Microtrauma, which is tiny damage to the fibres, may play a significant role in hypertrophy. When microtrauma occurs (from weight training or other strenuous activities), the body responds by overcompensating, replacing the damaged tissue and adding more, so that the risk of repeat damage is reduced. Damage to these fibres have been theorized as the possible cause for the symptoms of delayed onset muscle soreness (DOMS), and is why progressive overload is essential to continued improvement, as the body adapts and becomes more resistant to stress.

So when you exercise and damage the muscle it grows bigger. No pain, no gain is true. It's been going on since there were muscles.

There is no plant analogy.

Bones get weak in weightlessness, so obviously they respond very well to being used to support the weight of the body. They heal faster and grow stronger when under compression forces.

http://en.wikipedia.org/wiki/Muscle_hypertrophy