Have you ever wondered why you feel alert in the morning and sleepy at night? Or why jet lag makes you feel so awful? The answer lies in your circadian rhythm, a 24 hour body clock that runs silently in the background of your biology, coordinating everything from when you sleep to when your hormones are released.
Understanding your circadian rhythm is one of the most practical pieces of health knowledge you can have. It affects your sleep quality, energy levels, mood, metabolism, and even your risk for various health conditions. In this beginner's guide, we will explore what circadian rhythm means, how scientists discovered it, and why it matters for your daily life.
Your Body Keeps Time
Every cell in your body contains molecular machinery that keeps track of time. This internal clock influences:
- When you feel sleepy and when you feel alert
- Body temperature fluctuations throughout the day
- Hormone release timing
- Hunger and metabolism patterns
- Immune system activity
- Mental alertness and cognitive performance
What Is Circadian Rhythm?
The term "circadian" comes from two Latin words: circa, meaning "about," and diem, meaning "day." So circadian rhythm literally translates to "about a day." It refers to the roughly 24-hour cycle that governs many of your body's biological processes.
Your circadian rhythm is not just a response to light and darkness. It is an internal biological program that runs even when you are isolated from all time cues. In experiments where people have lived in underground bunkers with no clocks, windows, or schedules, their bodies still maintained a roughly 24-hour cycle of sleep and wakefulness.1
An Important Discovery: In 1962, French scientist Michel Siffre spent two months living in a cave deep underground with no way to tell time. Despite having no sunrise, sunset, or clocks, his body continued to follow a daily rhythm. His sleep-wake cycle settled into a pattern of about 24.5 hours, proving that the circadian rhythm is generated internally rather than simply responding to the environment.2
This internal timing system exists in nearly all living things, from bacteria to plants to humans. It evolved to help organisms anticipate predictable changes in their environment, particularly the daily cycle of light and darkness that comes with Earth's rotation.
Three Key Properties of Circadian Rhythms
Scientists define true circadian rhythms by three characteristics:
Self-Sustaining
The rhythm continues even without external time cues. If you put a person in constant darkness with no clocks, their body still maintains an approximately 24-hour cycle. This shows the clock is generated internally by biological mechanisms.
Entrainable
The rhythm can be synchronized to external signals called "zeitgebers" (German for "time givers"). Light is the most powerful zeitgeber, but meal timing, exercise, and social activities can also influence your clock.
Temperature Compensated
Unlike most biological reactions that speed up when warm and slow down when cold, circadian rhythms maintain their roughly 24-hour period across different temperatures. This ensures your internal clock stays accurate regardless of whether you have a fever or are in a cold environment.3
Nobel Prize Research
The importance of circadian rhythm research was recognized in 2017 when Jeffrey Hall, Michael Rosbash, and Michael Young received the Nobel Prize in Physiology or Medicine for their discoveries of molecular mechanisms controlling circadian rhythm.4
Their work, conducted primarily in fruit flies during the 1980s and 1990s, revealed how cells keep time at the molecular level. They identified genes called "clock genes" that create a self-regulating feedback loop, producing proteins that rise and fall in concentration over a 24-hour cycle.
The Period Gene Discovery
The breakthrough came when scientists isolated a gene called period. This gene produces a protein that gradually accumulates in cells during the night and is broken down during the day. When enough protein builds up, it blocks its own production, creating a feedback loop that takes about 24 hours to complete.5
This molecular mechanism, refined by additional genes discovered since, exists in virtually every cell of your body, from your brain to your liver to your skin.
The Nobel Committee noted that the laureates' discoveries had "vast implications for our health and wellbeing." Their work explained why disrupting the circadian system, through shift work, jet lag, or irregular sleep schedules, can have such profound effects on health.
Why This Research Matters
Understanding the molecular basis of circadian rhythms has opened doors to new research in many fields:
- Chronotherapy: Timing medication delivery to match circadian rhythms for better effectiveness
- Cardiovascular health: Understanding why heart attacks are more common in the morning
- Mental health: Exploring connections between circadian disruption and depression
- Metabolism: Investigating why eating at night may contribute to weight gain
The Brain's Master Clock: The Suprachiasmatic Nucleus
While every cell has its own clock genes, your body needs a conductor to keep all these cellular clocks synchronized. That conductor is a tiny brain region called the suprachiasmatic nucleus, or SCN for short.
The SCN is a pair of small clusters containing about 20,000 neurons, located in the hypothalamus directly above where the optic nerves cross (the optic chiasm). Its position is no accident. This location allows the SCN to receive direct light information from specialized cells in your eyes.6
Size and Location
Despite controlling timing throughout your entire body, the SCN is remarkably small. Each of the two nuclei is only about the size of a grain of rice. Together, they contain roughly 20,000 neurons, a tiny fraction of the brain's approximately 86 billion neurons.7
Damage to the SCN eliminates circadian rhythms. Animals with SCN lesions lose their regular sleep-wake patterns and other daily rhythms, sleeping and waking randomly throughout the day and night.
The SCN coordinates your body's peripheral clocks through several methods:
- Neural signals: Direct nerve connections to other brain regions and the body
- Hormones: Controlling release of timing signals like cortisol and melatonin
- Body temperature: Your core temperature varies by about 1 degree Celsius over 24 hours, helping synchronize peripheral clocks
- Feeding signals: Meal timing affects liver and metabolic clocks
Think of the SCN as the conductor of an orchestra. Each section (organ, tissue, and cell) has its own musicians and sheet music (clock genes), but the conductor ensures everyone plays in time together.
Light and Melatonin: How Your Clock Stays Synced
Your internal clock runs at approximately, but not exactly, 24 hours. Left to its own devices, your clock would gradually drift out of sync with the actual day-night cycle. Light exposure is what keeps your clock aligned with the real world.
How Light Reaches Your Clock
Your eyes contain special cells called intrinsically photosensitive retinal ganglion cells (ipRGCs) that are different from the rods and cones used for vision. These cells contain a light-sensitive protein called melanopsin and are particularly sensitive to blue light, around 480 nanometers wavelength.8
When light hits these cells, they send signals directly to the SCN. This is why some people who are completely blind from damage to their rods and cones can still maintain normal circadian rhythms. As long as their ipRGCs are intact, light information reaches their clock.
Morning Light
Effect: Advances your clock (makes you wake earlier the next day)
When: Most effective in the first 2-3 hours after waking
Application: Get bright light exposure early if you want to shift your sleep schedule earlier
Evening Light
Effect: Delays your clock (makes you wake later the next day)
When: Most impactful in the hours before typical bedtime
Application: Avoid bright light in evening if you want to fall asleep earlier
The Melatonin Signal
Melatonin is often called the "hormone of darkness." Your pineal gland, a small structure deep in the brain, produces melatonin when the SCN signals that it is nighttime.9
Melatonin does not make you sleep directly. Instead, it signals to your body that it is biological nighttime, helping prepare various systems for sleep. Melatonin levels typically begin rising about 2-3 hours before your natural bedtime, peak in the middle of the night, and fall to nearly undetectable levels during the day.
Light Suppresses Melatonin
Light exposure at night, especially blue light from screens, suppresses melatonin production. Studies show that two hours of tablet use before bed can suppress melatonin by more than 50% and delay melatonin onset by over an hour.10
This is one reason why screen time before bed is associated with difficulty falling asleep and poorer sleep quality.
Circadian Rhythm and Hormones
Your circadian system controls the timing of hormone release throughout the body. Two of the most important circadian hormones are cortisol and melatonin, which work in opposition to regulate your daily alertness cycle.
The Cortisol Awakening Response
Cortisol, often called the "stress hormone," follows a strong circadian pattern. In healthy individuals, cortisol levels begin rising several hours before typical wake time, peak about 30-45 minutes after waking, and then gradually decline throughout the day, reaching their lowest point around midnight.11
Cortisol Peak (6-8 AM)
Cortisol surges to help mobilize energy, increase alertness, and prepare your body for the day ahead. This "cortisol awakening response" provides natural energy and mental clarity in the morning without any caffeine.
Melatonin Onset (9-11 PM)
As cortisol falls, melatonin rises. The pineal gland begins releasing melatonin about 2 hours before your typical bedtime, signaling to your body that biological night has begun. This prepares your systems for sleep.
Other Circadian Hormones
Beyond cortisol and melatonin, many other hormones follow circadian patterns:
| Hormone | Peak Time | Function |
|---|---|---|
| Growth Hormone | Early sleep (11 PM - 2 AM) | Tissue repair, muscle building, fat metabolism |
| Testosterone | Early morning (7-10 AM) | Energy, muscle function, mood |
| Thyroid Hormone (TSH) | Late evening (10 PM - 2 AM) | Metabolic rate regulation |
| Leptin | Midnight - 2 AM | Satiety signaling, appetite control |
When your circadian rhythm is disrupted, these hormone patterns can become dysregulated, contributing to a wide range of health issues from metabolic problems to mood disturbances.
What Disrupts Your Circadian Rhythm?
Modern life presents numerous challenges to circadian health. Understanding what disrupts your body clock can help you make better choices to protect your natural rhythms.
Shift Work
Working during biological night and trying to sleep during biological day puts your behavior directly at odds with your circadian programming. Shift workers face ongoing conflict between what their clock says and what their schedule demands.12
Long-term shift work is associated with increased risks of cardiovascular disease, metabolic disorders, certain cancers, and mental health problems. The World Health Organization's International Agency for Research on Cancer has classified shift work that involves circadian disruption as "probably carcinogenic to humans."13
Jet Lag
Rapid travel across time zones creates a mismatch between your internal clock and local time. Your SCN can only shift by about 1-1.5 hours per day, so crossing multiple time zones means your clock will be misaligned for several days.14
Direction Matters
Traveling east (advancing your clock) is typically harder than traveling west (delaying your clock). This is because the human circadian clock naturally runs slightly longer than 24 hours, making it easier to stay up late than to go to bed early.
A general rule: recovery takes about one day per time zone crossed when traveling east, and slightly less when traveling west.
Blue Light at Night
The light from smartphones, tablets, computers, and LED lighting is rich in blue wavelengths that strongly affect the circadian system. Evening exposure to these devices can suppress melatonin, delay sleep onset, and reduce sleep quality.15
Irregular Sleep Schedules
Going to bed and waking up at different times on weekdays versus weekends, sometimes called "social jet lag," can keep your clock perpetually misaligned. Studies show that people with more than 2 hours difference between weekday and weekend sleep timing have increased risk of obesity, depression, and cardiovascular problems.16
Other Disrupting Factors
- Late-night eating: Food is a zeitgeber; eating late can shift peripheral clocks
- Caffeine: Can delay circadian phase when consumed in the evening
- Insufficient daylight: Without bright daytime light, your clock may not be properly anchored
- Late-night exercise: Physical activity can shift the clock, potentially delaying sleep
How Scientists Study Circadian Rhythms
Researchers use several methods to study the circadian system in both laboratory and real-world settings.
Constant Routine Protocol
To observe the true circadian rhythm without environmental influences, researchers use a "constant routine" protocol. Participants stay awake for 24-40 hours in constant dim light, with small identical meals at regular intervals and semi-recumbent posture throughout.17
This removes masking effects from sleep, light, food, and activity, allowing researchers to see the underlying circadian rhythm in measures like body temperature, melatonin, and alertness.
Forced Desynchrony
In forced desynchrony studies, participants live on artificial day lengths that are far from 24 hours, such as 20 or 28 hours. Because the circadian clock cannot entrain to these unusual schedules, it "free runs" at its natural period while the imposed schedule runs at a different rate.18
This allows researchers to separate circadian effects from sleep effects, since participants end up sleeping at all different circadian phases over the course of the study.
Measuring Circadian Phase
Researchers commonly use these markers to determine circadian timing:
Dim Light Melatonin Onset (DLMO)
The gold standard for measuring circadian phase. Researchers collect saliva or blood samples in dim light during the evening hours and measure when melatonin levels begin to rise. This typically occurs 2-3 hours before habitual sleep onset in people with normal circadian timing.19
Core Body Temperature
Body temperature follows a circadian rhythm, dropping to its minimum in the early morning hours (around 4-5 AM for most people) and peaking in the late afternoon or early evening. Continuous temperature monitoring can reveal circadian phase.
Real-World Monitoring
Outside the laboratory, researchers use actigraphy (wearable motion sensors) and sleep diaries to track rest-activity patterns. While these don't directly measure the circadian clock, they provide useful information about sleep timing and regularity in everyday life.
Newer technologies including continuous glucose monitors and wearable temperature sensors are expanding options for studying circadian rhythms in natural settings.
References
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- Siffre, M. (1964). Beyond Time. McGraw-Hill.
- Pittendrigh, C. S. (1954). On temperature independence in the clock system controlling emergence time in Drosophila. Proceedings of the National Academy of Sciences, 40(10), 1018-1029. https://www.pnas.org/doi/10.1073/pnas.40.10.1018
- The Nobel Prize in Physiology or Medicine 2017. NobelPrize.org. https://www.nobelprize.org/prizes/medicine/2017/summary/
- Hardin, P. E., Hall, J. C., & Rosbash, M. (1990). Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature, 343(6258), 536-540. https://www.nature.com/articles/343536a0
- Moore, R. Y., & Eichler, V. B. (1972). Loss of a circadian adrenal corticosterone rhythm following suprachiasmatic lesions in the rat. Brain Research, 42(1), 201-206. https://pubmed.ncbi.nlm.nih.gov/5047187/
- Welsh, D. K., Takahashi, J. S., & Kay, S. A. (2010). Suprachiasmatic nucleus: cell autonomy and network properties. Annual Review of Physiology, 72, 551-577. https://pubmed.ncbi.nlm.nih.gov/20148688/
- Berson, D. M., Dunn, F. A., & Takao, M. (2002). Phototransduction by retinal ganglion cells that set the circadian clock. Science, 295(5557), 1070-1073. https://www.science.org/doi/10.1126/science.1067262
- Claustrat, B., Brun, J., & Chazot, G. (2005). The basic physiology and pathophysiology of melatonin. Sleep Medicine Reviews, 9(1), 11-24. https://pubmed.ncbi.nlm.nih.gov/15649735/
- Chang, A. M., Aeschbach, D., Duffy, J. F., & Czeisler, C. A. (2015). Evening use of light-emitting eReaders negatively affects sleep, circadian timing, and next-morning alertness. Proceedings of the National Academy of Sciences, 112(4), 1232-1237. https://www.pnas.org/doi/10.1073/pnas.1418490112
- Chung, S., Son, G. H., & Kim, K. (2011). Circadian rhythm of adrenal glucocorticoid: its regulation and clinical implications. Biochimica et Biophysica Acta, 1812(5), 581-591. https://pubmed.ncbi.nlm.nih.gov/21320597/
- Kecklund, G., & Axelsson, J. (2016). Health consequences of shift work and insufficient sleep. BMJ, 355, i5210. https://www.bmj.com/content/355/bmj.i5210
- Straif, K., Baan, R., Grosse, Y., et al. (2007). Carcinogenicity of shift-work, painting, and fire-fighting. The Lancet Oncology, 8(12), 1065-1066. https://pubmed.ncbi.nlm.nih.gov/19271347/
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- Gringras, P., Middleton, B., Skene, D. J., & Revell, V. L. (2015). Bigger, brighter, bluer-better? Current light-emitting devices: adverse sleep properties and preventative strategies. Frontiers in Public Health, 3, 233. https://www.frontiersin.org/articles/10.3389/fpubh.2015.00233/full
- Roenneberg, T., Allebrandt, K. V., Merrow, M., & Vetter, C. (2012). Social jetlag and obesity. Current Biology, 22(10), 939-943. https://www.cell.com/current-biology/fulltext/S0960-9822(12)00394-7
- Duffy, J. F., & Dijk, D. J. (2002). Getting through to circadian oscillators: why use constant routines? Journal of Biological Rhythms, 17(1), 4-13. https://pubmed.ncbi.nlm.nih.gov/11837947/
- Dijk, D. J., & Czeisler, C. A. (1995). Contribution of the circadian pacemaker and the sleep homeostat to sleep propensity, sleep structure, electroencephalographic slow waves, and sleep spindle activity in humans. Journal of Neuroscience, 15(5), 3526-3538. https://www.jneurosci.org/content/15/5/3526
- Lewy, A. J., & Sack, R. L. (1989). The dim light melatonin onset as a marker for circadian phase position. Chronobiology International, 6(1), 93-102. https://pubmed.ncbi.nlm.nih.gov/2706705/
Disclaimer: This article is for educational purposes only and does not constitute medical advice. The information provided is based on scientific research and is intended to help readers understand circadian biology. Consult qualified healthcare professionals for advice about sleep disorders, circadian rhythm disorders, or other medical conditions. NullField Lab is a research tool for personal experimentation, not a medical device.
