You two seem to be in the minority on that point. You're the first people I've heard criticize it (though obviously there are others), most people I know who've read 'Windup Girl' adored it.
Well, I put that down as a corruptive influence of reading too much fantasy (which is more popular than science fiction nowadays, but which doesn't have to take principles of science to any consideration), to the poor science education in schools. :-)
As I said I liked the writing and characterization. But the science sucked BIG TIME.
I could write a long essay of the stupidities in this book. Starting from the fact that in energy poor situation the only alternative energy used is methane produced by compost (sic!) piles, and that is used apparently mainly for lighting. I wonder how much of the energy produced by burning methane is released as light? 1%? 2%? Springs which are wound by "mastodonts", apparently gene modified elephants, are used as another energy source. I find it hard to believe that it would efficient to feed giant animals to produce mechanical labour and save it in that form loaded in springs, instead of using the food as a direct source of bio energy. The thermodynamics of the windup girl are really stupid, as she heats up from too much exercise (sometimes from from fairly little amount of exercise, sometimes from a lot lot of it),and then she cools down by drinking a class of icewater. One glass of 0 centigrades water cools down on 60-70 kg body which has temperature, lets say 39-40 centigrades, by something like 0.1 centigrades. And so on, and so on.