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.

Companies like GenoCAD allow users to piece together
their own designer DNA.

“Synthetic biology” seems like a contradiction in terms, doesn’t it? I mean, if it’s biological, it’s natural, right? And if it’s natural, then it’s not synthetic.

Sure. Except that modern science has sorta blurred all those nice convenient boundaries.

Nothing has demonstrated this more clearly than Craig Venter’s latest feat of building out an entire bacterial genome from scratch. It’s the second episode of a three-part plan, devised by the venerable entrepreneur who brought the world its first look at the human genome, to create an organism with a manmade DNA sequence. First, he took a genome from one bacterium, stuck it into an empty cell, and then got it going. Now he’s pieced together a copy of the DNA of Mycoplasma genitalium, the second-smallest known bacterial genome. The last in this troika of tricks will be to combine these two steps, inserting the manufactured genome into a cell and starting it up.

Some scientists believe that success in this endeavor will soon lead to the creation of organisms with new, artificial genomes. Couple that idea with the announcement that researchers at Scripps have devised two new molecules that can function as DNA bases and the question of what’s alive, even what counts as biology, gets a little fuzzy.

I first heard about synthetic biology several years ago, at a lecture for science writers. The speaker had culled together sections of DNA that he hoped would produce a medically useful enzyme, inserted the sequences into a bacterial genome, then let the bug do its work copying the gene and producing the chemical, which the speaker could then harvest.

This seemed to me to be a fundamentally different way of thinking about biology. Here was a scientist who wasn’t asking: “How does this work?” or “Isn’t the living world amazing?” He was asking: “How can I employ this system to manufacture a specific product for my benefit?” He was harnessing the ingenious mechanisms of biology as tools. Being able to put together sequences of DNA seemed akin to the invention of movable type, a letter here, a letter there, till you spell the words (or in this case, genes) you want.

At some level, I was offended by this, though I’m still not exactly sure why. It seemed like a disrespectful exploitation of life. Who are we to manipulate the code defining living things and make them do our bidding? And how far will we go with this? Will the precious genomes of my plants, or my pets, or even me for Godsakes be manipulated one day, ordered to pump out some substance that a distant researcher has deemed desirable?

On the other hand, I was fascinated. The potential this technique held for research was enough to send a geek’s mind reeling. What amazing ingenuity. What creative thinking. How wholly human, actually, to devise a new purpose for knowledge we’d gained. This engineering feat struck me as demonstrating a deep appreciation—almost a reverence for—the power within the systems that the living world has evolved.

So there I was, conflicted.

Since then, this process of connecting DNA bits together has become more commonplace. So common, in fact, that a variety of companies, like Gene Design and GenoCad invite you design a gene online and have it sent to you (Go ahead, try it. It’s easy to make up valid sequences.). This is, in fact, what Venter did: ordered sequences of DNA and pieced them together, discovering that he could make an exact copy of the genome he desired.

Synthetic biology’s proponents promise microbes that can clean up pollution, produce drugs, signal changes in the environment, help with medical diagnoses, and a slew of other useful tasks. Its detractors fear the creation of new biological weapons, and new organisms that aren’t well understood but which may be able to reproduce and evolve.

Since this sort of talk makes a sci-fi world of ready-made critters seem like it’s just around the corner, it’s easy to forget how much work remains before our best (or worst) dreams come true. Just because we can string functional bits of DNA together, even whole (though relatively small) genomes, doesn’t mean that we actually know much about how they work. Venter, after all, didn’t invent a new genome, he just put an already-known one together. The goal, of course, is to be able to someday make new genes that do specific things. But for the moment, synthetic biologists hope to use the technologies they’re developing to learn much more about how genes work in the first place.

What does wait for us around the corner is a set of questions similar to those that accompany all new and emerging technologies. How do we create policy to protect ourselves from the risk but not quash research? Who decides what research directions and questions are most important to pursue? How do we create profit incentives for technology that benefits the common good?

And will I ever resolve my mixed feelings about this new science? Is it better off that I don’t?

Robin Marks is a journalist and science writer who current serves as a Multimedia Projects Developer for the Exploratorium in San Francisco, CA.

latitude: 39.1067, longitude: -77.1623