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Stanford University researcher Thomas Jaramillo is overseeing a million-dollar research project that explores ways to create liquid fuel from sunlight and carbon dioxide. A Stanford colleague, Yi Cui, has nearly $2 million to research solar energy and high-energy batteries.

UC Berkeley researcher Jamie Cate is part of a multimillion-dollar effort to determine how to make an alternative fuel out of crops such as switchgrass.

For all three projects, the money is coming from Big Oil, and the research is at the core of a growing debate about whether the work carries the taint of corporate influence.

"We're all proposing to do the science exactly how we would want to, without any constraints," Jaramillo said.

"I have lost zero freedom," he said, echoing the views of Cui and Cate.

Not everyone agrees.

The author of an October report offering a blistering assessment of such arrangements said, "Every researcher says that. And I think it's true."

But Jennifer Washburn, author of "Big Oil Goes to College," a report from the Center for American Progress, said the oil industry deals pose a far...