I completely agree with all the points that are being made in this article. I don't believe we can control or get rid of the negative thoughts because, as Manson says, they are natural processes of the brain.
However, I do believe we can counteract those negative thoughts through positive self talk. As I said in my first post, if I have a thought that I'm crap, then I tell myself that I'm really not. Manson seems to agree that this thinking, this self talk, is a good idea. In the article he says that he acknowledges the negative thoughts and tells his thinking mind "that it's full of shit" and then tries to act despite the negative thoughts. That's exactly what I was trying to say, although maybe not very eloquently. So me telling myself that I'm not crap is, in my view, the same as Manson's suggestion that if we have the thought that our boss is an idiot we should take possession of it and instead tell our thinking mind "My boss is not an idiot. But I am having the thought that my boss is an idiot."
I don't think any of the literature on self affirmation would disagree with Manson either. I don't think anyone has suggested that it is some panacea that, if practiced, will get rid of negative thoughts and emotions. Rather the idea is that when we have negative thoughts, we recognise that they are negative and we challenge them through positive self talk. Through doing this we can try to ensure that the negative thoughts and emotions don't control our behaviour.