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From a physiological perspective, all that is done during exercise is the expending of energy in the form of ATP to fuel muscle contraction and extension.

When I looked up why muscle grow due to exercise, there is the claim that recovery of micro lesions formed during exercise enables slight growth of muscle. I am not sure how micro lesions are formed and intuitively, these micro lesions should cause atrophy of the muscle rather than strengthening of the muscle fibers.

Further there is no logical connection as to why muscle fibers would be strengthened rather than just restored to its previous form during rest.

Can someone help me make the mental leap from the consumption of ATP through exercise to muscle growth?

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Muscle growth and development is mediated by "trophic factors" not biochemical reactions (ATP) or muscle contraction directly. The best method of releasing tropic factors is exercise and not electrical stimulation or biochemical reactions (ATP) or biomechanical contraction.

Nerve ending release growth or tropic factors which stimulate muscle growth and for example if the nerves die off either due to injury or disease (ALS) the muscles will atrophy.

Not all of the tropic factors are as of yet known, but it is these tropic factors that stimulate muscle growth, not the biochemical or biomechanical reaction of the muscle (contraction). One can not as of yet stimulate muscle growth by delivering electrical energy to the muscle, for example (it has been tried to in an effort to maintain muscle mass in critically ill patients).

There is a review of the trophic factors here - http://neuromuscular.wustl.edu/lab/trophic.htm

And a review of electrical stimulation - http://www.medword.com/MedwordStore/PCP/EMS_truth.html

There are many claims of benefit for electrical stimulation, such as regeneration of the facial nerve in facial paralysis, such as Bell's palsy.

The "problem" is that the prognosis in Bell's palsy is very good, even without electrical stimulation, and so it is difficult to "prove" benefit with electrical stimulation:

With or without treatment, most individuals begin to get better within 2 weeks after the initial onset of symptoms and most recover completely, returning to normal function within 3 to 6 months.

http://www.ninds.nih.gov/disorders/bells/detail_bells.htm

Statistically, the natural history without treatment was described in a study of 1011 patients in 1982 [8]. One-third had an incomplete paralysis, and two-thirds had complete paralysis. Overall, 85 percent showed signs of recovery within three weeks, 71 percent had complete recovery, 13 percent had slight sequelae, and 16 percent had residual weakness, synkinesis and/or contracture. Patients with incomplete lesions had a 94 percent rate of return to normal function, while only 60 percent of those with clinically complete lesions returned to normal function.

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