Since this column began three years ago, Scientific American has commented on President George W. Bush's science-related policies--often, though not always, critically. Many readers have complained that we shouldn't mix politics and science. If only it were within our power to keep them separate. Science bears on some of the most important issues of the day, and increasingly, politics bears on how science is done. Although science is not, and should not be, the only factor guiding our choice on November 2, it is up to scientifically literate citizens to take it into account.

Embryonic stem cells. This issue brings out the sharpest disagreements between the candidates. Bush all but banned federal funding for studying these cells and opposes both therapeutic and reproductive cloning. Senator John Kerry of Massachusetts vows to lift the restrictions and to allow therapeutic cloning with ethical oversight.

Climate change. Bush now accepts, as Kerry long has, that the planet is warming and that humans are at least partly responsible. Both men disavow the Kyoto Protocol. What distinguishes them is where to go from here. Bush has set modest goals for industry to meet (or not) voluntarily. Kerry calls for mandatory emissions restrictions, higher car fuel-economy standards and renewed negotiations on international environmental treaties.

National missile defense. Both candidates support it. Bush's advocacy has been more forceful and consistent; a prototype system is now being deployed. Although physicists and engineers fault the design [see "Holes in the Missile Shield," by Richard L. Garwin], Bush argues that an imperfect system is better than none and will improve with time. Kerry asserts that deployment is premature and supports more rigorous testing.

AIDS. Both candidates deserve credit. Bush committed the country to the first substantial global initiative: $15 billion over five years. Kerry has a distinguished record on the subject, often working with Senator Bill Frist of Tennessee, now the Senate majority leader. The differences lie in how to spend the money. Bush's initiative requires organizations to buy brand-name drugs, rather than cheaper generics, and to emphasize sexual abstinence even if other approaches would save more lives. Kerry promises more money with fewer strings.

Science policy. Bush speaks highly of science and has increased research funding. The fields of defense, medicine, space and nanotechnology have done well, basic science less so. But his five-year budget plan imposes cuts. And many scientists say his administration has suppressed scientific reports and stuffed technical committees with ideologues or lobbyists. Kerry has echoed these critiques. He calls for increases in funding, although his overall budget numbers don't add up any better than Bush's do.

We hope that whoever wins will reestablish a tradition of nonpartisan thinking about science. Both the political left and right have been guilty of ignoring scientific findings they don't like and elevating their gut feelings above the judgment of people who spend their lives studying a subject. It's one thing to oppose embryonic cell research on moral grounds, and quite another to deny, as have some opponents, its great potential for curing disease. It's one thing to consider global warming a low priority compared with other problems, and quite another to deny that it is a problem at all. It's one thing to want a missile shield, and quite another to deny scientific critiques that could make it better. Science may not be the only factor in decision making, but the dilemmas and tradeoffs it identifies should be faced squarely.