Genomatica was founded in 2000 based on a set of computational tools used to predict how changes to metabolic pathways--series of reactions by which cells metabolize nutrients--could cause them to produce desired products, and to sort through the thousands of different pathways to find the best ones to try in experiments. Recently, the company has added the ability to produce organisms designed with this software, including tools for inserting and removing genes and selectively evolving the organisms to survive in high concentrations of the desired product. In addition to BDO, Genomatica is developing biological processes for making ten other chemicals, including the solvent MEK, which it says it can produce in idled corn ethanol plants.

The company will face difficult challenges as it moves toward a commercial-scale process for making BDO. Schilling says that the productivity of the organism still needs to be doubled. He expects that the increased productivity will be achievable, noting that the company has already improved the productivity of the bacteria by 20,000 times, having started with only trace amounts 18 months ago. But the last doubling of output could be difficult to achieve, as the organism's output becomes increasingly optimized.

What's more, moving from a lab scale to commercial scale can take years, and there's no guarantee that it can be done without incurring deal-breaking costs. Some things that are easy to do in lab flasks, such as delivering oxygen to the organisms in a solution, are much more difficult in commercial-scale vats, Pierce says. It took DuPont 11 years to begin producing its biologically made PDO. And there are other practical considerations. Are the organisms vulnerable to viruses? If there's a power outage, interrupting the flow of oxygen or nutrients, how fast can the organisms recover?

If it is able to scale up the production of BDO from the small amounts produced in a lab to the one-ton-per-day demonstration plant, the company plans to form partnerships with large chemical manufacturers, such as Dow Chemical, BASF, or DuPont, rather than attempting to build its own commercial plants, Schilling says.