FallenMadonna,
Really interesting article, makes some very valid points - but it has to be said that Perutz is attacking from a 'hard' science point of view, and in his field it is quite likely that things can be proved.
I do agree with his take on how the social sciences operate in terms of teaching that everything is subjective - strictly speaking I am a social scientist (Prehistoric archaeology) but there is much in archaeology that is all about physical observation - stratigraphy, dating techniques and microscopy and pollen analysis, all fairly 'hard' science branches in the field. I am of the opinion that many social scientists are bending over backwards to be culturally sensitive at all times, hence the 'everything is relative' approach - which is why I found the anthropology subsections of my field hard to take and specialised in the more hands-on stuff.
I especially like the way Perutz differentiates between using scientific methods to oppose Creationism and people setting out to offend people who have faith - as an atheist I've always felt that not believing is as much about respecting other beliefs (whilst disagreeing with them) as about non-belief itself.
I still think this thread deserves some sort of stamp of approval from MN - something like 'Guaranteed gluten-free - no bunfights on this thread'
Lastly I'd like to say that Popper and Kuhn are not the be-all and end-all of scientific practice IMO - they are just a useful, relatively simple to explain example of how science can work as opposed to how religion works.