aelephant comments on Exercise isn't necessarily good for people - Less Wrong Discussion
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This is what came to mind to me too. If you have someone who is thoroughly unhealthy & metabolically broken, adding a bunch of exercise on top of that is not a positive stressor, it is likely to knock them down even further. You have to approach things in order, like fixing the diet & addressing potential issues like hypothyroidism before you start training them to be an athlete.