UCSF biologist Jeff Tabor holds up an ecoli culture designed to display the shape of a squid.

Synthetic biology portends big changes in our lives by ushering in a dizzying array of applications in everything from medicine to biofuels, environmental remediation to agriculture. Though many of these applications haven’t yet come on line, researchers are hard at work to synthesize new drugs and devices made from genetic parts.

For example, there’s an enzyme that exists in plants which makes methyl halides, a molecule which can be catalytically converted into gasoline and other chemicals. Imagine if you could put this enzyme-making gene into yeast, then you could brew the yeast to churn out the methyl halides and after some optimization of the production pathway, you could scale up production to pump out this carbon neutral gasoline precursor for use in today’s automobiles. This is the idea behind an innovative biofuels project that has taken off in the lab of Chris Voigt at UCSF’s School of Pharmacy.

Voigt and his team surveyed the genetic database for the presence of the gene that encodes for the enzyme that makes methyl halides. Lo and behold, the gene exists in plants as diverse as ice plant, which dots the northern California coast, bok choy and pinot noir grapes. After building a library of about 100 enzymes from these diverse plants, the researchers had to determine which of these would function best in the yeast. They zeroed in on an enzyme from ice plant and then used the tool of DNA synthesis to translate the gene for the enzyme that makes methyl halides into something that would work in yeast.

The remarkable thing about this project is that the researchers never actually touched any of the plants. They simply “Googled” a genetic database to find all the genes out there in plants that produce the enzyme that makes methyl halides. As Professor Voigt says, “it’s incredible that synthetic biology is something that could really unlock the potential of using organisms in order to produce fuels.”

Watch the video made by the Voigt Lab demonstrating the combustible property of their synthetically derived methyl halides:

QUEST on KQED Public Media. Video courtesy of
Prof. Chris Voigt, UCSF School of Pharmacy

Watch the Decoding Synthetic Biology television story online.

Sketch drawing of the proposed San Francisco-Oakland Bay Bridge (1913) from Overland Monthly, April 1913.

The Bay Bridge will be closed from September 3rd at 8:00 p.m. until the 8th at 5:00 a.m. During these 105 hours, Caltrans will perform an "essential and unprecedented construction feat."

It turns out there was a lot I didn't know about the Bay Bridge. Its official name, for example is not the Bay Bridge. It's "The James 'Sunny Jim' Rolph Bridge," after the California Governor who died in 1934, two years before the bridge opened (The Golden Gate Bridge opened 6 months later). Around 280,000 vehicles traverse the bridge every day—nearly $7 in bridge tolls per second; The Yerba Buena Tunnel that connects the eastern and western segments is the world's largest diameter bore tunnel; Much of the eastern span is supported by old growth Douglas Firs, driven into firm mud.

As construction grows increasingly noticeable, the new eastern section rising out of the bay, more people are wondering: How will it attach? What happens to the old bridge? What's with the retrofit of the western suspension? And what is this unprecedented feat of construction happening over Labor Day weekend?

The construction website, baybridge360, just received a Webby award in the Government category, and is worth a visit. Videos and slide shows are overlaid on a satellite image of the bay and provide answers to these and other engineering questions. There's a bit of Troy McClure style narration, epic synthesizer for the construction scenes, and techno pop for the fast-forward time lapse photography. At one point, the “Governator” dons a pair of terminator sunglasses for a ceremonial blowtorching.

The new site may be sleek, but some of the most interesting information is buried in the old stalwart: baybridgeinfo.org. The western span's retrofitting, completed in 2004, added some 17 million pounds of structural steel, and included new rollers between the roadway and the bridge supports. The new eastern segment (slated for rebuilding since a section collapsed in the 1989 Loma-Prieta earthquake) will include the world's longest Self-Anchored Suspension (SAS) bridge, connected to a pier-supported "Skyway" (elevated roadway over a mile of mudflats), sloping down to the "Oakland Touchdown."

The 2,047-foot asymmetric SAS will be supported by a single steel tower, embedded in rock, rising 525 feet above sea level. While most suspension bridges use a pair of cables, the new SAS employs a single cable, anchored on the east side, wrapped over and around the tower, and down to the west. The Skyway is supported by a set of steel pipes, driven 300 feet into deep bay mud by a massive hydraulic hammer.

Amidst the construction clamor, considerable attention is afforded to local wildlife. Dense columns of air bubbles helped dissipate shockwaves from the hammering to ease construction-related stress on local fish. For the birds, platforms under the new east span provide cormorant nesting habitat, and the crew is building a 500 square-foot island for the pleasure of the snowy egret and ruddy turnstone. And at the Oakland touchdown, a turbidity-controlling curtain was installed to protect eelgrass, which in turn serves as a filter, improving water quality.

So consider all this next time you lament the $4 bridge toll. The original 1936 toll, collected in both directions, works out to over $20 in 2009 dollars. The bridge is scheduled for completion in late 2013.

Hydrogen is not exactly a fuel. That is, we don't burn it to make energy. It's used more as a medium for storing and transporting energy.

The science of hydrogen fuel cell systems is based on a simple concept. When you combine hydrogen with oxygen, energy is released. You get electricity. What makes it such a clean technology is that the byproducts of that chemical reaction are just heat and water.  So when a fuel cell takes hydrogen from a fuel tank and combines it with oxygen in the air, it produces electricity and emits only a wisp of heated water vapor from the tailpipe.

Hydrogen is combustible (remember the Hindenburg?), and needs to be handled carefully. However, there are easy ways to demonstrate electrolysis, which breaks water apart into oxygen and hydrogen, and the opposite process of joining those chemicals. In fact, you could make a type of fuel cell in your kitchen, with a popsicle stick, battery clips, Scotch tape and a few other household products. You do need one item that can't be found in your kitchen: platinum wire or platinum-coated nickel wire.

Hydrogen is the most abundant element in the universe. And hydrogen fuel cell conversion is a squeaky clean technology. But the production of hydrogen for use in fuel cells — that can produce a lot of carbon dioxide. In fact, most hydrogen is currently made by stripping, or re-forming, natural gas. That's one of the ongoing criticisms of fuel-cell technology, that it generates greenhouse gas emissions just to get the hydrogen in the first place.

Fuel cells also can store energy generated by solar-powered electrolysis, as well as similar energy generated by wind and hydropower. That's the kind of hydrogen generation that advocates hope to eventually use in fuel cells. But being able to store energy also makes it extremely attractive to harnessing wind, solar and hydropower.

For example, California could generate a lot of wind energy at night, but since electricity has to be used right away, that nighttime, offpeak energy is less valuable. But if it could be stored in a fuel cell through the electrolysis process, that would make it much more lucrative.

Listen to the Where's my Hydrogen Highway? radio report online, and watch our Web Extra Slideshow.

Cal Poly's CP-4 mini-satellite in orbit. Credit: The Aerospace
Corporation.

It's a classic engineering story – a garage inventor spends years working in isolation, only to produce something that gets the attention of the world. Ok, the CubeSat story may not be quite as romantic, but it does have a lot of the same ingredients.

Professors at Stanford University and Cal Poly created CubeSats – 10 by 10 by 10 centimeter mini-satellites – as enginneering projects to give their students hands-on experience. Compared to standard satellite missions, which can run hundreds of millions of dollars and take years to complete, CubeSat missions are mean to be done cheaply and quickly.

CubeSat is also a standard – a basic blueprint that any university program can use. CubeSats are actually known as "FedEx satellites," since universities can mail them to Cal Poly to arrange a ride into space. They've created launching devices called P-Pods (a box that fits the CubeSats perfectly) so they can piggyback on larger rocket launches. Once the main cargo is deployed, the P-Pod releases the CubeSats into orbit. Depending how high they are, CubeSats can orbit for more than a decade before they burn up in the atmosphere.

What started at universities has spread – NASA, Boeing and other aerospace companies all have mini-satellite programs. Despite the small size, CubeSats are actually able to do valuable research. They can space test new technology, submitting it to all the rigors of space travel like solar radiation and launch stress. Recreating those conditions on the ground can be very expensive.

CubeSats can also gather scientific data. On Tuesday, NASA will be launching Pharmasat, which they hope will be their second nano-satellite in orbit. It will carry yeast samples, and once in orbit will hit them with an anti-fungal to see if their resistance is increased in space. NASA has previously observed that some bacteria are more resistant to antibiotics in space, something that could be dangerous for future human space travel.

You can tune in on Tuesday evening for the Pharmasat launch. Three other CubeSats from Cal Poly and other organizations will also be getting a lift into space.

Listen to the Do-It-Yourself Mini-Satellites radio report online, and see our Web Extra: Mini-Satellites Slideshow.

In our radio story, we feature the stylishly high tech Vineyard 29 and the Robert Mondavi Winery, but scores of other wineries are using a similar toolbox of technology to help them monitor the soil's water content to grow better grapes. The technology ends up conserving water, too. Remote sensing, ground penetrating radar and satellite technology have helped Mondavi cut back on water use by 30% in recent years.

Winemakers are using some of the same technology that NASA uses to study Mars and engineers use to build hi-rises and freeways. A typical toolbox includes multi-spectral imaging, weather stations, neutron moisture probes, and pressure bombs and there is a plethora of newer technologies in the pipeline. But enough with all the high tech gizmos. How does wine from high tech vines taste? The answer might be found in the success of the winery. Mondavi has won numerous awards over the years and there is a two-year waiting list just to purchase Vineyard 29 wines.

Check out our slide show to see some of these technologies or listen to our radio report on high tech in the vineyards.

The Stanford Linear Accelerator. Credit: SLAC.

Luckily, there is a particle accelerator right here in the Bay Area. Last year, I took an intrepid group down to the Stanford Linear Accelerator (SLAC) to learn more about the these giant expensive research labs.

SLAC maintains an extensive public outreach program. An extensive tour (mine was 2 hours with very in-depth exploration of the facility), public lectures, weekly colloquia, and even science competitions for high schoolers.

I was surprised to find a wealth of research beyond the typical particle colliding at the facility. Many researchers use the state of the art facilities to study basic elements of our life, including water.

On Tuesday, Anders Nilsson is discussing his research on water at SLAC, an in-depth look at some of the stranger properties of water: its high heat capacity, how it is more dense than ice, even insight on using water as a power source (by splitting it into hydrogen and oxygen). Water: The Strangest Liquid, Tuesday February 24th 730-830PM at the Stanford Linear Accelerator.

However, our continued economics woes are threatening physical science research. SLAC is getting the brunt of money cut, missing out on $23 million of requested funding. In response, SLAC laid off 125 of its 1600 employees and shut down its PEP-II collider last year.

SLAC Public Lecture Series
The SLAC Public Lecture Series opens the doors to the inner workings of SLAC for the local nonscientific community. Find out what SLAC is all about: the research, the facilities, and the people that make this a world-class research institute.

SLAC Colloquium
The intellectual watering hole for the entire laboratory, where you can hear talks intended for a general audience on a wide variety of subjects. The colloquium will be returning later this year.

SLAC Science Bowl for High School Students
SLAC hosts an annual Regional Science Bowl for teams of high school students. The Science Bowl is a question-and-answer competition with buzzers, judges, and time keepers for high school teams of 5 students and 1 faculty coach. This year's competition is on February 28th.

SLAC Tour Information
Tours of SLAC will be available again later this year. On the tour, you get an extensive look at the operation of the accelerator, including a peek into the Klystron Gallery.

Probably the hardest thing to get your hands on for this project will be the four gold-plated neodymium-iron-boron magnets. Not something you usually find at the local 5-And-Dime. (Or maybe I was just looking in the wrong aisle.) But I'm sure Make Magazine can point you where to get them. Once you do, here's a safety tip: The magnets are very powerful, so make sure they are securely taped down or they might slam together and shatter. Then you'll have to go out and find more gold-plated neodymium-iron-boron magnets.

Do try this at home. But be careful out there. Adult supervision is always a good idea. And make sure to aim your Tabletop Linear Accelerator away from your little brother.

Download Instructions for the Tabletop Linear Accelerator (419.3 KB .pdf)

Watch the Make At Home Tabletop Linear Accelerator television story report online.

Bio-inspired design borrows its creative inspiration from models and systems in nature, that is, plant and animal parts that have been slowly tweaked for over 3.8 billion years. But that doesn't mean that nature's designs are perfect. In fact, that's what makes the process of engineering things based on natural models so difficult. You have to figure out how to pull the aces from the evolutionary discard pile. As professor Bob Full at U.C. Berkeley explained in our first phone conversation, that's also why scientists now use the term "bio-inspiration" rather than the more commonly known term "biomimicry." Biologists and engineers are not looking to simply mimic nature, because there are all kinds of dead ends and redundancies in natural systems that would be pointless to recreate in an optimized, man-made piece of technology. One of the examples he gave me is a kind of grasshopper that if you were to copy it, you would copy neurons that go to nothing, they don't connect to any muscles, and that's because during evolution the adults lost their ability to fly. The neurons going to the muscles are still there, but the muscles aren't there anymore. No need to copy that, right?

So what a biomimeticist does is look to nature to find plants & animals with remarkable performance abilities, and studies their adaptations for inspiration to design something new. For example, if you want to make a tiny robot that can fly, then look at the best fliers. If you want to design a blade that moves quickly through fluids, or an Olympic swimsuit that minimizes drag, then look to the most efficient swimmers. Now that's what I call "intelligent design!"

Watch the Bio-Inspiration: Nature as Muse television story report online.

Credit: California High Speed Rail Authority

One of those outstanding questions is: Where will the train go?

In the Bay Area, that has been a huge issue. There are two proposed routes (check out an interactive map here) — one through the East Bay and the Altamont Corridor toward Sacramento, and the "preferred alternative," which runs down the Peninsula, through San Jose, Gilroy and the Pacheco Pass, and then loops back around to Sacramento.

Some rail advocates filed a lawsuit, pushing the state to do more study, particularly environmental study. The Pacheco Pass route cuts through some pristine landscape, and that worries environmentalists. And the Altamont route runs through some of the heaviest traffic corridors in the Bay Area, so a high speed train could relieve some of the East Bay's congestion. In addition, the Peninsula communities of Menlo Park and Atherton joined the lawsuit, because they're concerned about the potential of massive above-the-street construction there.

The Rail Authority says it's working with communities to answer their concerns. For instance, it's possible that some of the high speed rail stations could go below ground on the Peninsula — and that they hope to build BOTH routes eventually. Right now, they say, the Pacheco Pass route is preferred, but they point out that it's a long way till the tracks go down and the train starts running, and there will be a lot to work out over the next decade.

Listen to the Fast Trains radio report online.

A confession: When I first got the assignment to do a story about air conditioner efficiency, I didn't exactly leap from my seat in excitement. (Which is why extra kudos go to those who've made it as far as this web page!) But, really, I should have known better.

AC seems mundane because it's ubiquitous – but because it's ubiquitous, its impact is astonishing. If you took air conditioning out of the picture, there might not be such thing as the California energy crisis. We could put dozens of power plants offline. In terms of global warming, it would be like taking hundreds of thousands of cars off the road, permanently.

Why air conditioning and not, say clothes dryers or refrigerators? Well, partly because AC sucks lots of power (especially central AC systems though, bought new, even those may be more efficient than your old window unit), partly because of the way we use them: all at once. When heat waves hit, Californians turn on their ACs practically in unison, hitting up a beleaguered electricity grid that fires up every creaky last turbine to handle the load.

So, it comes as no surprise that a number of Californians are putting serious energy into making air conditioning work better. At the top of that list is California Energy Commission Commissioner Art Rosenfeld, the efficiency guru who, perhaps more than any other person, can be credited for California's remarkable efficiency gains over the last 30 years. We also hear from AC inventor and entrepreneur John Proctor. And thanks also go to Jeff Scalier, of Antioch-based Blue Star Heating and Air Conditioning, who introduced me to his very satisfied customer, Al Mason, and whose mother I hope enjoys the CD we send her.

If you want to retrofit your central AC system to tailor it to California climate (and make it 20 percent more efficient) a number of Bay Area installers are ready to do it. Here are some of them, courtesy of Proctor Engineering:

– Vtech HVAC Services, Antioch, 925-752-6075

– Bland A/C & Heating, Inc., Bakersfield, 661-836-3880

– Herrera Heating & Air Conditioning, Bakersfield, 510-750-6972

– Action Air Conditioning, Clovis, Fresno, 559-292-8640

– California Indoor Comfort, Fresno Area, 559-276-7457

– Certified Heating and Air Conditioning, Fresno County, 559-273-8048

– ReNu, Marin County, 415-462-0245

– Queirolo's Heating & Air Conditioning, Inc., San Joaquin County, 209-464-9658

– Leo's Heating & Air Conditioning, San Joaquin Valley, 209-271-7873

– Air Solutions Heating & Air, Stanislaus County, 209-380-3032

– Air Flo Pro, Stockton, 209-915-4730

– University Refrigeration, Stockton, 209-609-8400

– CPR Sheet Metal, Inc., Vacaville, 707-628-7495

– Right Now Air, Vacaville, 707-447-3063

Listen to the Air Conditioning Reinvented radio report online.