The climb up the steel steps is dizzying--like ascending the tower of a European church, except the steps lead to a platform bolted to the side of a gleaming new chemical plant. Here in Brazil, under a brilliant blue sky, Eduardo Loosli, the plant manager, pauses to explain a vision of the future. "I used to manage a Molson Coors beer manufacturing plant, and its not all that different," he says, leaning on a railing and surveying the scene around us. Directly below is a cityscape of huge stainless-steel tanks. Out beyond the tanks, and stretching far into the distance, are dense greenfields of sugarcane.

Yeast turns grain into beer, Loosli says. Here, in this new plant, genetically engineered yeast created by the plants owners--the California biotech company known as Amyris--turns sugar into liquid fuel. At the end of the platform, Loosli points to two special "seed" tanks. "The yeast enters the system here," he says. When production starts, a glass flask of Amyriss special strain will be poured into each tank, and the yeast will multiply until it becomes a thick, hungry broth. For two weeks, the yeasty stew chews up as much as 1.2 million liters of energy-rich cane syrup. The end product is farnesene, which can be adapted to a seemingly perfect replacement for petroleum-based diesel. Not only does farnesene-based diesel cut pollutants from vehicle exhaust pipes, but since it derives from cane syrup, it is also a renewable resource. These cane fields surrounding the plant are thus the rough equivalent to bottomless oil wells.

Amyriss great innovation is deep inside the genetically modified yeast that chews up the Brazilian sugarcane. The yeast serves as a host for a set of DNA instructions--scientists call the organism a chassis, as if it were a simple platform, waiting for an engine. Depending on their goals, engineers at Amyris can outfit the yeast with a variety of genetic material that tells the yeast how to digest what it is fed. The result is a cell that can (at least in theory) ingest simple sugars and produce virtually anything. Indeed, if the yeast cells work as theyre supposed to, they promise not merely to change the energy industry by producing farnesene. They may also be programmed to transform the way many commodity materials are made. The first step would be petroleum-type materials. Rubber, chemicals, and medicines would follow.

At least thats the idea. Already, in the short lifetime of the biofuels business, Amyris has become legendary--a stand-in for the sectors breathtaking promise and now for its troubling descent. The companys 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, Amyriss 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.

Everything now rides on success at Paraiso. This summer, as the final bolts were tightened and the last pipes sealed, Loosli readied himself to take command and find out what the plant can do. 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.

A few weeks before I travel to Brazil to see the Paraiso plant, I discuss Amyriss perilous situation with one of its founders, chief technology officer Neil Renninger. We meet at the companys Emeryville, California, headquarters, in a small lounge decorated with black-and-white photos of Red Sox players and filled with comfortable leather couches. He reminisces about growing up in California--his dad had worked as an engineer at Intel, his mom as a schoolteacher. As he speaks, his slender fingers sometimes search for his iPhone, sometimes hang in the air, and sometimes touch tip-to-tip as he considers a thought.

Circles of exhaustion rim his eyes. His company is ailing and he wears it on his face. Just before my visit, Amyris had announced it had produced a million liters of farnesene in 2011, rather than the 6 million it promised. Its executives declared they would no longer make predictions about future production. "Id be lying to you if I said that I didnt look at the stock price," Renninger admits.

He always knew a startup is a gamble. As an undergraduate at MIT in the mid-1990s, before casino bouncers recognized MIT kids on sight, Renninger played on the institutes notorious Black Jack Team. On nights and weekends, between engineering classes, Renninger traveled to Vegas and Mississippi River casino boats. He wadded up $100,000 of the teams betting money in his pockets, and when a table ran hot, hed clean up. The experience forged him. "The biggest thing I learned at MIT was go ahead and take risks because if you fail, youll land on your feet," he says.

He felt that way about Amyris. Ten years ago, 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. Keaslings 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. This is the vision that Renninger signed on to and what he spent years working toward. Today at Amyriss California lab--downstairs from where Renninger is recounting the companys history--a team of 40 scientists works on a computer program called Thumper. Essentially, the program allows scientists to rearrange a yeasts genetic makeup and create new strains; more than 400,000 new strains are screened each week. In a sealed room, the fittest move from plates of colonies to half-liter fermenters--glass containers filled with soups of yeast and sugar, like mocha and cream. The fermenters resemble Cuisinart food processors. From there, the most promising strains are shipped to Brazil.

Back in 2002, Renninger recalls, before any of this was built, Keasling and his colleagues began sharing the details of their work with outside companies. One day, a postdoctoral student under Keasling named Vince Martin said, "We have some good technology and good people. Why dont we do something with it?"

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The Rise And Fall Of The Company That Was Going To Have Us All Using Biofuels