Entrainment is the word scientists use to explain how we all, as human beings, "set our clocks." Our human body clocks, to be specific. Our bodies have multiple "clocks" in specific organs as well as inside each and every blood cell, and like clockwork they help us to manage our daily rhythms, which inform the behaviors that make us functioning human beings.
Think about hunger, sleep, sex, digestion. These are all physiological processes that require some precise timing on the part of our personal clocks. This is what our circadian rhythms are all about. When our rhythms fall out of synchronicity, that is when we can experience disease, general malaise or other kinds of biological confusion. We really can't live healthy lives without adhering to circadian rhythms.
The most obvious way that we entrain ourselves to life's rhythms is through our perception of light. Light is what marks the day/night cycles; the sun rises, the sun sets. Sunlight, and its absence, also helps the body to detect seasonal shifts. These are primal communications we share with the earth. All living things require the light-dark cycles, as established by the rotations of our planet, to manage these critical life rhythms.
Light is perceived by the eyes, of course, but also through the skin via melanopsin. Signals collected by these organs are sent to the body's main pacemaker, the suprachiasmatic nucleus (SCN), which issues orders to all others parts of the body to function according to a preset pattern of rhythms that, by and large, most human beings are commonly entrained to using light.
For the vast majority of human beings, light is the key influence over when we sleep and when we wake up. For those with circadian rhythm disorders like Non-24 Sleep -Wake Disorder (also known as free-running disorder) or shift work disorder or even a temporary case of jet lag, light doesn't deliver the same influence over sleep-wake cycles.
The person who suffers from these kinds of disorders struggles to maintain a normal life on an abnormal schedule. They have fallen out of entrainment and need to find a way to "reset" or else they are forced to adjust their schedule in ways that are not typical, even unorthodox, in order to simply get by.
Imagine the person who can only feel awake and alert in the later afternoon; maybe they have a job working at the toll both during the morning commute. Or imagine the nurse who can only work night shifts but who has children to watch during the day at home. Or the musician who cannot stay awake long enough to attend the gigs he is scheduled to perform at nightclubs.
Having pattern disruptions in one's rhythms can absolutely devastate the efforts of many to live normally (in this case, meaning "by society's schedule"), and that includes having the ability to earn a living, care for family or function at their maximum potential while on the job. Circadian rhythm disorders also seriously disrupt relationships and social lives.
Believe it or not, there are other cues besides light--in science, they call them zeitgebers, which translates as time markers, external or environmental cues that synchronize our biological rhythms--which have a powerful impact on our lives, including our time while sleeping. These are also ways we are entrained to healthy--or unhealthy--rhythms.
Eating and digesting do not require light or even sight to take place. They require that the gastrointestinal system follow specific cues that dictate that you eat and digest while you are awake. While you sleep, the digestive system goes into sleep mode as well. This is why, generally speaking, most people do not get up in the middle of the night to have a bowel movement. The digestive system does not expect food to enter the alimentary canal at this time. Instead, the act of moving food through the system slows dramatically.
Large meals eaten right before bed, however, can create problems with sleep disruption; the digestive system is suddenly working overtime when it had fully expected to be in bed like the rest of you. Poor sleep can result, as can reflux disease and other health problems related to metabolism. There are lots of studies to suggest that eating out of synch with one's normal body rhythms (meaning, late at night) can lead to imbalanced secretions of certain hormones like melatonin, orexin, leptin and ghrelin, which can impact metabolism in negative ways.
Finally, there is a circadian shift in metabolism that occurs in the morning as part of your biological rhythms. This is normal; it prompts hunger and stimulates the body to recommence digestion. Now you know why we almost always need to use the restroom first thing in the morning: wakefulness stimulates digestion and the elimination of wastes that have been in your "holding tanks" (meaning, the bladder and the bowel) overnight.
Activity levels are other non-light time markers that can inform sleep-wake cycles and metabolism. If you exercise too late at night, this could mess with your ability to fall asleep. Physical activity (it could be running a mile or doing laundry) amps up adrenaline and other hormones which encourage wakefulness.
Similarly, body temperature, which is influenced by how physically active you are, impacts your ability to entrain to patterns that allow for consistent sleep-wake patterns. If you do not get enough physical activity during the day, you may find it hard to fall asleep, as well--with no normal rise and fall in daytime body temperature, the body may not be able to read your activity markers clearly enough to signal sleep to occur.
Also, the act of sleeping itself is marked by specific patterns of body temperature shifting that prepare the brain and body systems for specific kinds of sleep. If your body temperature is out of whack as you are heading off to bed, you might be missing out on sleep stages that are critical to your body and brain to function at maximum potential.
Temperature-related breaks in entrainment are experienced by people with major stress disorders like PTSD or severe depression: they may generate higher body temperatures at night while in stress response even as they are hoping to fall asleep. Women, because of their monthly cycles, can also experience temporary periods of sleep disruption due to normal alterations in body temperature caused by menstruation or other major changes in hormone balance like pregnancy or menopause.