# Animal Behavior/Biological Rhythms
## Biological Rhythms

Our surrounding undergoes predictable, cyclical fluctuations as a result of changes in seasons, or the time of day. When events and conditions repeat in a rhythmic pattern, the ability to predict, anticipate, and prepare for them is a highly beneficial trait. Not surprisingly, most animals are able to adjust their physiology, behavior, and life cycles to the upcoming conditions. Owls begin to stir in the late afternoon and evening, awaiting the emergence of small mammals at dusk. Ground squirrels gather rations and pack on fat reserves in the fall in preparation for cold winters spent underground. Moose reproductive cycles match the birth of fawns in the spring to the rich emergence of forage at that time. Human core body temperature cycles with a low during the middle of their sleep cycle and highs around lunch time and early evening. Bioluminescent fireworm of Bermuda time their romantic gettogethers to diurnal as well as lunar cycles. Adult emergence of 17-year cicadas, or bamboo flowering every few decades, is closely timed across entire populations. Chronobiology, the science that describes timing in biological clocks and their associated rhythms, makes extensive use of terms and concepts derived from engineering disciplines. Rhythmic events are described as to their period (i.e., the amount of time it takes to go from peak to peak), frequency (i.e., the number of cycles completed within a specific unit of time), amplitude (i.e., the distance between peaks and average), and phase (i.e., the timing of the rhythm relative to some objective, external point in time).
The timing of a cycle's events can operate at many different time frames. Some cycles are link to obvious external patterns including:
* sun: circadian refers to 24h period length, ultradian to cycles exceeding 24h
* moon: lunar cycles, lasting 24.8h, are controlled by the phase of the moon, while tidal rhythms of 12.4h are determined by the timing of its gravitation pull
* tilt of earth's spin axis: a circannual rhythm spans events that repeat on a 12 month basis corresponding to the Earth's seasons

### Biological Clocks

Many observed rhythms in physiology and behavior often crucially depend on the presence of endogenous cycles and their production through biological clocks. Periodic rhythms, which are not simply responses to external periodic cues, have been documented for most living beings, including bacteria, fungi, plants, and animals. Biological clocks are self sustaining oscillators which will continue a period of free-running cycling even in the absence of external cues. However, clocks are usually linked to and can be reset by the environment via cues (i.e., Zeitgeber). Such entrainment keeps an organisms clock synched to its surrounding conditions.
Circadian clocks must contain a minimum of three basic elements: (1) input pathway(s) relay environmental information to a circadian pacemaker; (2) the endogenous pacemaker (oscillator) generates temporal patterns; and (3) output pathway(s) for the pacemaker to regulate output rhythms. A search for biological clocks commonly attempts to isolate an organism from its external cues and to search for the continuation of rhythmic patterns. Isolation from all possible (e.g., geophysical, magnetic, or radiation) cues remains a difficult task, however, animals will display cyclical activity patterns even when maintained in constant conditions aboard a spacecraft orbiting far above the earth.
Genetic components of the biological clock have emerged from research on the fruit fly where mutant lines of flies displayed abnormal cycling, including a shorter period, a longer one and its complete absence in yet another. All three mutations were mapped to the same gene - termed period or per. Disruption of the same gene in human sleep disorder underscored the conserved nature of the molecular circadian clock throughout evolution.
Biological Clocks exhibit a high degree of inheritance, independence of temperature and social conditions, strong resistance to pharmacological and chemical disruption, and may even be expressed at the level of single cells. Entrainment is often limited to a narrow range of possible outcomes, may utilize a small set of cues, and its timing is critical. Human circadian rhythms free-run at slightly longer than 24 hours and are reset to the normal 24h day by light cues. Humans are able to readily adjust to a 23-25h day but not to a 22 or 28h day. Biological rhythms may be expressed over many different time frames, and entrainment of one clock may disrupt multiple rhythmic changes suggesting a basic linkage of patterns (e.g., circadian activity and estrous cycles in mammals).
Karl von Frisch's search for biological clocks characterized a periodic, night-time lightening of skin chromatophores in minnows. These cyclical changes in skin pigments persisted even in blinded individuals. With damage to the pineal gland, however, fish were no longer able to change skin color in rhythmic fashion. The existence of extra ocular light perception in the brain's pineal gland allowed the fish to change color even when ocular light perception was disrupted.

#### Molecular Basis of Cellular Clocks

The presence of rhythmic patterns even at the level of single cells indicates the presence of cell-autonomous circadian mechanisms. In the fruit fly (Drosophila) two proteins (PER and TIM) play a role in rhythmic patterns at the cellular level. The two proteins form a dimer complex in the nucleus, bind to the gene's promoter, and inhibit production of further per and tim RNA. With gene transcription of the component proteins turned way down, few new PER and TIM proteins are made. Existing PER-TIM complexes are gradually degraded, and decrease in numbers as they are not replaced. The protein-induced inhibition of per and tim transcription weakens, mRNAs for them increase, leading to enhanced PER and TIM protein, complex formation between them, and renewed inhibition of per and tim gene transcription. In the mammalian suprachiasmatic nucleus entrainment derives from light-induced expression of transcription factors (i.e., immediate early genes, IEG), which control the expression of timing genes down-stream. At the output level, the circadian clock controls the transcription of a number of genes such as CREM (i.e., CRE modulator).

#### Suprachiasmatic Nucleus

The mammalian circadian system relies on oscillating neurons grouped within the suprachiasmatic nucleus (SCN), a distinct group of cells located in the hypothalamus. Its destruction results in the complete obliteration of regular sleep/wake rhythms. Cultured SCN cells maintain their own rhythm in the absence of external cues. The SCN receives information on day length from the retina, interprets it, and during the dark phase enhances secretion of the hormone melatonin from the pineal gland.

### Sleep

Sleep, an essential state of natural rest, is observed in most animals. It is characterized by reduced voluntary body movement, decreased reaction to external stimuli, and a loss of consciousness. Humans sleep an average of 7.5 hours, during which they proceed in around 100 minute cycles of two broad types. Rapid eye movement (REM) occupies roughly 25% of sleep time. During this stage the body shows a loss of skeletal muscle tone while the brain is quite active. Electroencephalography (EEG) shows a mixture of frequencies that is similar in appearance to the wakeful EEG and coincides with periods of intense dreaming. Non-rapid eye movement (NREM) sleep occupies most of the sleep time and is characterized by frequent limb movements and sleep walking while the brain exhibits reduced activity and little dreaming.
The inherent function of sleep is not yet completely understood. Sleep, which affects the immune system and metabolism, supports a restorative function with increases in wound healing and the production of anabolic growth hormones. Sleeps is marked by a variety of physiological processes of growth and rejuvenation of the organism's immune, nervous, muscular, and skeletal systems. In newborns sleep appears to play a critical role in establishing proper functional connectivity in the brain. A number of studies suggest the existence of a correlation between sleep and the many complex functions of memory. Memory and learning involve nerve cell dendrites sending information to the cell body to be organized into new neuronal connections. Sleep which reprocesses the days events in the absence of external information is processed by these dendrites as memories are solidified and knowledge is organized [Saper and Stickgold 2005].