Here is Polanyi in his essay “The Nature of Scientific Convictions” on why positivism should not provide the basis for the autonomy of science:
the freedom of science cannot be defended today on the basis of a positivist conception of science, which involves a positivist program for the ordering of society. Totalitarianism is a much truer embodiment of such a program than is the free society; as, indeed, consistent positivism must destroy the free society. A complete causal interpretation of man and human affairs disintegrates all rational grounds for men’s convictions and actions. It leaves you with a picture of human affairs construed in terms of appetites checked only by fear. All you have to explain then in order to understand history, and with it politics, law, science, music, etc., is why at certain moments the appetite of one group gets the upper hand over its rivals. (Reprinted in Scientific Thought and Social Reality, at p. 64.)