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When you do heavy exercise like running, your heart rate, and breathing increases, is it because of the sympathetic nervous system controls it? Or the Sympathetic nervous system only activates on the fight-flight situation? Or is the exercise considered a fight-flight situation by our brain?

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Interestingly, intense exercise elevates levels of cortisol, which is the primary stress hormone. However, since this intense exercise usually only lasts for a short time (except maybe for ultra-marathon runners), it is considered acute rather than chronic stress. Other "intense" activities, like sex, also elevate levels of stress hormones. This just goes to show you that some stress is good. Generally, only chronic stress is bad (or brief very intense stress from trauma).

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The sympathetic nervous system's primary process is to stimulate the body's fight-flight-or-freeze response. It is, however, constantly active at a basic level to maintain homeostasis (Brodal, 2004).

The heart rate and breathing increase is needed for homeostasis due to the need for more blood oxygen and fuel by the muscles.

References

Brodal, P. (2004). The Central Nervous System: Structure and Function (3 ed.). US: Oxford University Press. pp. 369–396. ISBN 0-19-516560-8.

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