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President Barack 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 that sets forth broad parameters for how his administration would choose expert advisers and use scientific data.

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 itself.

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 should have no illusions about whether they make policy — they don’t,” said Harold Varmus, president of the Memorial Sloan-Kettering Cancer Center and co-chairman of a panel that advises Obama on science matters. The directive, he said, was simply intended “to provide the best available scientific information” to those who make policy decisions.