is to develop a new class of supercomputers 1,000 times more powerful than those in existence today.

—Local IP service provider Telekenex raised $5.5 million in debt financing from Wellington Financial, a specialty firm out of Canada. Though headquartered in Seattle, Telekenex was founded in San Francisco in 1994, and is backed by a number of Bay Area firms, including Walden Venture Capital, Altos Ventures, and Industry Ventures. The funding will provide the company with the necessary capital to “continue its growth and penetration of the managed voice and data service market,” according to Wellington.

—Bend, OR-based search engine marketing company G5 closed a $15 million round led by Boston-based Volition Capital. The funding will be used to further the company’s software development platform. As part of the deal, Volition managing partner Roger Hurwitz and principal Sean Cantwell are joining the G5 board of directors.

—Bellevue, WA-based Intelius, an online background check and information commerce company, agreed to pay $1.3 million in a legal settlement with the Washington State Attorney General’s office, according to a report by TechFlash. The dispute was part of an ongoing effort on the part of the Attorney General to prevent “post-transaction marketing” tactics. Intelius has been called out in a number of class action lawsuits recently, including one case in October accused the company of violating the state’s Consumer Protection Act.

—DepotPoint, a Bellevue, WA-based Web company that develops a tracking platform for the real estate foreclosure market, raised $2 million in equity out of a $4.5 million offering. In 2008, as the mortgage meltdown accelerated, the company launched a free site that provided access to street addresses for some 1.2 million properties undergoing foreclosure across the U.S. In the same year, it raised a $7 million Series C found led by OVP Ventures Partners and Trident Capital.

—Woodinville, WA-based Calico Energy Services  told  Xconomy of an recent partnership with the U.S. Environmental Protection Agency Energy Star program. Although the energy management company hasn’t officially announced the deal yet, Calico chief marketing officer Thomas Doggett said the partnership, which has no financial terms, validates the company and acknowledges its ability to help utilities companies and energy providers “meet Energy Star certification goals.”

—San Francisco-and Seattle-based Jambool, the virtual currency and virtual goods management developer, was acquired by Google for an undisclosed amount. The four-year-old company behind the Social Gold platform, has raised $6 million in venture financing to date from Palo Alto, CA-based Bay Partners and Seattle’s Madrona Venture Group.

—A brand new online travel venture here in Seattle—AirlineTickets and Airport Parking—received $90,000 in startup financing out of a $200,000 round. A number of local angel investors contributed to the round, including Andy Liu and David Niu of BuddyTV, Geoff Entress, Bob Senoff, and Fred Hsu, the co-founder of oversee.net. The sites, led by former Internet marketer and first-time entrepreneur Sujan Patel, will take a new spin on the online travel searching and booking market—making the process of traveling easier and more enjoyable, Patel says.

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Seattle-based supercomputing company Cray (NASDAQ: CRAY) is part of a team that has been awarded a $25 million U.S. Defense Advanced Research Projects Agency (DARPA) grant for the further development of supercomputer technology.

The team, led by graphics processing unit (GPU) developer Nvidia (NASDAQ: NVDA), also includes Oak Ridge National Laboratory and six U.S. universities. According to a statement released Monday, DARPA is funding the project “to address the challenge that conventional computing architectures are reaching the practical limits of energy usage.”

The four-year research contract, part of DARPA’s Ubiquitious High Performance Computer program, will finance the development of GPU software and hardware technologies needed to equip a new class of supercomputers that could be 1,000 times more powerful than the best supercomputer in existence today—dramatically increasing computing performance, programmability, and reliability.

Steve Scott, Cray’s senior vice president, chief technology officer, and principal investigator on the team, said in a statement that the DARPA program “is attacking technical issues that are key to the future of high performance computing,” and could lead to “radical improvements to the state-of-the-art in the coming decade.”

Cray has had a long history of ups and downs in the supercomputing sector. In the second quarter of 2009 the company reported $62.7 million in revenue. Despite inking a number of extensive deals in 2010—including a $45 million Department of Defense contract, a $45 million National Nuclear Security Administration (NNSA) contract, a $20 million deal with Brazil’s Foundation for Space Technology, Applications and Science, and a $47 million Department of Energy contract—Cray reported only $28.7 million in revenue in the second quarter of 2010.

The company attributed the fluctuation in revenue to the recent rollout of its XE6 supercomputer, adding that it expects higher profits for later in 2010.

“I remain very excited about our 2010 prospects, led by a number of significant wins and continued strength in custom engineering,” Cray president and CEO Peter Ungaro said in a statement last week. “[We] are in the midst of one of the largest production ramps in our history. In fact, in a five month period this year, we expect to ship over six-times more compute power than we did in all of 2009.”

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After last week’s resurgence of activity surrounding Seattle-area technology companies, I have to say I’m somewhat surprised by how few deals were made this past week. But just because there weren’t very many straight deals over the last few days, doesn’t mean there weren’t any big news stories—or big dollars—being tossed around the local tech scene. This past week we’ve seen a number of key players in local business shuffle in and out of executive positions and a local billionaire pledge the majority of his money to charity, and we’ve gotten a number of interesting glimpses into the future of Seattle-area startup culture and the emerging industries that seem to be taking center stage. Take a look at the highlights:

—Seattle-based energy retrofitting company EcoFab joined the McKinstry Innovation Center, becoming the third cleantech company to set up shop at the still growing “accelerator” for clean and alternative energy startups. This announcement, however, falls into a larger context about the future of northwest industry. Could the emerging green sector become Seattle’s newest boom industry?

—Stealthy Seattle-based startup PhotoRocket hired on its interim president Gary Roshak as the company’s first CEO. Though founder and chairman Scott Lipsky, former Amazon executive and aQuantive co-founder, hasn’t revealed exactly what the company will be doing yet, this recent announcement may be a sign that the company, which says it is planning on “changing the landscape of the photo sharing space,” may be coming out of stealth soon.

—Madrona Venture Group managing director Tom Alberg has been appointed to President Obama’s new National Advisory Council on Innovation and Entrepreneurship. The 26-person council, which includes co-founders from big web companies including Yahoo!, AOL, and Zipcar, is charged with helping the administration develop policies to foster entrepreneurship, create jobs, and drive economic growth.

—Paul Allen threw some big money around this last week. The Microsoft co-founder commemorated the 20^th anniversary of the Paul G. Allen Family Foundation by giving $100,000 in special grants to the founders of five local nonprofits and vowing to donate the majority of his own estimated $13.5 billion estate to philanthropy. Allen, 57, was diagnosed with non-Hodgkin’s lymphoma last fall and said he intends to ensure that his “philanthropic efforts will continue after my lifetime.”

—Microsoft Research Redmond named Peter Lee as its new managing director, succeeding Rico Malvar, who will stay on as chief scientist. Lee was previously the director of the Technology Office at the U.S. Defense Advanced Research Projects Agency (DARPA), and head of Carnegie Mellon University’s computer science department.

—TechStars, a startup mentorship program and seed-stage investment with operations in both Boulder, CO, and Boston, is opening up a Seattle program in August. Before leaving for Boston himself, Greg got a sneak peek at TechStars Seattle’s new 14,000-square-foot South Lake Union space, fully equipped with a bar put in by the former tenant, who had been planning to open a speakeasy of sorts in the basement. What better environment to foster Seattle’s next generation of tech startups?

—Speaking of blossoming startup scenes, Seattle seems to brimming with new group buying deal-a-day sites—from Tippr, DealPop, and Yubit to the national names, Groupon and LivingSocial. And while this may not exactly be a deal, the onslaught of new daily deals and bargain sites in the local sphere definitely makes for an interesting analysis of where this market is going and what it means for consumers seeking new deals in the local marketplace, and merchants looking for ways to draw in new customers.

—In perhaps the only actual deal this week, Portland, OR-based Puppet Labs, a developer of data center automation software, raised $5 million in Series B financing led by Kleiner Perkins Caufield & Byers, a venture firm out of Menlo Park, CA. The completed funding round came at the same time as the open-source software startup rolled out its newest product, Puppet 2.6, which improves upon its flagship product and targets the needs of “enterprise environments.”

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Microsoft Research announced today that Peter Lee has been named the managing director of Microsoft Research Redmond, effective this fall. Lee was previously director of the Transformational Convergence Technology Office at the U.S. Defense Advanced Research Projects Agency (DARPA). Before that, he was head of Carnegie Mellon University’s computer science department and had served as the university’s vice provost for research. His technical expertise includes software security and reliability. Lee will succeed Rico Malvar, the current head of Microsoft Research Redmond, who will stay on as chief scientist of Microsoft Research.

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