Simply, if you HAVE to choose, go with free weights. Stabilizer muscles come into play. And with the basic movements like squats, deadlifts, cleans, and even bench presses, the whole body becomes involved working as a unit to move the weight. I believe that more growth hormone is released when your whole body is involved. Therefor...better gains.
However, after someone has been training a while good machines can be rotated into the routines to keep things from getting stale. Most fans of free weights won't flinch to do leg extensions and leg curls after a good squat workout. For people with strong calves, it's hard to balance 800 -1000 lbs on an olympic bar to do calf raises on a toe-block. Heres where a calf raise machine works well. There have also been times that I've been confronted with the fact that I'm not invulnerable, and I have used machines to continue training around those injuries.
Machines have their place. I would suggest though that as a beginner that all or at least 90% of your training come from free weights.
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