To what extent can the brain cause physiological change?

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I'm looking for opinions/theories based on the current scientific understanding of the brain and it's associated glands/systems (pineal, pituitary, thyroid, adrenal, endocrine, etc) on as to what extent the brain can incite physiological change in it's host body.

For example:
-Can they incite changes in the metabolic processes of specific parts of the body (for the purpose of accelerating mitosis)?
-Can they promote the generation of stem cells in specific parts of the body?
-Can they cause tissue growth such as to expand olfactory senses or tactile senses?
-Can they be used to effectively select what traits would be represented in the host body from it's DNA and overtime restructure the body to that select trait type?

All of this is under the pretense of the brain being externally caused to do so vice doing so naturally and with complete disregard to the sustained health or wellbeing of the host body.