For those who haven't yet read/understood Taubes book Good Calories Bad Calories or his latest Why We Get Fat: And What to Do About It here is a full text paper that examines his ideas critically.
REVIEW Obesity and energy balance: is the tail wagging the dog?

It's fairly detailed but not too difficult to understand. Certainly a lot more concise than Taubes original version. However I think it's probably worth downloading to your PC and reading from a PDF file.

The way I look at it (and I need to lose 20 pounds), is that if you have 2 slices of bread, white and whole grain and the package says 150 calories per slice, you will absorb all 150 of the white cones but the whole grains, some of the 150 calories they get in the calorimeter are undigestable fiber, so they are not absorbed.

It's true the faster your body is able to absorb calories the less satiating they are. It's probably why sodas and juices are increasing obesity.
I think in general the idea that Whole Grains are safe is probably not true for most people. They may well be less bad than refined grains but that's about the best you can say.
Whole grains and another smoking gun?