Biological Rhythms

The earth spins on its axis once every 24 hours, submitting plants and animals to highly predictable daily rhythms of light, dark and temperature. The availability of food and the activity of predators are in turn affected by these periodic variations, therefore it is not surprising to discover that the behavior and metabolism of most organisms follows a 24 hour schedule.

The most obvious explanation for such 24-hour cycles is that plants and animals passively respond to the cycles in their environment. However, when an organism is isolated from all environmental time cues; when light, food, temperature and sound are kept constant around the clock - the biological rhythms of many organisms persist with an independent period, which is known as a free-running period (when isolated from environmental cues, behaviors and physiological processes maintain a roughly 24 hr rhythm of highs and lows).

The physiological system responsible for measuring time and synchronizing an organism's internal processes with the daily events in its environment is known as the circadian timing system. The word circadian (Latin; circa = about; dies = day).

Other kinds of rhythms also exist which have either a shorter or longer period than the circadian period.

Ultradian refers to very short rhythms of minutes to hours, such as the cycle of REM sleep, which has a period of about 90 minutes.

Infradian rhythms are those which last for more than one day, such as the menstrual cycle in human females which has a rhythm of about 28 days, or the estrous cycle in rats and hamster, which is about 3 - 4 days.

Circannual rhythms refer to rhythms that have a period of about a year, such as rhythms which control the onset of the breeding season in many animals such as deer and sheep.

A little history:

1. Jean Jacques d'Ortous de Mairan (1729), an astronomer, was the first to determine that organisms might not be passively behaviorally responding with rhythmic behavior to exogenous cues. He noted that the heliotrope plant, which opens its leaves during the day and folds them at night, will do so even when placed in constant darkness.

2. In 1832 Augustin de Candolle discovered that the daily leaf movements of Mimosa not only persist in constant darkness but that the opening occurred an hour earlier each day, indicating that the endogenous rhythm of leaf opening had a period of about 23 hours (not 24 hours).

This was the first demonstration that circadian clocks would free-run with their own endogenous period when they were no longer synchronized to a 24 hour light-dark schedule.

3. The investigation of the nature of circadian rhythms in mammals first occurred in 1866, when William Ogle observed that body temperature in humans rises in the early mornings and falls in the evening, and he demonstrated that this rhythm was not directly dependent on obvious environmental influences.

4. In 1906, Simpson and Galbraith demonstrated that the body temperature rhythm of monkeys persisted in constant darkness or constant light, and that the rhythm appeared to be synchronized by the 24 hour light-dark schedule, since if the schedule of light and dark was reversed, the body temperature rhythm gradually shifted to follow it.

5. The conceptual advance that stimulated scientific inquiry into the field of biological rhythms was the recognition that rhythms are the output of a neural system whose function is to measure time. This was a shift in emphasis from considering rhythms as a biological curiosity to realizing that circadian rhythms are critical, time-measuring devices and are physiologically and behaviorally important.

This observation can be traced back to the findings of a Swiss physician, Auguste Forel in 1910. He and his family were vacationing in the Swiss Alps and it was their custom to have breakfast on the terrace. One morning, a bee arrived from a hive about 125 meters from the house and ate some of the marmalade on the table. Within a few days, so many bees were arriving at breakfast time, that they had to abandon the practice of eating outside, however for several days following, the bees continued to arrive at breakfast time. The physician noted that that the bees must have some kind of time-keeper, or a memory for time that enabled them to arrive just at breakfast time and no other time.

6. von Frisch (1929) enlarged on this casual observation by experimentally determining that bees could be trained to arrive at an artificial feeding place; although they could only do this when the interval was close to 24 hours. They could not be trained to find food, for example, every 19 or 48 hours, indicating that it must be an endogneous rhythm that was stimulating this behavior.

7. Beginning in 1932, Bunning laid the foundations for much of our current understanding of biological clocks. He demonstrated that:

8. In the 1950s, Colin Pittendrigh published a paper that demonstrated that the time of day that a fruit fly (Drosophilia) emerges from its pupa is controlled by the circadian clock and has nothing to do with other environmental variables such as temperature. Although most metabolic processes speed up with increases in body temperature, the circadian clock does not. Circadian clocks are thus temperature-compensated, which of course is necessary if the clock is to be a viable time-keeping device.

9. Renner (1955) decided to determine for once and all if there was something else in the environment which was cueing bees to collect food. He trained 40 bees to collect sugar water between 8:15 PM and 10:15 PM each night in a closed room in France. He then transported the bees overnight to New York City where they were placed in a similarly organized laboratory. The next night, the bees arrived at the feeding table between 8:15 and 10:15 PM, French time. These experiments showed that no environmental cue was telling the bees when the food was available, but that an internally generated time-keeping device must be in place. This internal circadian timing system thus enables bees to avoid wasting energy in futile visits to flowers, which, following a circadian schedule themselves, offer their nectar or pollen only at restricted times of the day. Many flower species have a characteristic time of opening and closing their petals. Once a bee has identified a flower with nectar available at a given time of day, the bee and others from the same hive can return each day at the appropriate time, no matter what cues the other environmental conditions are giving (for example, it might be very cloudy).

10. In 1962 Aschoff and Wever conclusively demonstrated that human circadian rhythms were endogenous. They isolated individuals in a sealed cellar below Munich for 8 - 19 days. This revealed that the free-running period of of the human rest-activity cycle is about 25 hours (meaning that a free running human would get up an hour later every day) (although later more rigorous work indicates that it is closer to 24 hr in length).

11. In 1972, two independent groups (Moore and Eichler; Stephan and Zucker), found that found that lesions of a small, bilateral pair of nuclei in the anterior hypothalamus (SCN) would eliminate circadian rythmicity in many physiological and behavioral variables; including sleep and wakefulness.

Requirements of a circadian clock:

  1. First, the clock must measure the passage of time independently of any periodic input from its environment. A researcher looking for a clock, looks for the smallest entity, whether it be an organ, a cell, or a sub-cellular fraction, that can measure circadian time in the absence of time cues in the environment.

  2. Second, the clock must be used to time biological events.

  3. Furthermore, in order to keep time, a clock must have resolution. The resolution of a clock is a measure of its ability to detect the temporal order of two events closely spaced in time. If the events are closer together than the clock can resolve, then the clock will not be able to tell which event follows the other. Circadian clocks have relatively high resolution.

  4. Clocks must have uniformity. Uniformity is a measure of how uniformly the clock measure times, and therefore predicts how well the clock can predict the occurrence of other regularly timed phenomena.

  5. Circadian clocks must be able to be reset each day by cues in the environment, such as light, so that the variable they control is synchronized with external variables. Thus, although the human sleep-wake cycle is longer than 24 hours long (if you were allowed to free-run, you would go to bed later each day), this resetting each day by light keeps us on a 24 hour period.


Like many fields, the study of biological rhythms has its own jargon, or terminology.

Zeitgeber: Literally time-giver. The Zeitgeber is the environmental cue that synchronizes the endogenous circadian rhythm with the environment. For most organisms, the strongest Zeitgeber is sunlight.

Local Time: The time of day during which the biological measurement was taken.

Circadian Time: This is an artificial construct which standardizes the relationship of the biological variable to the Zeitgeber cycle by defining CT 0 as dawn; (CT 24 = CT 0; onset of activity of diurnal animals) and CT 12 as dusk (onset of activity of nocturnal animals). When measuring entrained rhythms, it is OK to use local time but if you are measuring free-running rhythms, you need an artificial time such as CT time; CT time is the standard time that is used to measure all rhythms.

Period: Identified for both the rhythm which is being measured and the Zeitgeber are the mean values, and the minimum and the maximum; and the ranges of the oscillation (r and R) and the periods of the oscillations (length of time between any two similar points in the rhythm, such as onset to onset, or maximum to maximum; designated by the Greek letter tau).

Rhythm maximums, minimums, and period

Phase: The Greek letter psi, is used to designate the relationship between any two reference points on the Zeitgeber and the rhythm.

Entrainment: The daily resetting of the clock by some exogenous cue such as light so that rhythms are synchronized or entrained to the 24 hour exogeneous cue.

Subjective Day and Subjective Night: The part of a circadian cycle during the free-running state that corresponds to the illuminated or dark segment during entrainment by a light-dark cycle. The time of day or night an animal thinks it is. This is a lab construct, since in the lab you can put animals on any photoperiod you like, so that their subjective day might be during the hours when it is actually dark outside.

What kinds of behaviors do researchers measure experimentally?

The ideal rhythmic behavior should be measurable within an individual animal at many times per circadian cycle for many successive cycles. Ideally, also, the behavior that is being measured should not be influenced by the process of measurement and the process of measurement should be automatable unless you can find a large number of researchers who are willing to work around the clock.

An example of the kind of behavior which meets these criteria is wheel running activity in rodents. Hamsters, for example, will run with a highly reproducible pattern at the same time each day. Many successive circadian cycles can be monitored for the animal's whole lifetime if necessary. Other rhythms that are often monitored are those of feeding and drinking and body temperature rhythms via telemetry from an implanted capsule.

Sinauer link (see 14.1, 14.9 and animation 14.2)

Exogenous cues which act as Zeitgebers to entrain rhythms:

  1. Light-dark cycles: The LD cycle is an important cue in all mammalian species, both nocturnal and diurnal, including humans.

  2. Food availability: Cycles of eating and fasting might be expected to provide some important temporal restraints on an animal's behavior, especially under natural conditions when food may be available only at certain times of day. Richter was the first to demonstrate this in a laboratory setting. Using a rodent running wheel, he demonstrated that in constant darkness, a single meal once a day could synchronize the rest-activity pattern of a rat. He further found that the rhythm would persist over several days of food deprivation.

  3. Temperature cycles: Temperature cycles are not effective in entraining many rodent species, however it has been demonstrated that cycles of hot and cold will entrain the macaque monkey.

  4. Social cues: Cycles of social interaction can entrain some species of bats and mice (blind mice in rooms with sighted mice will entrain to the activity cycle of the sighted mice. The social cues used are probably sounds or smells emitted by the entraining animal. It appears that social cues are important for social animals, such as humans, and that social cues probably interact with other environmental cues to produce entrainment. It is also thought that in older humans, whose biological rhythm mechanisms deteriorate with age, that social cues are the primary method of entrainment.

Phase Response Curves (PRCs):

Phase Response Curve

Phase Response Curve Graphic

For a Zeitgeber to entrain a circadian rhythm, it must in each cycle reset the phase of an otherwise free-running rhythm by an amount that corrects for the difference between the period of the time cue (light) and that of the pacemaker (SCN-generated circadian rhythm of the physiological function). This resetting is achieved through a circadian rhythm of sensitivity of an organism to a time cue, such as light. Light, for example, will induce a phase delay, a phase advance or no phase shift at all, depending on when in its subjective day or night an animal is exposed to light (subjective day or night = the time scale as defined by the animal's own circadian rhythm). The largest phase delays occur in early subjective night, and the largest phase advances occur in late subjective night. The circadian system is relatively unresponsive to light during the subjective day and at mid-subjective night

This property of entrainable circadian rhythms - a periodically changing sensitivity to light - was first observed in plants and then later in mammals in 1956 when Rawson noticed phase shifts in the activity rhythm of mice free-running in constant darkness when he switched on the light at certain phases of their subjective night, but no phase shift when he switched on the light at other times.

The observed relationship between the time in the animal's subjective day when a light pulse is given and the phase shift obtained, can be conveniently plotted as a phase-response curve (PRC). The main features of the PRC, with phase delays in early subjective night and phase advances in late subjective night, are similar in all species whether they are single-celled algae or primates and whether they are nocturnally or diurnally active.

The first detailed examination of the phase-response curve of a mammal to short (10 min) light pulses was undertaken by Pat DeCoursey. She determined the phase shift in the wheel running records of a flying squirrel at hourly intervals throughout the subjective day and night. This was aided by the high uniformity of the flying squirrel's activity rhythm, so that phase shifts of a few minutes could be reliably detected.

The discovery of the phase response characteristics of the circadian system has contributed significantly to our understanding of how light-dark cycles and other Zeitgebers entrain an animal's circadian pacemakers. Because brief pulses of light are so effective, the daily light-dark and dark-light transitions have become recognized as major entraining features. Furthermore, the PRC has become important in the analysis of circadian systems because it enables us to study the properties of pacemakers independently of an animal's overt rhythms.

This example uses the rest-activity cycle of an animal in constant darkness with a free-running period of 25 hours being reset by 1 hr pulses of light. The horizontal bars represent wheel-running in a nocturnal animal (or sleep in a diurnal animal) plotted as a standard circadian actogram. Before the pulse was given, the free-running period was stable at 25 hours, with the rhythm phase-delaying by 1 hr every day as compared to 24 hour clock time. Panels A thru E illustrate the consequence of applying a single 1 hr light pulse at different times of subjective day or night. Not all light pulses produced phase shifts of the rest-activity cycle. In mid-subjective day (A) or mid-subjective night (not shown, CT 18), no phase shift was obtained.

PRC example

When an identical light pulse was applied in early subjective night, just after a nocturnal animal would start its activity, the onset of activity was more delayed (C). By the second day, the rhythm had stabilized at a net phase delay of -3 hours. In contrast, similar light pulses in late subjective night (D) and early subjective day (E), produced phase advances of +4 hours and +2 hours respectively, instead of phase delays.

With such data, we can quantify the response of the animal's circadian system to light. In the lower panel the resultant phase-response curve is shown, which has a waveform characteristic of the PRCs for mammalian species.

Sample problem:

An animal kept in constant conditions in the laboratory whose free-running sleep-wake cycle is 26 hours long and who is given a pulse of light at circadian time 21 and circadian time 12 would now demonstrate a sleep-wake cycle that was advanced or delayed how many hours? (3 pts). Please make it clear how you arrived at your answer. (use PRC and explain how long advances and delays would be and do the math). (3 pts).

Several points can be made about this schematic PRC:

  1. Responsiveness to light is confined mostly to subjective night in both nocturnal and diurnal species (dawn and dusk). Thus, for both, when placed in a suddenly shifted light-dark cycle, light falls on a different portion of the PRC and produces a corresponding phase shift of the circadian system.

  2. At the time when a diurnal animal is normally exposed to light (and a nocturnal animal is not) in mid-subjective day, light has no effect on the circadian system. Most of the daytime illumination falls on the inactive portion of the PRC and thus has little or no influence on the entrainment process. At the time when both nocturnal and diurnal animals are normally not exposed to light (CT 18 or mid-subjective night), neither is responsive to light.

  3. The PRC documents how the sun rising in the morning (during an animal's subjective day) tends to produce a phase advance (so a diurnal animal would start activity earlier), whereas light falling at dusk (late subjective day) causes a phase delay (so that the animal would continue activity longer). Thus a natural daily light-dark cycle is constantly nudging the circadian clocks of animals forward in the morning and backward in the evening with each 24 hour day (this works for both diurnal and nocturnal species).

  4. Notice that the dawn pulse (E) causes a phase advance of 2 hours each day, whereas the dusk pulse (B) causes a phase delay of only 1 hour. The net effect is a 1 hour phase advance per day, just sufficient to reset a 25 hour free-running period to 24 hours and therefore ensure entrainment to the 24 hr day-night cycle of the environment. Although this schematic diagram oversimplifies the process, it demonstrates the general principle of how the fine-tuning of the circadian system's phase normally occurs each day at dawn and dusk.

Sleep/wake cycles:

People tend to be segregated into two groups, larks and owls. Larks are people who like to get up early and go to bed early, and owls are people who like to get up late and go to bed late.

Bedtime11:30 +/- 1 hr
(for extreme larks, this is very late; 8:30-9:30 is more reasonable)
1 AM +/- 1 hr
(for extreme owls, this is very early, 2:00-4:00 AM is more reasonable)
Wake up7:00 AM +/- 1 hr
(or much earlier, 4:30-5:00 AM)
8 AM +/- 1 hr
(usually much later, 10:00 AM-1:00 PM)
Ease of Sleepeasyhard
Mood in AM goodbad
Variation in bedtime littlehighly variable
Napsbrief/rarelonger /frequent
Awake all nightvery raremore frequent
Sleep quality good but inflexiblepoor, but flexible

Do the Lark/Owl test; It should be done according to your preferred hours, not what you actually are forced into by school, work, parenting, etc.

It turns out that whether you are a lark or an owl is mediated by your body temp (BT) cycle. We have 1 clock that runs circadian rhythms, including the rest/activity cycle (or sleep/wake cycle) (SCN), but for body temperature, this clock appears to be modulated by other inputs (arcuate and MPOA are candidates).

Normally, these are synchronized to each other (in a particular phase relationship) and are also entrained to the light/dark cycle in the same phase. However, people who cross many time zones have been studied and their body temperature rhythms and rest/activity cycles desynchronize and can even re-entrain going in different directions (one rhythm phase delaying and one phase advancing), indicating that they can desynchronize (it is suspected this may be part of the trigger for the onset of some metabolic diseases).

Typically, we get sleepy when our BT starts to drop, about 3 hours after the max of the rhythm.

Body Temperature Circadian Rhythm

Body temperature rhythm compared to sleep onset and offset (and melatonin release)

Core Body Temperatures in Insomniacs vs. Controls

Graph of delays and advances in two kinds of insomnia

We know these physiological differences exist in Larks and Owls:

  1. Larks and owls body temperature and rest/activity cycles are synchronized to each other in different phase relationships.

    Body temperature cycles in owls vs. larks

  2. Differences in period of the temperature rhythm: owls may have a longer body temperature rhythm than do larks.

  3. Owls are less sensitive to the entraining Zeitgeber.

  4. SCN pacemaker may not be as strongly modulated by the neural inputs that affect body temperature in owls as it is in larks.

  5. Larks and owls have different clock genes.


The sleep-wake cycle (rest/activity; high alertness/low alertness) persists in the absence of environmental variation and has a period in humans of longer than 24 hours (originally reported as 25 hrs, now known to be closer to 24 than 25). Humans have some capability to postpone sleep, but there is a circadian rhythm that persists in the desire for sleep, even when you are denying yourself sleep. For example, if you have stayed up all night, you go through a period of alertness in the morning even if you haven't slept, and you go through a period of fatigue during the time you would normally fall asleep.

Circadian rhythms of low and high alertness

Human subjects who are not sleep deprived, but living in an isolation facility where their circadian rhythms are free running alternate between long (15 - 20 hrs) and short (6 - 9 hr) sleep durations with no consistent relationship to the duration of prior wakefulness. Ashoff recognized that when internal desynchronization occurs, the rest-activity cycle may free-run with a period much longer than that of the body temperature cycle. Under these conditions, the length of the rest-activity cycle is modulated as it passes through various phase relationships with the body temperature rhythm; thus sleep duration depends on the circadian phase of the body temperature rhythm when you go to sleep; short sleep episodes typically begin just at or just after the mid-trough of the temperature cycle, whereas the long sleep episodes occurred when sleep begin when the body temperature rhythm is above its mean value.

Americans are considered to be chronically sleep deprived. People may be divided into short sleepers (5 hrs or less per day) or long sleepers (more than 5 hrs per day). The majority of people appear to need at least 7 hrs of sleep to avoid sleep deprivation; 1 out of 4 Americans aged twenty and above reported getting 6 or fewer hours of sleep a night and over the last century, the average total sleep time has reduced by 20% or more.

American sleep habits

Across the human life span, amount and the timing of sleep vary considerably: