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A further problem is the design of the exercise study. Going from sedentary to 60 min of strenuous exercise is too quick of a ramp for most adults. They will not have recovered from one workout before they are doing the next. Being tired and sore limited further activity. Had the study gone on for a year it is likely the 60m group would have been fitter and thinner.

The actual study was designed to measure how the different levels of exercise provoked compensatory changes. As you point out, exercising beyond your fitness level (which is quite common among folk launching into a weight-loss/exercise programme)tends to cause you to rest up a bit more during the day and eat more both through hunger and "rewards"

To be able to work hard enough to burn 600 Cals in an hour, your have to be pretty darn fit. To be able to work hard enough to burn 600 Cals in an hour, you have to be REALLY fit. The sort of fitness level that can't be had with a few weeks or even months of "working out"

Incidentally, dieting also tends to cause this economy of movement to some degree. When we did our informal study at the start of the year, we all chose our own diet and noted and compared our results. I used a pedometer to track my movement before starting the diet and then for the few days I could manage to hack it before dumping it. My average step count went from about 12,000 steps a day to about 7-8,000. Not quite a couch potato but a noticable difference. I would never have guess without the pedometer, mind, as my volitional activity (housework, dog walking etc was the same)

The NYT article did as good a job of reporting as you could expect, but look how the duo touting the Perfect Health Diet presented it...
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