Though we all talk about the government as though it was this sprawling, monolithic behemoth single-mindedly devouring every liberty in its path, the truth is actually a lot more complicated. What we call government (in the singular) is really a patchwork of institutions, often brought to life on an ad hoc basis, which may bear little relation to each other and sometimes actually conflict with one another.
Take the National Action Committee on the Status of Women (the name alone should give it away). Before having its budget gutted, the NAC was a fairly lively critic of governmental practices, decrying systemic sexism at all levels of government and lobbying for change. Here you have a case of two branches of government acting at cross-purposes - and it's great! Conservatives love to hold cases like this up as examples of waste, inefficiency, etc., but what it amounts to is something of a government check on government power.
There is nothing worse than a troupe of like-minded, pointy headed bureaucrats all pulling the same way - just look at the Bank of Canada. With that kind of solidarity, it is next to impossible to effect any lasting changes in policy. A soup of different opinions and purposes, however, contains the seeds of real debate and eventual agreement, at least on an issue by issue basis, which takes away some of the grosser elements of ideology. When the government sponsors its critics, it forces itself to challenge its own assumptions.
Of course, there are risks. One of the best ways to co-opt your opponents is to fund them, and governments are notorious for silencing their critics by holding out the gravy train and then requesting more 'cooperation'. However, too much simplification of how governments work obscures more than it illuminates.
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