This is where science and the law, including the Endangered Species Act, are supposed to come in. The law requires the BPA and the Corps to operate the hydropower dams in such a way that fish recover. And the National Marine Fisheries Service -- also called NOAA Fisheries -- is charged with making sure BPA and the Corps comply.

This means NOAA has long been subject to tremendous pressure from pro-hydropower politicians, including former U.S. Sen. Larry Craig, R-Idaho, who used his powerful Senate committee positions to champion the hydropower industry and oppose spending on salmon recovery measures. He even tried to eliminate the federal Fish Passage Center after it demonstrated that court-ordered spill was boosting salmon survival.

Through politicians like Craig, says Wood, NOAA "has been swayed by the interests of BPA and the industries. And it has manipulated the science over the years to preserve the status quo that favors the industries."

Wood, Sando and other scientists and scholars believe Obama's appointment of Jane Lubchenco to run NOAA and his nomination of Jo-Ellen Darcy to run the Army Corps of Engineers will help turn this around. Both are smart, seasoned, known for a strong environmental ethic and accustomed to politicians trying to intimidate or outflank them.

Lubchenco, a highly regarded marine biologist at Oregon State University, has promised a new era at NOAA. While she has declined to comment specifically on salmon, she recently told The Oregonian that her agency "will be revisiting a number of different policies and asking ‘Are they consistent with the best possible science?' "

Lubchenco has already shown she's not afraid of tough decisions. She's pushing for changes to eliminate over-fishing in New England, a sometimes-hostile controversy that makes the Pacific Northwest salmon dispute seem like polite conversation. Lubchenco could dramatically improve the federal government's salmon efforts by calling for changes to the current biological opinion as part of a settlement offer.

Darcy, former deputy staff director for the Senate Environment and Public Works Committee, likewise gets high marks from government watchdogs.

Her committee position gave her a "great understanding of the Corps, warts and all," says Steve Ellis, vice president of Taxpayers for Common Sense. "She has congressional ties and she has the trust of a lot of people in leadership -- especially the Senate. And I think she understands the issues well, whether it's modernizing the Corps or salmon recovery."

The federal agencies defend their current salmon recovery plan and dismiss the need for dam removal. Last spring, they negotiated a $900 million settlement with some of the tribes that had long been their courtroom foes. They also point to better salmon runs. For example, approximately 246,600 spring/summer chinook and steelhead made it above the Snake dams last year, compared to the 172,400 tallied after the first lower Snake dam was constructed. However, that optimistic figure largely represents hatchery fish. Overall, the Snake's wild spring/summer chinook and steelhead runs have declined by nearly 75 percent since 1962. And many biologists and conservationists say where runs have improved, it's largely because of Judge Redden's orders for increased spill at the dams.

The agencies take strong exception to any suggestion that they politicize, bend or suppress science. "The Northwest Fisheries Science Center is physically removed from the regional office where policy is made," and has an independent director and a separate budget, NOAA spokesman Brian Gorman says. Some critics simply misunderstand the relationship between science and policymaking, he adds. If the agency makes a choice that doesn't mesh with someone's point of view, "the temptation is to say the science has been ignored. Somebody has to make a decision based on the best available science and other realities -- how much money do we have, how much economic and social disruption will take place."

"BPA has a long history of adjusting hydropower operations to protect fish, often at great cost," BPA spokesman Michael Milstein adds. "After flood control, which is a matter of public safety, the top priority for hydropower operations is fish protection. That's part of our mandate, and we support it."