Cynthia Warner was in Morocco on April 20 celebrating International Earth Day, when a friend emailed her with the news:

An explosion at a BP oil well off the Louisiana coast had killed 11 men and ruptured a pipeline almost a mile underwater, sending waves of crude into the Gulf of Mexico. “My first thoughts were for the people who died and the men there witnessing it and the horror of all that,” she says. “My heart sank. This is the kind of nightmare that everyone works hard to prevent from every angle.”

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Warner, known as CJ, has a more informed perspective on this species of nightmare than most observers. As the former head of global refining for BP, she was one of Big Oil’s highest-ranking woman executives until she abandoned petroleum to become president of Sapphire Energy in 2009. “I was never directly involved in drilling,” she says. “I couldn’t represent myself as an expert on this.” But as efforts to halt the spill failed, phone calls, text messages, and emails from the network Warner built during her 28 years in the oil business kept her in touch with what she calls the “huge drama underneath the surface — all the technical people who are working night and day, trying to figure out what to do. This one is really tough because it’s extremely deep water.” In such challenging situations, “it is just so much harder to resolve any problems that arise.” And that difficulty, she says, was at the heart of her decision to leave Big Oil. “They have to drill this deep because it’s getting harder and harder to find new sources of oil. The harder you work to find additional crude, the more environmental impact there is. What this does from a big perspective is illustrate the urgency of continuing to work to get solutions that are more in harmony with the earth’s cycles and more controllable.” Warner is not the only former BP executive to have come to this conclusion. For more than a decade, the company’s award-winning “Beyond Petroleum” campaign, with that heartwarming sunburst logo, seemed to promise a future of planet-friendly energy. Although alternative energy remained a very small part of BP’s business, that campaign may have succeeded all too well in raising expectations inside the company — expectations that were frustrated as new CEO Tony Hayward backed away from the clean-energy positioning. “Former colleagues of mine are all over renewables,” says Warner. Among them: John Melo of Amyris, Janet Roemer of Verenium, Mark Niederschulte of Ineos Bio, Richard Wilson of Cobalt Technologies, Lee Edwards of Virent, and K’Lynne Johnson of Elevance Renewable Sciences. “They’re the Beyond Petroleum generation,” says Jim Lane, editor of Biofuels Digest, “and Warner’s at the forefront of it.” The move from Big Oil to Big Algae, says Stephen Mayfield — aka “Dr. Pond Scum,” a founder of Sapphire and director of the San Diego Center for Algae Biotechnology — “might get CJ out of hell. She worked for, what, more than 20 years at BP and Amoco? That’s what I tell her: ‘CJ, keep working at this and you might not go down.’ “ Two weeks after the Deepwater Horizon catastrophe, with the oil still spilling into the Gulf, I meet Warner, 51, over Diet Cokes in Sapphire’s modest headquarters in an ocean-side biotech office park in La Jolla, California. She is a rangy woman with a warm smile and a flat Midwestern accent who runs three miles every morning with her dog. She dresses demurely in pastels and modest jewelry, like the wife of a Western politician. A chemical engineering major at Vanderbilt, Warner has become known for a collaborative approach to leadership even as she has fought against attempts to limit her career because of her gender. “Velvet hammer” is a phrase I hear more than once from her colleagues past and present.

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“I was kind of at that front end of the women’s-lib movement, where we started thinking everything is going to be equal,” Warner says. “My graduating class at Vandy was 10% women. But many of them dropped out as I was going on in my career. They were perfectly capable, but you just get tired of competing and having to prove yourself for the 15-millionth time.” Warner, however, was dogged. She set her sights on the oil industry, attracted by its technical challenges and by the teamwork required to get good results in such a complex business. “I wanted to know how to throw a wrench around a pipe and be able to crack a valve,” she says. “I had a refinery manager tell me it was over his dead body that I’d get out in operations. It wasn’t until he retired that I got out in the field.” She worked her way up slowly, at refining company UOP, Amoco, and then BP. “By the time I was running the whole refining system for BP, I pretty much knew almost every job.” One ladder she had to climb was a literal one. Early in her career, she was put in charge of an oil platform full of roughnecks who spent their onshore time with the Hell’s Angels. They told her she had to check a meter on the tallest tower — 200 feet up, on a ladder that swayed in the wind. “Then when you’re almost at the top, they radio you that there’s an emergency, so you panic.” There were 300 men, one woman, and a single bathroom with no door. “You put the hard hat over your lap,” she says with a grin. She met her husband, Dave, a mechanical design engineer, surrounded by refinery equipment. “We met at work, under a cracker, showing that residual oil can be very romantic,” she says. He telecommuted to his job in Chicago from her various postings around the world, before retiring several years ago to design and build a sailboat and help raise their children, a boy and a girl. By 2005, Warner was vice president of international refining, stationed at BP’s London HQ. In March of that year, an accident at BP’s Texas City refinery killed 15 people and resulted in the largest-ever fine from the Occupational Safety and Health Administration. She was put in charge of a new health, safety, and security group in BP’s refining sector, and assigned to work closely with the independent review panel headed by former Secretary of State James A. Baker and implement its findings across BP’s refining system. While some of the changes were technical and procedural, others were cultural, such as establishing that whenever a manager walked into a control room, he or she would always check the logbook to make sure shift changeovers were handled properly. In 2006, Warner was promoted to head of global refining. Environmentalists say BP — which has paid $725 million in fines, settlements, and civil-suit judgments since 1999 — hasn’t worked hard enough to prevent accidents like Texas City or Deepwater Horizon. “There’s an established pattern of workplace rule violations, skimping on investments in its energy infrastructure assets, and now this latest tragedy in the Gulf,” Tyson Slocum, director of consumer-advocacy group Public Citizen’s Energy Program, tells Fast Company . “Had it been another company, you could say it’s an isolated incident, but you’ve got a clear pattern of negligence.” (Asked for comment, BP referred Fast Company to its annual safety report.) Warner won’t comment on the causes of the Deepwater Horizon incident, but she attributes the accident at Texas City not to corporate negligence but to general human-cognitive errors. “It was the biggest accident that had occurred in its time frame, so BP is going to get that kind of reputation from someone who’s not paying deep attention to the industry,” she says. “But what the Baker panel found, and what I know is true, is that process-safety accidents” — those involving hazardous materials that may affect the public as well as employees — “are very high impact and low frequency. Everybody gets all focused and concerned about it. And then nothing bad happens for a really long time, and the excitement and concern goes away.”

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But Warner had concerns about the oil industry that weren’t going away. “I had a slow but growing realization that the industry was maturing, the current fields were falling off in volume more quickly than anticipated, and the feats required to find new oil were becoming more and more heroic.” She was deeply affected by The Long Emergency, James Howard Kunstler’s thundering 2005 screed about the end of the oil era. Although Kunstler is witheringly dismissive of any technological fix, Warner took his post-peak-oil Stone Age scenario as a challenge. “He gets to the human psychology, which is that ‘They,’ with a capital T — and I’m one of those They — They are going to figure it out,” she says, making finger quotes. “Well, I’m proud to be one of They, but I’m only one, and if They don’t hurry up, it won’t be okay.” She had been involved in alternative-fuel experiments within BP as early as 2000, but she was troubled that the projects were too small scale. “There were things I could do to move the ball forward within a large organization, but it simply wasn’t fast enough, or radical enough, of a change.” Eventually, she says, “I had an epiphany that if I was going to put so much personal energy into making something happen, it was a lot better to create the key to the future than to nurse along the dying past.” What motivated her above all was her two kids, a feeling she describes in a typically homey metaphor: “What I want to do is leave a legacy for my kids where energy is secure. I don’t want them to have to go out and fight for it — I don’t want to leave them a world where we’re fighting for the last slice of the pie, but one where we’re baking new pies.” The particular pie Warner wanted to bake was industrial-scale production of liquid hydrocarbons. While solar, wind, and geothermal work for electricity, she argues, the transportation sector needs energy-dense, portable fuel. Electric cars are still limited-range and expensive, and no one has yet debuted an electric jet. “Besides transportation, we use hydrocarbons for chemicals precursors and a lot of our building materials today. We would denude the planet if we had to go back to just building with wood.” Some of her former colleagues had gone into biofuels, but she saw problems with the so-called first-generation biofuels brewed from corn, soy, sugarcane, or plant waste. All compete with food crops for arable land and potable water. “Most of the alternative choices I could see were short-term fixes with a lot of resource trade-offs,” she says. Plus, she was convinced that it was essential to find a solution that could “drop in” to the existing energy infrastructure, from pipelines to refineries to tanker trucks, representing a sunk cost of trillions of dollars. Alternatives like hydrogen, liquefied gas, and ethanol require new investment in processing, storage, and distribution. “Think of the savings to society and the environment of not utilizing all these new resources and tearing everything up. It just makes so much more sense.” On a gray January day in London two years ago, Warner first met with emissaries from Sapphire over tea and biscuits in a wood-paneled conference room at BP’s headquarters, a Georgian-style building in historic St. James’s Square with a view of Buckingham Palace. At one end of the table sat Sapphire CEO Jason Pyle. A biotech PhD and entrepreneur with a boyish flop of hair, a wide smile, and a tendency to invoke management theory in conversation, he had raised more than $100 million in venture capital from the likes of Bill Gates and the Wellcome Trust. Accompanied by Steve Goldby, one of Sapphire’s VC investors, Pyle was looking for a board member from Big Oil who could envision the transformation of the energy industry.

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“I was really planning to be just polite — here’s another one of these interesting biofuel ideas,” recalls Warner. “But the more I spoke to Jason, the more it was obvious that this would be potentially interesting.” The infant science was compelling. “When I heard about algae,” she says, “I had that state of readiness that enabled me to recognize that it was the solution. It’s not going to compromise food production, it’s not going to compromise potable water, it doesn’t require land that is in high demand for alternative uses, and it’s very low carbon, so it’s not creating a negative environmental footprint.” Second- and third-generation biofuels grown from algae and other single-celled organisms are “absolutely hands-down the most exciting thing going on in bioenergy,” says Lane of Biofuels Digest. The single-celled photosynthesizer produces a little sack of fat so it can float on top of a body of water. Its prehistoric ancestors were the world’s original source of hydrocarbons, making it more similar to petroleum than corn or palm oil or jatropha. The U.S. Department of Energy’s Office of Fuels Development funded the obscure Aquatic Species program to develop fuels from algae from 1978 to 1996, but the real action has come in the past few years, as scientists like Mayfield at UC San Diego have started to apply techniques from pharmaceuticals research to breed algae that grow faster, produce maximum amounts of oil, and are disease resistant and easier to harvest. In Sapphire’s lab, as many as 8,000 strains a day are created and tested. The most promising move up from trays of 96 petri dishes as tiny as pillboxes to containers the size of milk bottles, all gently shaking to keep the algae dispersed and active; to bladders that hang like IV drips; to tanks several meters long that are mixed with a paddle wheel; and finally outside to a greenhouse. Sapphire produced what it says are the world’s first drops of 91 octane gasoline made from a renewable resource in May 2008. Weeks later, Pyle was back in London. He went straight from the airport to a steamy, un-air-conditioned conference room in a hotel, where he and Warner talked algae and strategy from 12:30 p.m. to 7:30 p.m. She was won over by Pyle as a person and by the position he was offering her — not to join the board, but to become president of the company. His aim was not just to license technology but to build an energy company, a producer of green crude on a large scale. In exchange for Warner’s refining and distribution expertise and her credibility in the industry, he was willing to give up a chunk of his equity and to create a role for her that would be equal to his own as CEO. Warner would be risking her career and her reputation on a pilot-phase technology, and moving her family from the U.K., where her children had grown up, to California. She would go from having 11,000 reports on five continents to sharing one assistant in a startup of 100 employees. “I have to say it did sort of destabilize me at first,” she says. “You’re thinking you have your whole life planned out. But it became the bar against any other opportunity I could think of, and it was too compelling to say no.” She sought and received her family’s support for the move, and resigned from BP at the end of 2008. “Frankly, from a woman’s perspective, if my career is taking this much time away from the family, it better be important and meaningful,” she says. “Everything came together for me once I understood what the algae-technology potential was. I realized I can’t afford to leave it to chance that someone — They — will figure it out.” “On CJ’s first full day at work,” Pyle says, “she’s staying in a hotel. She’s jet-lagged. She gets up early and can’t go back to sleep, so she decides to go for a run on the mesa. And what happens at 4 o’clock in the morning? She was bitten by a rattlesnake.”

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“He didn’t envenomate me,” Warner interjects with a smile. “And she’s promptly at work at 8 a.m.,” Pyle continues. “And of course the joke around the company was that the snake bit her, and it died.” The three of us are having lunch at the Torrey Pines Golf Course on the day of the company’s third anniversary party. Pyle, 39, is sporting an oversize, sapphire-colored belt buckle that Warner bought him so he could dress like the Big Oil executive he aspires to be. Although they reminisce about Sapphire’s early days, most milestones are still ahead of them. In September of this year, the company is scheduled to break ground on a 300-acre demonstration plant in New Mexico, funded by a competitive Recovery Act grant of up to $50 million from the Department of Energy and a $54.5 million loan guarantee from the Department of Agriculture. By 2011, the plant should be producing 100 barrels per day. If all goes well, Sapphire will move on to a commercial plant that by 2018 should be producing 10,000 barrels per day — a single “basket” of fuel, the smallest amount a procurement manager of a refinery would consider purchasing. “The really big refineries will bring in 20 to 30 baskets of crude at any given time,” Warner says. “An average refiner isn’t going to be interested in a smaller volume than that. So that’s what we’ve targeted for ourselves.” Algae’s time frame is long and the numbers are daunting. Mark Bünger, a top biofuels analyst at Lux Research, says today’s technology is still too pricey and delicate to scale. “Algae makes corn ethanol look like the most above-board business you’ve ever seen.” He says Sapphire is particularly secretive about its research. (Its headquarters has no sign, and I’m greeted by a burly security guard before I’ve even gotten out of my car.) “It causes a baseline assumption that this isn’t going to work,” Bünger says, “if that secrecy isn’t just a front for being in the same place everybody else is.” He adds, “You might say, people like CJ aren’t going to bet their careers on something that’s not going to work. But smart people can make mistakes. It’s not necessarily insurance that there’s a there there.” Byron Washom, an alternative-energy consultant for two decades and now the director of strategic energy initiatives at UC San Diego, is more optimistic. “From my due diligence days, I used to have a saying to clients,” he says. “When you go to the horse races, do you bet on the horse or the jockey? I always bet on the jockey, because the jockey knows how to pick the mount and the jockey knows how to win the race. I would say a company like Sapphire has the silks.”

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But even algae boosters agree that basic questions remain. The race to create better strains by manipulating genes is ongoing. “We’re trying to do in 10 years what agriculture has accomplished in 100,” says Mayfield. “But we have two enormous advantages. One is that we’re in the molecular era, so we can take things down to a single gene. Two is that we’re dealing with single cells, so we can grow 25 generations of crops in a year.” Then there’s the issue of how to grow millions of acres of the stuff — a prospect that concerns people uncomfortable with genetically modified crops. The top companies have very different approaches, which suggests that there is not yet a clear winner. (See “Algae Fuel’s Pioneers“.) And the true challenge is not only to figure out how to breed the best pond scum, grow it as easily as rice, and bring it to market, but to do it all at a cost approaching that of conventional gasoline. The really inconvenient truth is that no one in the biofuels world anticipates that green crude will earn any real premium from consumers over the Deepwater Horizon brew. The challenge excites the competitive spirit that Warner has nurtured since she joined a swim team at 5 years old. She’s made her decision: She’ll dedicate 100% of her energy to advancing a radical energy solution that has at least the potential to scale. “It’s a long-term undertaking, not just for me, but for the world,” she says. The alternative? To sit back and hope that They come up with a better answer. Meanwhile, one month after the accident, thousands of barrels of crude are continuing to pour into the Gulf.