Table of Contents (click to expand)
You wake up at the same time every morning because your circadian rhythm runs on a tight 24-hour cycle. About two to three hours before you normally wake, the suprachiasmatic nucleus in your hypothalamus starts ramping cortisol up and pulling melatonin down, lightening your sleep and timing your awakening to the minute. Born and colleagues (Nature, 1999) showed this anticipatory cortisol rise tracks the time you expect to wake up, which is why you often beat your alarm by a few minutes."
While being young, free and spontaneous has a certain allure to it, most people eventually find themselves in a situation where they have to set an alarm clock to ensure their life doesn’t get thrown into chaos. Whether it is taking care of your newborn baby, making it to your 9am lecture, or getting on the road to beat the commuter traffic, waking up and starting the day is pretty important.
However, have you ever experienced the strange phenomenon of waking up only moments before your alarm clock? Or even if you aren’t an alarm clock owner, do you notice that your body tends to naturally wake up at the same time? Why – and more importantly, how – does that happen?
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The Cycle Of Our Days
You may not like being classified as such, but the fact remains… human beings are creatures of habit. Based on the fact that we are diurnal animals – primarily active during the daytime – we know that something in our genetic makeup and evolutionary history has made our bodies “aware” of the passage of time. Based on our energy expenditures, nutrient intake, hormonal fluctuations and habits, we do exist on something of a schedule.
In fact, we exist within a number of rhythms and patterns that we collectively call our Circadian rhythm. You also might know this by different names, such as internal clock, biological clock, Circadian oscillator, etc. However, this Circadian rhythm is reactive to certain external cues, the primary one being daylight. This Circadian clock is located in the hypothalamus, more specifically, in an important bundle of nerves called the suprachiasmatic nuclei (SCN).

Although the SCN contains only about 20,000 neurons across both nuclei (a tiny number against the brain's ~86 billion), it has key connections to other parts of the brain that regulate our day and night schedule. This tiny bundle of nerves is the ticking clock that guides our sleeping and wakefulness. Not only that, it also guides our heart rate, body temperature and blood pressure, among other key aspects that can affect how tired or active we happen to be.
Over evolutionary history, the suprachiasmatic nuclei has become very good at recalibrating our daily cycle based on the 24 hours of each day, and while some people have a cycle that is slightly longer, and others a cycle that is slightly shorter, we are basically preprogrammed to operate within a 24-hour day. Over the course of this cycle, we see changes in melatonin secretion (which can help us relax and fall asleep), bowel movement, blood pressure, body temperature, coordination, reaction time, testosterone production and stress hormone levels.
This tightly packed bundle of nerves is the operating center for our alertness, and while it is extremely powerful and can affect our lives in countless ways, we do need to help it stay on track, particularly if we want to wake up on time.
Underneath the SCN, every cell in your body runs its own molecular clock. In 2017, Jeffrey C. Hall, Michael Rosbash and Michael W. Young won the Nobel Prize in Physiology or Medicine for working out how that clock actually ticks: two genes called period (PER) and timeless (TIM) make proteins that build up during the day, accumulate in the cell nucleus at night, and then suppress their own transcription, creating a 24-hour feedback loop. The SCN keeps all those cellular clocks in sync.
Why Do I Wake Up At The Same Time Every Day?
While the SCN takes care of the many hormonal and neuronal aspects of our Circadian rhythm, our choices and behavior have a great deal to do with when our body begins to “wake itself up”. The body prefers to get 7-8 hours of sleep, which typically includes 4 to 6 sleep cycles of roughly 90 minutes each, with a REM episode in every cycle (the REM bouts get longer towards morning). The body also prefers a routine, so if you begin going to bed every night at 10 pm, and setting your alarm for 6 am, the SCN can definitely get on board with that.
Within a matter of days or weeks, it will time your melatonin so that levels begin rising two to three hours before your usual bedtime, making you feel drowsy on cue. Cortisol then climbs steadily through the second half of the night and peaks about 30 to 45 minutes after you wake (researchers call this the cortisol awakening response). The combination of falling melatonin and rising cortisol thins out your last sleep cycles until you naturally awaken, right on time.
You see, the body spends a lot of time and energy perfecting this system, and a gradual wake-up makes for a smoother adjustment into the day and a more rested feeling. Although many people NEED an alarm clock to pull themselves out of bed, your Circadian rhythm (and your nerves) hate it! That sort of jolting shock is disorienting and floods the body with stress hormones, essentially undoing the smooth transitional work your system had been doing while sleeping.
Over time, if you remain on the same schedule, your body’s clock is so precise that it will occasionally wake you up a few minutes or even seconds before your alarm is set to go off. No, you’re not psychic, but your mind is an incredibly powerful thing. Research has even shown that if you fall asleep with the idea of waking up at a certain time, or earlier than normal, and measure out the hours, your body will naturally adjust its hormone levels to help you wake up earlier by releasing stress hormones hours earlier than it normally would have!
Breaking The Routine
Clearly, Circadian rhythms can have a major effect on our lives, but if you don’t live a lifestyle that allows for this sort of routine (e.g., going to bed at the same time and waking up at the same time), then your body will have to constantly guess what you’re going to do next, and you’ll end up being a slave to your alarm clock.
Regularity and routine is the key if you want to master your Circadian rhythms and get to the point where you are always waking up around the same time. Have a nighttime schedule, avoid electronic consumption in the hours before bed, and try to start your day around the same time every morning. Pretty soon, you’ll be living the dream – or at least waking up without the blaring of your alarm clock disturbing your peaceful slumber!
References (click to expand)
- Saper, C. B., Scammell, T. E., & Lu, J. (2005). Hypothalamic regulation of sleep and circadian rhythms. Nature
- Born, J., Hansen, K., Marshall, L., Mölle, M., & Fehm, H. L. (1999). Timing the end of nocturnal sleep. Nature, 397, 29-30
- The Nobel Prize in Physiology or Medicine 2017: Hall, Rosbash and Young. Nobel Foundation
- Stages of Sleep. US National Heart, Lung, and Blood Institute













