Whenever the Workout of the Day on CrossFit.com requires rest periods of unspecified duration between exercise bouts, there are always many questions about it on the comments page. This is understandable, as rest and recovery within a workout can be quite a complex issue, and the rest period should depend on the activity you are doing and the goal of the workout.
As many of you are aware, there are three systems that a human can draw on to produce the energy required to do physical work. These are the phosphagen, glycolytic, and oxidative systems (these are discussed in terms of sustaining maximum efforts in issue 10 of the CrossFit Journal).
A muscle must produce a chemical compound called ATP to fuel contraction. There is a very small amount of ATP already in the muscle, but the rest must be synthesized from other fuels in the body-- creatine phosphate (CP) stores, glucose, fat, or protein. The chemical processes that produce the ATP from these different fuels are different, and some also require oxygen to be available while others don't.