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.

We see or hear about explosions practically every day on TV–
most people have no idea what an explosion really is.We were asked to surrender all of our communications devices before entering the High Explosives Applications Facility at Lawrence Livermore National Laboratory in Livermore, CA. After handing over our cell phones, checking our IDs and getting our badges, we were led through a labyrinth of Cold War-era concrete hallways where there is a definite atmosphere of secrecy and caution.

It’s true that the majority of the work done there is in support of Department of Defense and Department of Energy programs. But contrary to what one might imagine, the scientists there are work that goes on there isn't ALL about figuring out how to protect the U.S. from Communism. The scientists here are chemists, physicists and engineers who are delving into everything from warhead electrical systems to enhanced mammography.

We’re led into the "firing chamber" to meet our explosives guy, Jon Maienschein, who has promised to blow something up for us. I’m excited. It’s hard to make a bad TV segment when an explosion is involved. If you watch television, you will see that many shows live and die by that rule. Maienshein is surprisingly mild-mannered for a guy who blows things up for a living. After interviewing him for about 30 minutes on camera, we finally had a very basic understanding of what’s happening during a detonation.

There are several different kinds of explosions: chemical, natural, mechanical and nuclear, electrical, astronomical, etc. The most common "artificial" explosives are chemical usually involving a violent, rapid oxidation reaction. The fine folks at LLNL demonstrated just such and explosion for us then gave us the super-cool, ultra-slow-motion footage that they shoot in order to study what actually goes on inside an explosion.

We see or hear about explosions practically every day on TV, the movies and in the news, most people have no idea what an explosion really is. What’s happening on the chemical and molecular level? And how do the people who know about explosives actually study explosions? And why is it necessary to understand this stuff? The whole thing is surprisingly complex.

Watch the Inside an Explosion television story online.

The new FOCE experimental chamber being developed by MBARI scientists.

The scientists at the Monterey Bay Aquarium Research Institute (MBARI) are already well-known for uncovering some of the most extreme marine animals in the deep sea, like the incredible vampire squid. But recently, they're using their unique blend of biology and engineering to study one of the least-discussed impacts of climate change: ocean acidification.

When we hear about climate change, we tend of think of the atmosphere – and for good reason. But as MBARI scientists describe, the oceans are a key part of the process. The ocean acts like a giant sponge, absorbing carbon dioxide emissions from the air. And as we add more and more CO2 to air by burning fossil fuels, the ocean is absorbing it. On one level, it's done us a big favor. Scientists say that we would be experiencing much more extreme climate change were it not for the ocean's ability to remove the heat-trapping gas.

However, the carbon dioxide that the ocean absorbs is making the water more acidic. This isn't the first time that the oceans have become more acidic. But as is the case with many impacts of climate change, it's the rate at which acidification is happening that worries scientists the most.

As you can probably guess, the ocean is an incredibly complex system. So ocean acidification poses an interesting question to scientists: what will the impacts be on marine species and ecosystems? What they know already is that there will be winners and losers in more acidic waters. Some creatures may do fine, while others won't be able to adapt in time. Either way, food webs may feel the effects – including webs involving species that humans depend on , like salmon.

Another major concern has to do with marine animals with certain kinds of shells – known as "calcifiers." Corals, clams and others all use carbonate in the water to build their shells out of calcium carbonate. But ocean acidification reduces the amount of carbonate in the water, making it more difficult for them to make shells. That could be devastating for coral reefs, who are already facing a number of stresses.

Even if you're an animal without a shell, ocean acidification could make things difficult. Scientists are studying how much stress this could put on animals that can't regulate their internal pH, or how it could affect the larvae or reproduction of certain species. MBARI scientists are hoping that the flume they are developing to conduct FOCE experiments will help researchers answer some of these questions.

Check out the whole story – watch the "Acidic Seas" audio slide show online.

Scientist Alex Gash prepares the "frozen smoke."
I've always loved cooking shows. There's something so satisfying about watching an expert gather, wash, peel, macerate, combine and assemble ingredients. And because of the magic of television, we get the whole enchilada neatly packaged within a half hour program. Everything's perfectly cooked, presented and served. And I don't have to do the dishes.

So when I conceived this Aerogel segment, I had a cooking show in mind. I imagined the mad scientist, standing at his bench in requisite white lab coat and safety glasses, Bunsen burner bubbling away. And the big reveal at the end, pulling a perfectly-formed cylinder of Aerogel from the supercritical extractor. Well, it turns out that the process of making Aerogel isn't terribly visual. Essentially, there's a lot of clear liquid being added to clear liquid. Which becomes clear gel. Then it's put into a machine and it comes out Aerogel.

So, it's a good thing that our chemist, Alex Gash, was a rock star. He was such a good sport, saying the same thing over and over in just slightly different ways without a single complaint. And even though he works with Aerogel (Sol Gel chemistry) every day, it still seemed like he was pretty excited about it.

So, while it's not exactly a cooking show, we hope that our little segment piques your interest to find out more about how Aerogel is made as well as its really interesting applications. Maybe you can even print out the recipe and make it at home.

Watch the "QUEST Lab: Aerogel" TV Story online, as well as find additional links and resources.


Amy Miller is a Coordinating Producer for television on QUEST.