This paper analyzes the roots and implications of conflict between the conduct of science and government predilections in the United States, including the security state and neoconservative control of Washington. Three major conflicts are discussed: the emergence of new security and secrecy regimes that seek control of science; religiously derived moral viewpoints that seek to limit scientific research; and the purposeful shaping and censoring of scientific findings for political gain. All three policy issues, argues the author, have their roots in a growing public mistrust of science and its purposes, but also the actions of the current presidential administration. What is needed, he states, is a set of rules rooted in several common understandings or rules. First, policies resting on scientific or technological issues, like all public policies, are decided in the end not just by experts but by a variety of people and interests. Second, objective scientific results, tested by repeated efforts at confirmation, are necessary (though not sufficient) elements in such policy decisions. Third, if the scientists responsible for those findings are controlled or silenced by particular policy interests, or committed in advance to any particular category of policy outcome, the resulting decisions are likely to be wrong. If adopted in advance of the installation of the next administration, or at the outset, such a set of rules could be seen a forward-looking improvement in governance, rather than as yet another criticism of what has been going on in this one.