The reason that our bodies do this, as opposed to making all muscles strong all the time, is to avoid wasting energy on muscles you aren't using. It is basically using what muscles were used recently as a heuristic for which muscles need to be strong to ensure survival.
2 - It turns out that your mind does control it directly. The greatest predictor of improved muscular strength is how strongly you can intentionally contract that muscle. Unfortunately, you learn to do that through exercise :|
A lower level example is feedback mechanisms. Mechanical stress from motion are used to maintain bone strength. The cells involved in bone breakdown and repair can detect damage and reinforce where needed, but they also remove bone where it’s not needed. Without that kind of feedback our bones would either be weak or heavy.
The same thing happens with your circulatory system, you grow new capillaries in response to demand. Or for a “negative” example fat cells reproduce when you can store more energy.
Exercise raising the heart rate is a consequence, that (the increased heart rate) is not the singular magic thing improving your health. With exercise there's a positive, body-comprehensive event going on.
Exercise strengthens the heart.
Cocaine (for example) damages the heart. It doesn't just elevate the heart rate, it does some vicious things to the heart, causing damage:
https://www.webmd.com/connect-to-care/addiction-treatment-re...
Cocaine on the other hand seems to raise your resting heart rate because it damages your cardiovascular system [1]. Your heart has to work more to achieve the same result, the opposite from what you want to achieve with exercise.
1: https://journals.plos.org/plosone/article?id=10.1371/journal...
Mammals are highly adoptive by the design, a living organism consists of trillions programmed and partially controllable nanomachines.
Body has autonomous and centralised systems, which checks and sends hormonal signals and redistribute resources from other parts and could directly command specific cell groups to grow or change behavior in a chance to increase organism survivability.
The low-level mechanism could be the endocrine system and its production of anabolic hormones, depending on how 'low-level' you are looking for.
1) Body by Science: A Research Based Program for Strength Training, Body building, and Complete Fitness in 12 Minutes a Week by John Little and Doug McGuff.
2) The Energy of Life: The Science of What Makes Our Minds and Bodies Work by Guy Brown.
Human cells (controlled by DNA algorithm) repair the wear out parts via reinforcement learning.
Elastic bands are relatively just static objects.
I'm hoping someone can answer a question to which I've never heard a really satisfactory answer: Why does human health benefit from exercise whereas any kind of simple machine wears out with exercise? For example, doing a hundred stretches per day improves my health whereas stretching an elastic band 100 times per day will cause it to lose elasticity and soon destroy it. So what's the low-level mechanism by which exercise improves health in people but not in simple machines?