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Are there real physical differences between a morning person vs a night person that can be measured and used to explain the difference?

Or is it just an adapted preference randomly varying from person to person?

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(see also this Q&A over at Biology.SE: https://biology.stackexchange.com/questions/93965/why-do-morning-people-have-shorter-biological-clocks/93966)

It's a real thing, but that doesn't necessarily mean it's set in stone or that preferences can't be changed/learned.

At least some portion of these preferences seem to be genetic and related to regulation of circadian rhythms. In brief: animals, including humans, have a system of molecular "clocks" that keep track of roughly the length of a day. These clocks most often run naturally slightly longer than 24 hours: if you keep someone (or, preferably, a lab animal) in constant darkness, they will still keep a daily sleep/wake cycle, but it will drift over time, corresponding to a >24 hour day.

To actually follow the real cycle of day and night, light is used to resynchronize the clock every day.

If someone's "natural" clock (without light synchronization) runs a bit shorter (faster) than average, you'd expect that person would tend to feel like waking up a bit earlier as well as feeling tired a bit earlier in the evening - a morning person. If someone's natural clock runs a bit slower than an actual day, then morning will come a bit sooner than they prefer, and in the evening they won't quite feel tired yet.

That said, like most traits of this nature, the biological underpinnings of these tendencies only explain part of it, and you would not expect to find people sorted neatly into "morning" and "night" but rather to follow something like a Gaussian distribution, with most people in the middle.

Here's a recent genome-wide association study and a review of some others on "chronotype" (the morning/night preference you ask about):

Jones, S. E., Lane, J. M., Wood, A. R., van Hees, V. T., Tyrrell, J., Beaumont, R. N., ... & Weedon, M. N. (2019). Genome-wide association analyses of chronotype in 697,828 individuals provides insights into circadian rhythms. Nature communications, 10(1), 1-11.

Kalmbach, D. A., Schneider, L. D., Cheung, J., Bertrand, S. J., Kariharan, T., Pack, A. I., & Gehrman, P. R. (2017). Genetic basis of chronotype in humans: insights from three landmark GWAS. Sleep, 40(2).

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