Peer review sucks?

The New York Times has an article that reviews the problems with peer review. I don't know what to think, as it has something of the "and the other side says" air to it, never really coming to any conclusion. There's a lot of shoddy crap being published in stuff like the Tuvan Journal of Entomology, and always has been, but the big issue is when crap gets into Science and Nature. Ultimately science is a social enterprise based on trust and long term self-correction. There's a lot of noise in the system, but I don't see any other alternative out there. One issue that I've been wondering about is that in many of the biological and social sciences many new mathematical and computational techniques are being pushed really quickly, and I'm not totally sure if there's enough comfort with these methods for the scientists to utilize them without error ...