Obama's "War on Science"?

There was a pretty disturbing story in the Los Angeles Times recently about how much trouble some government scientists are having in the Obama administration--which has not formally issued its promised scientific integrity rules yet. Now, organizations whose work I trust, like Public Employees for Environmental Responsibility (PEER) and the Union of Concerned Scientists, are going on record saying that there are some serious cases of science being suppressed or interfered with in various government agencies. I have not independently investigated any of the cases here, but you have got to take these kinds of charges seriously. Let's go through some claims from the Times article, to list and also to comment: