Mascoma, a Lebanon, NH-based developer of cellulosic ethanol, said yesterday that its CEO, Bruce Jamerson, is leaving his post to be chairman of the company and its subsidiary Frontier Renewable Resources. Mascoma is working with executive recruitment firm Russell Reynolds Associates to find a new CEO. Jamerson plans to focus more time on Frontier Renewable Resources’ project to build a commercial-scale biofuel plant in Kinross, MI, according to Mascoma. In April, the company revealed it would reduce staff levels from 27 to 15 workers and relocate its corporate headquarters from Boston to Lebanon.

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Plankton Power, a Wellfleet, MA-based company developing ways to turn algae into renewable biofuel, announced in a press release today that it will plans on opening a manufacturing plant to produce biofuel from algae on the Massachusetts Military Reservation (MMR) in Bourne, MA. To build the factory, Plankton Power, along with the Regional Technology Development Corporation of Cape Cod, the Massachusetts National Guard, Woods Hole Oceanographic Institution (WHOI), the Marine Biological Laboratory (MBL), and the Cape Cod Commission have formed the Cape Cod Algae Biorefinery Consortium. Plankton Power said it expects pilot-scale production to begin next year.

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We’ve got several different venture deals to talk about this week, as well as an acquisition, a sizeable secondary offering, and other interesting transactions from New England’s tech and life sciences firms.

—Cardiac implant maker HeartWare International (ASX: HIN) of Framingham, MA, agreed to a $282 million acquisition offer from Pleasanton, CA-based Thoratec (NASDAQ: THOR). The half stock, half cash deal is expected to close in the second half of 2009.

—Boston’s Globespan Capital Partners participated in an $18.5 million financing for Longmont, CO-based data-archiving-hardware maker COPAN Systems. Westbury Partners led the round, which was joined by Austin Ventures, Firstmark Capital, and Credit Suisse.

—GlaxoSmithKline paid Lexington, MA-based Synta Pharmaceuticals (NASDAQ:SNTA) $10 million for reaching an operational milestone in the development of the drug elesclomol as a treatment for metastatic melanoma.

—Oasys Water—a Cambridge, MA-based startup developing technology for converting salt water into potable drinking water—raised $10 million in a financing led by Advanced Technology Ventures, Draper Fisher Jurvetson, and Flagship Ventures.

—North Bridge Venture Partners of Waltham, MA, participated in a $15 million Series B funding round for OfferPal Media, a Fremont, CA-based marketer targeting consumers who use social networking sites like Facebook, Bebo, and MySpace. D.E. Shaw Ventures led the round and InterWest Partners also participated.

—Cambridge, MA-based Verenium (NASDAQ: VRNM) forged a joint venture with British Petroleum (NYSE: BP) to build commercial-scale biofuel plants in the United States. BP will put $22.5 million into the venture, and Verenium, whose proprietary microbes break down sugar cane and other high-cellulose materials into ethanol, will contribute “development assets,” including two planned biofuel plant projects valued at $22.5 million.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX) announced a secondary public offering of 10 million new shares, priced at $32 apiece; the offering was underwritten by Merrill Lynch and Cowen & Co. Luke learned more about the deal and Vertex’s strategy from its CFO, Ian Smith.

—Burlington, MA-based thermal imaging camera maker RedShift Systems raised $6 million in a second round of financing led by new investor Emerson (NYSE:EMR) of St. Louis.

—Vaccine-discovery startup Genocea Biosciences of Cambridge, MA, raised $23 million in a Series A funding round led by SR One. New investors Auriga Partners, Cycad Group, and Alexandria Real Estate Equities participated in the deal, as did return backers Lux Capital Management, Polaris Venture Partners, and Morningside Ventures.

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It was the week before Christmas, and the deals were flying. Could San Diego’s economy be downturn defying? Heed the tech news and be of good cheer! We wish you an Xconomy Xmas and Xponential New Year!

—The big deal of the week came Wednesday, when Abbott Labs (NYSE: ABT) exercised its option to acquire Ibis Biosciences from Isis Pharmaceuticals (NASDAQ: ISIS) for $215 million—plus continuing payments from sales of Ibis’ diagnostics products.

—San Diego’s Ligand Pharmaceuticals (NASDAQ: LGND) also scored with a big pharma partner, GlaxoSmithKline, (NYSE: GSK) by awarding exclusive rights to Glaxo for its drug candidate shown recently to effectively boost blood platelet cells. Glaxo agreed to pay $5 million now and as much as $158 million later, not including royalty payments.

—San Diego’s Solera Holdings, which makes software for the auto claims industry, announced it has paid $117.4 million to buy HPI Ltd, a British firm that compiles a data base of used car histories. Solera was founded in 2005 by Tony Aquila, a former president of Mitchell International, a rival auto claims software developer also based in San Diego.

—San Diego’s Huntington Capital raised $78 million in capital commitments for its second fund, which the boutique venture lender launched in May. The firm hopes to raise a total of $100 million for “Fund II” by early next year.

—Privately held Sierra Nevada Corp. of Sparks, NV, completed its buyout of SpaceDev, which is based in the suburban San Diego community of Poway, in a deal estimated at roughly $30 million. SpaceDev said its shareholders approved the deal Monday.

—Ardea Biosciences (NASDAQ: [[ticker: RDEA]]), the San Diego biotech developing small molecule drugs for inflammatory diseases, raised more than $30 million in a private stock placement.

—Pfizer (NYSE: PFE), sensing new opportunities in stem cell research for treating diabetes, formed a two-year collaboration with San Diego’s Novocell.

—Serial entrepreneur Michael Robertson, who made his fortune as the founder of MP3.com, launched a new version of Gizmo5 technology at SIPphone. The new technology, GizmoCall.com, enables users to log onto a Web site to make VOIP calls (Voice Over Internet Protocol) and can be used with any computer running a Windows, Macintosh or Linux operating system.

—Finally, the government awarded a couple of noteworthy contracts this week to San Diego’s SAIC, (NYSE: SAI) the research and engineering company also known as Science Applications International Corp. The first, from DARPA, the Defense Advanced Research Projects Agency, was for a $14.9 million biofuel contract to develop ways of using algae to make JP-8 grade jet fuel. The second deal, from NASA, could be worth as much as $69 million over the next five years to SAIC for engineering services and support for the Constellation program, which calls for returning astronauts to the moon.

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

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Boeing Begins Jet Biofuel Initiative

Aircraft manufacturer Boeing has teamed up with 10 airlines, including Air France, Continental, and Virgin Atlantic, to form a Sustainable Aviation Fuel Users Group. Flightglobal reports that the group will look for ways to make renewable jet fuel, with the goal of at least partially replacing fossil fuel used in airplanes with biofuel by 2013. Boeing is funding two studies on making jet fuel from algae or the plant jatropha, being done at the Natural Resources Defense Council and Yale.

Digitizing Health Records Still a Challenge

Healthcare could be dramatically improved if every doctor a patient ever saw had access to all that patient’s health records, which could happen if the records were all digital. But only 15 to 18 percent of U.S. doctors use electronic records, partly because of the upfront costs of going digital. Technology Review talks to Karen Bell, who’s in charge of promoting digital records at the U.S. Department of Health and Human Services, about what the problem is.

Bacteria Can Produce Plastic

Not all of the fossil fuel we use goes to power our cars or heat our homes: Some is used to make plastic. The Discovery Channel tells us that researchers at Genomatica, a company in San Diego, CA, say they’ve developed bacteria that make an important ingredient of the plastic that’s used in products from Spandex to car bumpers. The company says it can go into production as early as next year, and that its product will be cheaper even if the cost of oil drops as low as $50 a barrel.

New Method Produces Stem Cells from Adult Cells

A new method of producing stem cells from adult cells may provide a route to new therapies without the controversy of stem cells derived from embryos. New Scientist reports that researchers at Massachusetts General Hospital in Boston have been able to turn liver cells from an adult mouse into stem cells, which now have the potential to become any cell in the body. Earlier this year, Japanese scientists also turned adult cells into stem cells, but their method used a virus that left behind genes that could lead to cancer.

Activists Say, Put Debates on the Internet

When the presidential and vice presidential candidates debate, they should take advantage of the Internet, say people on both the left and the right of the political spectrum. A group including liberal activist Arianna Huffington and the director of Newt Gingrich’s organization, American Solutions, signed a letter calling for the candidates to put footage from the debates on the Internet, and to take “Town Hall” style questions submitted online. CNET News reports that the group says that effective use of the Internet ensures “bottom-up democracy.”

Leaders Plan to Wipe Out Malaria in Seven Years

Malaria is one of the world’s greatest public health problems, killing more children than any other disease. Now world leaders, including United Nations Secretary General Ban Ki-moon, say that better science, improved record-keeping, and increased philanthropy make them believe they can reduce the number of malaria deaths to zero by 2015. The Washington Post reports that donors have given more than $3 billion to the Global Malaria Action Plan.

Tracking System Could Make Social Sites Profitable

Google is applying a system similar to its PageRank system for ranking websites to profiles on social networks such as Facebook and MySpace. BusinessWeek says the system looks at how often people post to others’ pages and measures whether users convince others to read a news story or watch a video clip. If it works, the system should allow advertisers to target ads more precisely, allowing the sites to charge more.

Obama Releases Science Funding Plan

Democratic presidential candidate Barack Obama has released an 11-page “plan for science and innovation.” Nature reports that the plan calls for doubling the funding of the National Institutes of Health over 10 years, and spells out science policies in more specific details than had been released previously.

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Cyber Command Offline for Now

An Air Force project to coordinate the defense of military computer systems and launch offensives against enemy systems has been put on hold while higher-ups review the plan. The so-called Cyber Command was scheduled to go operational in less than two months before the Pentagon called a time out. InformationWeek says it’s possible the plan will be scrapped entirely.

Military Probes Frontiers of Cognitive Science

Soldiers who control machines with their brains and mind-reading systems for interrogating terror suspects are some of the possible benefits of applying advances in cognitive science to military aims, a new report says. The Department of Defense asked a committee of the National Research Council to evaluate cognitive science research to see what it might lead to, Wired reports. Among the possibilities: brain scans that can tell whether a suspect is lying, and machine-brain interfaces that allow people to control robotic prostheses or software at a distance. As one wag wonders, haven’t they ever seen “The Terminator”?

Genome Scans Could Improve Biofuels

Understanding the genomes of the organisms involved could allow scientists to engineer better plants and improve the biofuel-producing microbes that feed on them, according to a paper appearing in the journal Nature. Ars Technica says there’s already been a lot of work looking for ways to improve the characteristics of cellulose in plants, which contains more potential for fuel than the less complex sugars in corn kernels. And although researchers know of many bacteria that can break down cellulose, they don’t yet understand how they work.

Poet Announces Cellulosic Ethanol Plan

At least one company says it’s ready to start making ethanol from cellulose, at least on a small scale. Poet, of Sioux City, IA, which is the country’s top ethanol producer, has started building a pilot facility in Scotland, SD, and plans to produce ethanol from crop waste by the end of the year, Reuters reports. The company’s hope is to increase the supply of ethanol without driving up food prices.

Disclosing Bugs is Best, Experts Say

While MIT students and the Massachusetts Bay Transportation Authority argue in court about whether the students can talk about flaws they found in the MBTA’s fare-card system, computer security experts say that suppressing such research could ultimately make computers more vulnerable to attack. Technology Review quotes experts as saying that security flaws won’t get fixed if the public doesn’t hear about them, and that the students should be viewed as providing a free service rather than posing a threat.

Lab Breaks Solar Cell Record

The National Renewable Energy Laboratory says it has set a new record for efficiency in solar cells, the Associated Press reports. The NREL developed a solar cell that converts 40.8 percent of the light striking it into electricity, and that can probably be improved, a spokesman said. Raising conversion efficiency is one way to bring the cost of solar power down to where it can compete with coal.

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Companies Developing Wireless HD Standard

As wireless high-definition video emerges, various groups within the industry are competing to create a standard on which wireless HD devices will operate. Ars Technica says that Hitachi, Motorola, Samsung, Sharp, and Sony have come together to support a standard being developed by Israeli startup Amimon. The company says its Wireless Home Digital Interface standard will surpass other technologies in range and bandwidth.

Security Holes Widespread in Bank Websites

More than three quarters of websites for banks have design flaws that could be exploited by criminals, a new University of Michigan study finds. Information Week reports that the study, being released this week, found a variety of flaws that aren’t fixable with a simple patch. The authors cite another study, which found that $16 million was lost to computer intrusions in the second quarter of 2007.

There’s Gold in That Thar Cow Plop

Converting cow manure into methane and burning that instead of coal could cut greenhouse gas emissions in the U.S. by about 4 percent, according to scientists at the University of Texas at Austin. The researchers tell Discovery News that the plan is a two-for-one win. Switching from coal to cow patties not only cuts the use of fossil fuel, it also keeps methane and nitrous oxide — two very powerful greenhouse gases produced by the decay of manure — from entering the atmosphere. Get out the shovels.

Garbage-to-Fuel Making Gains

Scientists have long considered converting garbage and crop waste into biofuels, but until gasoline hit record high prices it didn’t make economic sense. Now, the New York Times reports, several companies are building plants to convert waste into fuel, and their products could be on the market within months. Big-name companies such as Honeywell, DuPont, and General Motors are starting to invest.

DuPont Backs Cellulosic Ethanol Project

A major problem with using corn to make ethanol for fuel is that it eats up material that could otherwise be used to feed livestock or humans. Now DuPont has joined an initiative to use non-edible materials such as corn stalks and switchgrass, that are high in ethanol-producing cellulose as a feedstock. The Associated Press says the initiative is managed by the University of Tennessee and includes Genencor, a subsidiary of the Danish company Danisco.

Should Homeowners Buy Their Own Internet Hookups?

U.S. consumers are used to leasing the conduits that bring information into their homes – the telephone line, the cable for the TV. But an analyst at Google’s Public Policy Blog wonders why it shouldn’t be the other way around, with users buying a fiber connection to their homes and Internet service providers hooking up to sell them access. He argues it might save consumers money, give them more choice of provider, and make their houses more valuable.

Could Expiring Subsidies Push Solar Investment?

The renewable energy industry wants the U.S. government to make tax credits for clean energy more permanent, saying it’s hard to build an industry on two-year subsidies. But a writer at the Wall Street Journal argues that short-term subsidies may actually boost the industry, as consumers rush to install solar panels before the tax credit expires.

Google Gets Into the Green Car Business

Google has begun investing in green-car startups, announcing $2.75 million in funding split between green-car maker Aptera Motors and ActaCell, which develops rechargeable batteries for the cars. Earth2Tech calls the move “significant” as it starts to position Google as an incubator for the next generation of electric vehicles.

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Online Crime Gets More Organized

Cybercrime, once the province of unaffiliated hackers, is coalescing into to a more organized structure that resembles the Mafia, according to a report from the web security company Finjan, of San Jose, CA. As described by Ars Technica, Finjan found that cybercriminals are often organized into a system with a boss and several underbosses and lieutenants. Leave the computer virus, take the cannoli.

Biofuel Spending Doesn’t Cut Carbon, Group Claims

Between them, the United States and the European Union are spending $11 billion to promote biofuels. But Bloomberg reports that, according to a study by the Organization of Economic Cooperation and Development, all that spending is having little impact on carbon dioxide emissions. The report predicts a reduction in greenhouse gas emissions by vehicles of, at best, 0.8 percent by 2015.

Sprint Moves to Higher-Speed Broadband

Sprint has announced plans to convert the core of its network to handle data traffic at 40 gigabits per second, GigaOm tells us. That’s up from the current standard of 10 Gb/s. The increase in speed is needed as video downloads and third-generation data transmission become increasingly popular, the company says.

CERN Previews Network of the Future

Today’s Internet capacity will seem incredibly limited in a decade or two, but some of the steps needed to increase bandwidth are being previewed in a large-scale physics project in Switzerland. As CNET News reports, CERN, the European Organization for Nuclear Research, has built an ultra-high-speed network so scientists can share massive amounts of data collected from the world’s largest particle accelerator, scheduled to go online next month. The people who built the network are learning how to handle data moving at speeds about 1000 times as fast as the average home broadband connection.

U.S. Lags on Creating Science Graduates

The United States has not made as much progress on attracting more students to the sciences, engineering, mathematics, and technology-related fields as businesses had hoped, reports the Chronicle of Higher Education. In 2005, 16 business groups called for the U.S. to double its number of bachelor’s degrees in those fields, from 200,000 in 2005 to 400,000 in 2015, to keep up with foreign competition. So far, the number has only grown to 225,000.

NASA Aids Fight against California Wildfires

Aerial sensing drones designed by NASA for research on global warming and general Earth science turn out to be great volunteer firefighters. As the San Jose Mercury News reports, the drones, equipped with infrared sensors, are able to identify trouble spots that firefighters don’t know about, allowing them to successfully adjust their strategy in combating the blazes.

Republican Spider Tracks Obama’s Website

Republican Presidential candidate John McCain may not, by his own admission, have much use for e-mail. But his campaign is employing an Internet spider to crawl Barack Obama’s website and keep track of any changes on an hourly basis, according to Wired. The campaign’s hope is to highlight any shifts in policy Obama might make.

EPA Creates Rules for Storing Carbon

One proposal for limiting greenhouse gas emissions is to capture carbon as it is produced at power plants and store it underground, perhaps in exhausted oil wells. The Environmental Protection Agency is taking a step toward making that possible by publishing a draft of a rule governing such underground storage. The New York Times quotes a carbon storage expert as saying the rule is an important step, but not the only one needed to make carbon storage a reality.

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