PSYC 388 Study Guide - Circadian Clock, Carl Linnaeus, Epigenetic Clock

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Rhythms of life
-Time embedded in our genes; Biological clocks found everywhere (bacteria, worms, us)
-Biological clock regulate sleeping, most of what happens in our bodies, our physiology + biochemistry = shows strong day-night differences (heart beat, blood pressure, liver
function, metabolizing alcohol, generation of new cells, body temperature, production of many hormones) ~ rhythmic
-Biological clock – medical implication = action of drugs vary depending on time of day
-No time cues our rhythms slowly drift out of alignment with outside world
-Natural world= fully of daily, monthly, annual rhythms
-Daily circadian rhythms are orchestrated by a central clock to keep our bodily systems working in harmony, but if disrupted = suffer mild symptoms of jet lag to serious conditions
such as depression and sleep disorders
-Clock keep ensemble of body beating to a collective time = keeps everything from happening all at once and ensures biochemistry of body runs on time and in order
-Biological clocks synchronise times of activity and rest of both diurnal (daytime) and nocturnal (nighttimes) organisms and those that are crepuscular (active at dusk and dawn) to
ensure peak activity occurs when food, sunlight or prey is available = enable us, etc. to anticipate the predictable rhythmic changes in environment: light, temperature, humidity,
UV radiation
-Biological clock impose structure that enables organisms to change their behavioural priorities in relations to time of day, month, or year = reset at sunrise and sunset each day to
link astronomical time with organisms internal time
-Today; 24/7 society = employed in utilities, transport, retail, etc. = imposed structure conflict with our basic biology
-Most of what we know about the genetic basis of behaviour comes from study of Drosophila, fruit-fly; = Pittendrigh = study biological rhythms
Chapter 1: The day within and The Day Without
-Rhythmany process that repeats itself at regular intervals
-Oscillatordevice that produces a rhythm; 1. Can measure duration/elapsed time by counting cycles or portions of a cycle and triggering events at certain intervals 2. Can be
synchronized to an external cycle and then consult as clock to recognize local time (ex. Arbitrary time of day)
-Pacemaker –the oscillator that ultimately sets the rhythms long-term periodicity if more than one oscillator is involved in regulation of a rhythm
-Entrainmentprocess of matching the phase and period of an endogenously rhythmic circadian clock to an environmental cycle
-Clocks rule our lives = instruct us when to sleep, wake, and work, eat, etc.
-Modern world = need to now time to tell us what to do = unnatural
-Our basic internal clocks are often masked by artificial timing of modern world (inventions), but notice if travel to different time zones
-Believe there no connection between internal clocks and rhythmic cycles of nature (dawn/dusk, lengthen days, shorten night) but could be wrong
-Internal daily rhythms (biology) isolate individual from environment reveals it = study: underground in constant light; RESULT: body rhythms start to drift out of
synchronisation with outside world than about a month = back in synchrony with outside world then drift again
-Almost everything we do shows circadian (day) rhythms = time for everything = regularity stop everything from happening at once ( separate bodily events from time)
-Kidney function and urine produce reduced at night because sleep cycles out of phase; body temperature + heart beat + blood pressure higher in day, cognitive abilities change
rhythmically over 24 hour period, tooth pain lowest after lunch, proof reading + sprint swimming best in evening, labour pains mostly begin at night, most natural births in early
hours, sudden cardiac death mostly I morning
-Variations in physical, emotional, cognitive performance therefore depending on task performance change between daily high point and daily low point. complex problem
solving or reasoning good at noon, physical coordination best in early evening
-Most vulnerable in early morning hours (internal clock disrupted) = symptoms Low point of circadian cycles, body least able to resist cardiac or respiratory difficulties =
accidents, etc
-Modern world = people knew time by what they were doing = harmony between daily bodily rhythms and external world ( holistic conception of time) constant repetition of day
and night, cyclic patterns of seasons and harvest
-Sundialsmeasure time by position of sun (shadow)/track slow motion of sunlight across a dial Mesopotamia (Iraq) = plot rotation of earth by follow shadow Tower of
Winds in Athens (astronomical observatory for sundial, weather vane and compass, water clock for cloudy days)
-First mechanical clocks = 1300 ADmodern clocks controls us = race against clock; work-life balance
-Rhythmic cycles in plant behaviour - Alexander the Great >>tamarind tree opening and closing its flowers in synchrony with the day
-Floral horologueclock made of plants that opened their flowers at different times of day
-Carl von Linneformalised idea of floral clock 2 species of daisy (1. Hawk’s beard 2. Hawkbit) opened and closed with period within half-hour each day (plants many species
in circle = hands of clock)
-Many plants open leaves in day and close at night + energy of sunlight to drive photosynthetic reaction = converts CO2 + H2O into sugars, and process release oxygen
-Each leaf cell must be exposed to surrounding air for efficient gas-water exchange and light for photosynthesis
-Plants: leaves droop if very hot
-Plants can’t move so circadian clock vital to ensure many physiological activities, ex. Related to photosynthesis, occur in right sequence at optimal time
-Tobacco plants, stocks, evening primroses release scent as sun go down = attract pollinating moths and night insects; plant cant release scent in timely manner in response to
environmental cue because need time to produce oils = need to anticipate nocturnal insects, and sunset to produce scent on circadian schedule
-Nocturnal animals = rhythms diametrically out of phase with diurnal animals
-Crepuscularactive at twilight or just before dawn
-All organisms need to somehow anticipate coming sunset and rise in order to be in right state and right place at right time; different species use same space but divided by time
-some species of fish and insects live in caves (no light) retained circadian rhythms of ancestors that lived in light place assumption: clocks used to keep some sense of internal
order = = stopping everything from happening at once
-rhythmany sequence of regularly recurring functions or events
-biological rhythmliving world, regular recurrence of an event through time ; ubiquitous (found everywhere)
-intertidal (about 12.8 days)
-heart beat: rhythmic but not constant same with blood pressure because varies with demands (ex. Run) + underlying circadian rhythm blood pressure lowest at about 4-6:00 a,
and rises steadily from then on and peaks in early afternoon before starting to fall
-Jean Jacques Ortous de Mairan: first to study biological rhythms scientifically interested in earth’s rotation and why leaves of plants rigid during day and drooped at night with
this rotation >> put mimosa in cupboard and observe = found leaves still opened and closed rhythmically even in dark + (seemed had own representation of day and night) =
subjective night drooped, subjective day stiffened up and leaves move at same time = identified first circadian rhythm (still move under constant conditions)
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~ Experiment first show daily rhythms were not response to changing light levels but were internal (endogenous)
-Henri duhamel reasoned mimosa leaf movements might have been response to changes in temperature so put plants in constant-temperature environment + constant darkness >>
RESULTS: still show regular pattern of leaf movements
-Alphonse de Candollefound period of leaf movement rhythm in constant conditions wasn’t exactly 24 hours = varied slightly from plant to plant = provide evidence clock is
internal, if its due to environmental cue than plants would move at same time
-Free-runningdaily pattern of an organism kept in constant conditions of darkness or light; rhythm innate, hard-wired into genome
-Light/dark cycle or other cues can synchronise rhythms but don’t cause them
-Free-running rhythm = ticking of genetically programmed clock
-Aperiodic environmentconstant temperature and illumination
-Erwin Bunning(lead to rigorous investigation of biological rhythms) >> found leaf movements of common bean Phaseolus oscillated in constant darkness with mean period 24.4
Established salient property of circadian clocks: when kept in constant conditions they run with period close to, but never exactly, 24 hours
-Pittendrigh – father of circadian research found fruit fly Drosophila” kept in constant conditions, free-running rhythm not quite 24 hours (varies 22-28 hours for different
species) + pulled into synchrony by specific signal, usually rise and set of sun = suggest independent, self-sustaining endogenous clock
-Limuluscrab with ancient daily rhythms >> unchanged for 350 million years but have 1000 photoreceptors clusters (ommatidia) in eye Barlow found circadian clock in
crab’s brain that transmits nerve signals to its eyes + eyes sensitivity varies on daily cycle even in darkness + have internal rhythm of ~24 hours, at night = signals can increase
eyes sensitivity to light to compensate for decrease in illumination between full moonlight and midday
When exposed to natural light = signals from photoreceptor cells in tail (stick out in mud) help keep circadian clock synchronised with actual cycle of day and night
-Cockroach Periplaneta” running wheel activity = in aperiodic environment its periodicity persisted indefinitely in absence of external driving factors (hence, internal clock ticks
~ 24 hours when kept in unvarying conditions) >> 24.5 hours = total darkness = starts its subjective day half-hour later each day
-Released from obvious light/dark switch that mimics daily sunrise and set, animal free-runs with natural period slightly longer than solar cycle >> free-running rhythm =
synchronised each day and forced exactly to 24 hour cycle by light
-Most organisms, light = main time –giver (Zeitgeber) that keeps mechanism synchronised to dawn and dusk
-Biological clock = temperature compensated because biological reactions are subjected Q10 biological rule (10 degree rise in temperature doubles metabolic rate so all biochemical
reactions in organism double in speed)
Chapter 2: Telling Time
-Most of us have instinctive sense of time( due to what we are doing)
-Bees in tune with daily solar cycle; their internal clock is reset by sun, on cloudy day they uses pattern of polarised light to deduce position of sun; have clocks with them, can
tell time and can tell other the times (time-sensing ability)
-Honeybee have time-sensing facility (Aristotle) saw sugar water set near hive no bees arrive then later once one had come other arrived too
-Zeitgedachtnismemory of time
-Dr. Forel studied whether bees have Zeitgedachtnis breakfast observation = bees came at same time even when no food outside= bees remember hours at which they had found
sweets = memory for time
-Ingeborg Beling showed bees could be trained to visit given site at given time; experiment which eliminated some external environmental cue = bee still punctual for food
-Bees have endogenous clock not memory or appreciation of time that does time-keeping for them
-Karl von Frisch believed bees had fixed memory for a 24 hour period an couldn’t remember significantly different time intervals; aware of bees capabilities especially timing of
their behaviour how bees communicate about direction and distance of new food source
Found figure-of-eight dance” - when return to hive describe direction of food source and distance
Vertical honey comb (dance floor)perform waggle dance”-Short straight run, waggling from side to side then turns left/right and walks in semicircle to starting
point then repeats short run down middle and make semicircle on opposite side and returns
Number of waggles and intensity of buzzing in each run indicate distance
Bees translates tree-dimensional location of food in outside world and its reference to sun into two-dimensional map on comb
In hive, gravity provides position of sun (up” locates sun) and direction of food given by angle that straight-line section of dances makes with the sun (imaginary
vertical line)
waggle dance”food sources further than ~50 metres; round dance”indicated food source near hive
Number of waggles during straight lines indicates distance to food source
Bees have distinctive language; challenged notions about cognitive abilities of insects
-Some biologists felt more likely bees located nectar-producing plants through odours and dancing was by-product as bees warmed down” after a flight (little to do with time
-Ocelli- photoreceptors in bees located on top of their head used for orientation
-James Gould experiment = make foraging bee lie” about location of food to rest of hive through its dance >>actual direction take and stance they fly is communicated through
dance; scent of nectar sample forager brings back analysed by other bees for quality and volume which plays part in decision whether to fly there or not
-Bees perform mindless tasks live by set of instructions (subroutines – do this until stop of code) = simple creatures, but have innate ability to work out location of food source
from position in relation to sun even on cloudy days by reading pattern of polarisation of light and pass information to other bees
-Bees can communicate distance up to 15 kilometres and allow for fact that sun moves relative to have by ~15 degree an hour and correct for this when they pass on information
(have own built-in global positioning system and language that enables them to refer to objects and events that are distant in space or time)
-Optical flow - pattern of apparent motion of objects, surfaces, and edges in a visual scene caused by the relative motion between an observer (an eye or a camera) and the scene 
bees have?
-Von Frisch >> bee measuring system in windy weather encounter headwind on flight to feeding-place, on return they indicate greater distance than if there had been no wind
(calculation of distance depends on time required)
-Honeybees acutely attuned to way their environment changes with time on daily basis - specialize in seeking gout one flower species at just right time
All information about flower is time-linked because produce nectar at approximately same time each day
Bees can tell time = can be trained to associate particular scent at particular time of day with food reward
Bees have circadian clock thats reset daily to run with solar cycle = can consult this clock and check off given time and associate this with particular event
If return too late in day for rest of hive to go out for food then bee wait until morning to dance
-Dogs, bees, bats and birds are good time keepers
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