by Daniel Grushkin (FastCoExist.com)  Amyris’s breakthroughs in bioengineering–and its plans to make biofuels from Brazilian sugarcane–promised to transform how the world’s businesses produce energy, cosmetics, and medicine. Then reality (and Wall Street) got in the way.

…Already, in the short lifetime of the biofuels business, Amyris has become legendary–a stand-in for the sector’s breathtaking promise and now for its troubling descent. The company’s Brazilian plant is referred to as Paraiso, Portuguese for “paradise.” It could be more aptly described as a grande esperanca, a great hope. Just a year ago, Amyris’s stock price soared to $33 a share. More recently, as the company reported $95 million in losses last quarter, it has plummeted to as low as $1.52. Meanwhile, a once-grand expansion plan has been scaled back. A plant at Sao Martinho, double the size of Paraiso, sits half-complete, vacant as of February. Amyris suspended production at another plant this year.

… The future has become a matter of simple economics. If Amyris can produce farnesene efficiently here, the company will gain precious time to perfect its genetic technology. And if not? Then Amyris will likely capsize and pull an entire sector–an entire vision of the future–down with it.

…Ten years ago, (Neil) Renninger was working in the lab of Berkeley chemical engineering professor Jay Keasling, a father figure in the field of synthetic biology. Keasling had come to believe that biology would ultimately follow the paths of engineering and computing, and that cells could in time be treated much like small factories, tiny machines whose insides behave like assembly lines. Keasling’s idea was that one day a biologist in front of a computer could piece together the virtual genes of a virtual organism, program and test it on a computer model, and then press print. From there, automated machines could produce the actual organism, which would behave exactly as the computer predicted.

…Oil giants make their profits on minuscule margins; going after diesel would mean making a commodity that generally sells for a dollar a liter. The Amyris team hoped higher-end chemical applications for farnesene, which could sell for upwards of $20 to $50 per liter, would support the company on the long road to fuels.

…The Amyris scientists balked when he (CEO John Melo) tried to apply big-company rigor to employee performance. “They didn’t want to be measured,” Melo says. “They said, ‘Metrics? What metrics? You can’t measure this stuff. It’s science–it’s about innovation, about us having space, about us thinking. Just leave us alone, and we’ll do great science for you.’”

…And on paper, farnesene appeared as if it could compete, in price, with petroleum. Whether Amyris could produce the chemical cheaply at a real plant, however, was still unproven. What’s more, no one had ever built a business like Amyris’s before. Getting its plants to run efficiently, getting its yeast bug to produce optimally–it could take decades to catch up with an oil industry that had a lead of nearly a century. Also, despite the incredible biotech tools Amyris had developed, company directors knew going public meant they’d have to open the books to the market, which only cared about one question: When would Amyris turn a profit?

… When various Amyris plants began to yield farnesene last spring, the selling price to customers was $7.80 a liter. It was reasonable for specialty chemicals, but far too expensive for the fuel market.

…When synthetic biologists announce they will treat microbes like tiny factories, investors and markets may be listening, but the microbes are not. Biology is not computing or engineering–at least not yet. Yeast has already been programmed by evolution. Inserting genetic instructions or working around ones already inside will be an uncertain business until scientists understand exactly how the organism functions. And that may take decades–if ever. “It’s not Google, Facebook, or Twitter,” Melo says of Amyris’s business. “It’s just not that model.” READ MORE