I found the article on “Political Science” at the New York Times interesting. Essentially the article is about allegations that the US government has been systematically distorting scientific views. With a petition by some 7000+ scientists alleging such behavior this is clearly a significant concern.
One thing not mentioned explicitly in this discussion is that there are fundamental cultural differences between academic research and the rest of the world. In academic research, careful, clear thought is valued. This value is achieved by both formal and informal mechanisms. One example of a formal mechanism is peer review.
In contrast, in the land of politics, the basic value is agreement. It is only with some amount of agreement that a new law can be passed or other actions can be taken. Since Science (with a capitol ‘S’) has accomplished many things, it can be a significant tool in persuading people. This makes it compelling for a politician to use science as a mechanism for pushing agreement on their viewpoint.
Most scientists would not mind if their research is used in a public debate. The difficulty arises when the use of science is not representative of the beliefs of scientists. This can happen in many ways. For example, agreement is uncommon in research which implies that it is almost always possible, by carefully picking and choosing, to find one scientist who supports almost any viewpoint.
Such misrepresentations of scientific beliefs about the world violate the fundamental value of “careful, clear thought”, so they are regarded as fundamentally dangerous to the process of research. Naturally, fundamentally dangerous things are sensitive issues which can easily lead to large petitions.
This combination of mismatched values is what appears to be happening. It is less clear what should be done about it.
One response has been (as the article title suggests) politicization of science and scientists. For example the Union of Concerned Scientists (which organized the petition) has a viewpoint and is pushing it. As another example, anecdotal evidence suggests a strong majority of scientists in the US voted against Bush in the last presidential election.
I would prefer a different approach, which is essentially a separation of responsibilities. Given a sufficient separation of powers, scientists should be the most reliable source for describing and predicting the outcomes of some courses of action and the impact of new technologies. What is done with such information is up to the rest of the world. This style of “sharply defined well-separated powers” has worked fairly well elsewhere. Supreme court judges (who specialize in interpretation of law) are, by design, relatively unaffectable by the rest of politics. A newer example is the federal reserve board who have been relatively unaffected by changes in politics, even though it is easy to imagine their powers could dramatically effect election outcomes. This last example is a matter of custom rather than constitutional law.
Neither of the above examples are perfect—the separation of powers has failed on multiple occasions. Nevertheless, it seems to be a useful ideal.