All About: Body Clock – Physician’s Notebooks


First, about the Body Clock, let us locate it in Brain (image below). It is part of the hypothalamus, a structure deep inside front of Brain; as its name implies, it is located between the thalamus, the brain’s central computer for connecting its many parts. The hypothalamus is the single small structure under the forward ends of the right and left thalamus.


The hypothalamus may be considered your body’s master neuro-gland. It contains neural centers that regulate sleep & wake, food & water intake, body temperature, and that tell time, i.e., it houses the body clock.



Every function of your body runs by your body clock’s time: sexual power, appetites, alertness & sleep patterns, energy, and your intellectual brilliance levels, and moods. They all cycle on the clock. You may not notice the cycles – they are chemically based and only documented by blood testing, and, as a modern civilized person, the external influences in your daily life allow you to override their cyclic patterns. However, it is important to be aware of the clock because it explains many variations in powers, feelings, and illnesses and can help you to be more efficient in your life.


The cellular time-keeper is based first on a biological clock in the hypothalamus: similar neurons, the suprachiasmatic nuclei (the SCN; right & left neurons located supra, or above the optic nerves crossing). These neurons tick your day’s time away. Their setting averaged out in humans, is 24 hours and 11 minutes plus or minus 16 minutes (95% of people fall within the plus or minus).


How did it get set and how may it be reset? In your retinas (the back cup that records your eye images) are special retinal ganglion time-keeping neurons. These cells have only one function: to signal the external light from the daytime/night-time cycle. These retinal neurons are directly connected each by a nerve fiber. The fibers run in the left and right optic nerve and together form a right & left tract (the retinal-hypothalamic tract or RHT) and they have set the SCN cell clock to the c.24-hour rhythm, called circadian (“circa”=approximate, and “-dian”= day)

But what about the artificial lighting in our modern life? Doesn’t it interfere with resetting the clock?

It sure does! The biological circadian clock is part of all animal and plant life on Earth. It evolved over billions of years since first life on our planet. For 99.9% of human existence, humans ran around without the benefit (and distractions) of artificial light. Everything was day-sunlight or night-time blackness (and in between a li’lle moonlight or firelight).

Over the millennia, human circadian rhythm by its daily resetting developed because we humans were daytime animals who slept at night. (Mice are night-time-active animals and as a result, tend to have a less than 24-hr circadian rhythm)
Today, with modern life, we override many rhythms and cues, but the basic rhythm is so deeply inserted in our DNA that each person’s SCN beats to the same human clock – the cells remember. This explains phenomena like jet lag and the problem of 24-hour shift work and most insomnia.


The RHT-SCN connection is key to the body’s biologic clock. All the vital organs function according to the clock with highs and lows in the 24-hour period. But the SCN is pure nervous system. So to signal other parts of the body, we have the pineal gland, a small midline structure like a little plum that grows out of the rear hypothalamus brain substance and dangles into the 3rd ventricle of the brain and is bathed in the cerebrospinal fluid.
Through the SCN, the pineal is part of the body clock, and during the unlit night, the pineal gland produces the sleep hormone melatonin and releases it into the cerebrospinal fluid and blood. So, the body knows when it is daytime or nighttime outside. It knows because light (sunlight or strong artificial light) excites the retina ganglion neurons to send a signal that stops the release of the sleep hormone melatonin.
And when darkness descends around each of us, the stop-melatonin retinal signal ceases, and melatonin gets released. This, in the natural state, results in a diurnal (day & night) absence and presence of melatonin from blood and CSF, and it signals cells all around the body what is the time of day, and the melatonin helps you fall asleep. But when it clashes with the realities of one’s daily living, insomnia develops.

With more research we may use knowledge of the body clock rhythms to help us succeed in daily chores, to prevent or cure illness, and, ultimately, to achieve the best healthy longevity. For examples, research shows that memory works best right after an undrugged good few-hours sleep, so if you are studying for a test, bone-up on the test subjects, arrange a condition where you are not sleep-deprived, study the subjects of the test and right away after you finished get at least 2 or 3 hours good sleep.

The body clock is something we all should learn more about and fund more research into.

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Physician’s Notebooks is a blog that teaches Healthy Longevity, which means living past age 80 on one’s feet with wit and wits. Reading and rereading should bring success and happiness. It may up your IQ, SAT, TOEFL (Test of English as a Foreign Language) and MCAT scores.

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*image courtesy of Riken



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