President Obama's directive on Monday to "guarantee scientific integrity" in federal policymaking could have a far-reaching impact, affecting issues as varied as climate change, national security, protection of endangered species and children's health.

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WASHINGTON — President Obama’s directive on Monday to “guarantee scientific integrity” in federal policymaking could have a far-reaching impact, affecting issues as varied as climate change, national security, protection of endangered species and children’s health.

But it will not divorce science from politics, or strip ideology from presidential decisions.

Obama delighted many scientists and patients by formally announcing that he was overturning the Bush administration’s limits on embryonic stem-cell research. But the president also went one step further, issuing a memorandum setting broad parameters for how his administration would choose expert advisers and use scientific data.

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The document orders Obama’s top science adviser to help draft guidelines that will apply to every federal agency. Agencies will be expected to pick science advisers based on expertise, not political ideology, the memorandum said, and will offer whistle-blower protections to employees who expose the misuse or suppression of scientific information.

The idea, the president said in remarks before an audience of lawmakers, scientists, patients advocates and patients in the East Room, is to ensure that “we make scientific decisions based on facts, not ideology”: a line that drew more applause than any other. Irv Weissman, a Nobel laureate who directs an institute at Stanford University devoted to studying stem cells, called the declaration “of even greater importance” than the stem-cell announcement.

It was also another in a long string of rebukes by Obama toward his predecessor, President George W. Bush. Bush was often accused of trying to shade or even suppress the findings of government scientists on climate change, sex education, contraceptives and other issues, as well as stem cells. But Obama’s announcement does not elevate science to some new and exalted place in his administration.

Scientists said they were thrilled by the announcement, as were advocates for patients, including Nancy Reagan, the former first lady who has made embryonic stem-cell research a personal cause. Obama said in his Inaugural address that he intended to “restore science to its rightful place,” and researchers said he had already made good on that promise by naming Nobel laureates like Varmus and Steven Chu, the energy secretary, to advise him.

“We’re not dumb — we know that policy is made on the basis of facts and values,” said Alan Lesher, chief executive of the American Association for the Advancement of Science and a former director of the National Institute on Drug Abuse under President Clinton and, briefly, Bush.

But by asserting “the centrality of science to every issue of modern life,” Lesher said, Obama is suggesting that science rather than ideology will be the foundation for his decision-making. “What you are seeing now is both a response to the last eight years, and a genuine reaction to President Obama’s enthusiasm for science,” he said.

During the Bush years, congressional Democrats and scientists themselves issued report after report asserting the White House had distorted or suppressed scientific information: from efforts to strip information about condoms from a government Web site to the editing of air-quality reports issued by the Environmental Protection Agency.

The Union of Concerned Scientists, for example, maintains an “A to Z” list on its Web site of “case studies” in what it calls the politicization of science under Bush, like his decision to devote federal money to programs promoting abstinence education despite studies showing such programs have limited effectiveness.

The House Committee on Oversight and Government Reform spent 16 months examining the Bush administration’s use of scientific data on climate change; it issued a lengthy report in 2007 documenting “a systematic White House effort to censor climate scientists by controlling their access to the press and editing testimony to Congress.” U.S. Rep. Henry Waxman, D-Calif., who led the committee at the time, said Monday that Bush had “exhibited a willingness to undermine science in order to further a conservative agenda.”

But Bush’s defenders see Obama as just imposing an ideology of his own. They say Bush did not ignore scientific facts; rather, he took the counsel of scientists and used it to make a policy determination that reflected his values, just as Obama is doing in lifting Bush’s restrictions on stem-cell research.

“Those who suggest that the Bush administration did not rigorously apply science are themselves ignoring the facts,” said Karl Rove, the former president’s political strategist. He called Obama’s declaration on restoring scientific integrity “simply hyperbole and hyperventilation,” and he disputed Waxman’s charge on climate change, saying the Bush White House “put more money into global climate research than any administration in history, by a significant factor.”

In the end, said Ed Gillespie, the former counselor to Bush, all administrations use science in service of a political agenda.

“Administrations come into office with a point of view,” Gillespie said. “The people in office tend to highlight those facts that support their point of view — not because they’re quashing dissent or not being scientific, but because this is what helps inform their thinking. A lot of scientific data can’t be refuted, but a lot of science is subjective. And even irrefutable science can be value-laden.”

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