Editing Brain (section)

== Function ==
[[File:Model of Cerebellar Perceptron.jpg|thumb|right|Model of a neural circuit in the cerebellum, as proposed by [[James S. Albus]]]]

Information from the sense organs is collected in the brain. There it is used to determine what actions the organism is to take. The brain [[multisensory integration|processes]] the raw data to extract information about the structure of the environment. Next it combines the processed information with information about the current needs of the animal and with memory of past circumstances. Finally, on the basis of the results, it generates motor response patterns. These signal-processing tasks require intricate interplay between a variety of functional subsystems.<ref name=CarewCh1/>

The function of the brain is to provide coherent control over the actions of an animal. A centralized brain allows groups of muscles to be co-activated in complex patterns; it also allows stimuli impinging on one part of the body to evoke responses in other parts, and it can prevent different parts of the body from acting at cross-purposes to each other.<ref name=CarewCh1>{{cite book |last=Carew |first=TJ |title=Behavioral Neurobiology: the Cellular Organization of Natural Behavior |publisher=Sinauer Associates |year=2000 |isbn=978-0-87893-092-0 |chapter-url=https://books.google.com/books?id=wEMTGwAACAAJ |chapter=Ch. 1}}</ref>

=== Perception ===
[[File:Hearing mechanics cropped.jpg|thumb|right|alt=Drawing showing the ear, inner ear, and brain areas involved in hearing. A series of light blue arrows shows the flow of signals through the system.|Diagram of signal processing in the [[auditory system]]]]

The human brain is provided with information about light, sound, the chemical composition of the atmosphere, temperature, the position of the body in space ([[proprioception]]), the chemical composition of the bloodstream, and more. In other animals additional senses are present, such as the [[Infrared sensing in snakes|infrared heat-sense of snakes]], the [[Magnetoception|magnetic field sense]] of some birds, or the [[Electroreception|electric field sense]] mainly seen in aquatic animals.

Each sensory system begins with specialized receptor cells,<ref name="Kandel 2000"/><!--Ch. 21--> such as [[photoreceptor cell]]s in the [[retina]] of the [[eye]], or vibration-sensitive [[hair cell]]s in the [[cochlea]] of the [[ear]]. The axons of sensory receptor cells travel into the spinal cord or brain, where they transmit their signals to a [[sensory system|first-order sensory nucleus]] dedicated to one specific [[Stimulus modality|sensory modality]]. This primary sensory nucleus sends information to higher-order sensory areas that are dedicated to the same modality. Eventually, via a way-station in the [[thalamus]], the signals are sent to the cerebral cortex, where they are processed to extract the relevant features, and [[Multisensory integration|integrated]] with signals coming from other sensory systems.<ref name="Kandel 2000"/><!--Ch. 21-->

=== Motor control ===
[[Motor system]]s are areas of the brain that are involved in [[motor control|initiating body movements]], that is, in activating muscles. Except for the muscles that control the eye, which are driven by nuclei in the midbrain, all the voluntary muscles in the body are directly innervated by [[motor neuron]]s in the spinal cord and hindbrain.<ref name="Kandel 2000"/><!--Ch 34--> Spinal motor neurons are controlled both by neural circuits intrinsic to the spinal cord, and by inputs that descend from the brain. The intrinsic spinal circuits implement many [[reflex]] responses, and contain [[central pattern generator|pattern generators]] for rhythmic movements such as [[walking]] or [[Aquatic locomotion|swimming]]. The descending connections from the brain allow for more sophisticated control.<ref name="Kandel 2000"/><!--Ch. 36 and 37-->

The brain contains several motor areas that project directly to the spinal cord. At the lowest level are motor areas in the medulla and pons, which control stereotyped movements such as walking, [[breathing]], or [[swallowing]]. At a higher level are areas in the midbrain, such as the [[red nucleus]], which is responsible for coordinating movements of the arms and legs. At a higher level yet is the [[primary motor cortex]], a strip of tissue located at the posterior edge of the frontal lobe. The primary motor cortex sends projections to the subcortical motor areas, but also sends a massive projection directly to the spinal cord, through the [[pyramidal tract]]. This direct corticospinal projection allows for precise voluntary control of the fine details of movements. Other motor-related brain areas exert secondary effects by projecting to the primary motor areas. Among the most important secondary areas are the [[premotor cortex]], [[supplementary motor area]], [[basal ganglia]], and [[cerebellum]].<ref name="Kandel 2000"/><!--Ch. 33--> In addition to all of the above, the brain and spinal cord contain extensive circuitry to control the [[autonomic nervous system]] which controls the movement of the [[smooth muscle]] of the body.<ref name="Kandel 2000" /><!--ch49-->

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Major areas involved in controlling movement
|-
! Area
! width="100" | Location
! Function
|-
! scope=row style="text-align:left" | [[Anterior horn of spinal cord|Ventral horn]]
| style="background: tan" | Spinal cord || style="background:#ffdead" | Contains motor neurons that directly activate muscles<ref>{{cite web |last=Dafny |first=N |title=Anatomy of the spinal cord |publisher=Neuroscience Online |url=http://neuroscience.uth.tmc.edu/s2/chapter03.html |access-date=2011-10-10 |url-status=dead |archive-url=https://web.archive.org/web/20111008172218/http://neuroscience.uth.tmc.edu/s2/chapter03.html |archive-date=2011-10-08 }}</ref>
|-
! scope=row style="text-align:left" | [[Oculomotor nucleus|Oculomotor nuclei]]
| style="background: tan" | Midbrain || style="background:#ffdead" | Contains motor neurons that directly activate the eye muscles<ref>{{cite web |last=Dragoi |first=V |title=Ocular motor system |publisher=Neuroscience Online |url=http://neuroscience.uth.tmc.edu/s3/chapter07.html |access-date=2011-10-10 |archive-url=https://web.archive.org/web/20111117070343/http://neuroscience.uth.tmc.edu/s3/chapter07.html |archive-date=2011-11-17 |url-status=dead }}</ref>
|-
! scope=row style="text-align:left" | [[Cerebellum]]
| style="background: tan" | Hindbrain || style="background:#ffdead" | Calibrates precision and timing of movements<ref name="Kandel 2000"/><!--Ch. 42-->
|-
! scope=row style="text-align:left" | [[Basal ganglia]]
| style="background: tan" | Forebrain || style="background:#ffdead" | Action selection on the basis of motivation<ref>{{cite journal |last1=Gurney |first1=K |year=2004 |title=Computational models of the basal ganglia: from robots to membranes |journal=Trends in Neurosciences |volume=27 |pages=453–459 |pmid=15271492 |doi=10.1016/j.tins.2004.06.003 |last2=Prescott |first2=TJ |last3=Wickens |first3=JR |last4=Redgrave |first4=P |issue=8|s2cid=2148363 }}</ref>
|-
! scope=row style="text-align:left" | [[Motor cortex]]
| style="background: tan" | Frontal lobe || style="background:#ffdead" | Direct cortical activation of spinal motor circuits<ref>{{Cite web|last=Knierim|first=James |title=Motor Cortex (Section 3, Chapter 3)|url=https://nba.uth.tmc.edu/neuroscience/s3/chapter03.html|access-date=2021-01-23|website=Neuroscience Online|publication-place=Department of Neurobiology and Anatomy at The University of Texas Health Science Center at Houston, McGovern Medical School}}</ref>
|-
! scope=row style="text-align:left" | [[Premotor cortex]]
| style="background: tan" | Frontal lobe || style="background:#ffdead" | Groups elementary movements into coordinated patterns<ref name="Kandel 2000"/><!--Ch. 38-->
|-
! scope=row style="text-align:left" | [[Supplementary motor area]]
| style="background: tan" | Frontal lobe || style="background:#ffdead" | Sequences movements into temporal patterns<ref>{{Cite journal |last1=Shima |first1=K |last2=Tanji |first2=J |year=1998 |title=Both supplementary and presupplementary motor areas are crucial for the temporal organization of multiple movements |journal=[[Journal of Neurophysiology]] |volume=80 |pages=3247–3260 |pmid=9862919 |issue=6|doi=10.1152/jn.1998.80.6.3247 }}</ref>
|-
! scope=row style="text-align:left" | [[Prefrontal cortex]]
| style="background: tan" | Frontal lobe || style="background:#ffdead" | Planning and other [[executive functions]]<ref>{{cite journal |last1=Miller |first1=EK |last2=Cohen |first2=JD |s2cid=7301474 |title=An integrative theory of prefrontal cortex function |journal=Annual Review of Neuroscience |volume=24 |issue=1 |pages=167–202 |year=2001 |pmid=11283309 |doi=10.1146/annurev.neuro.24.1.167}}</ref>
|}

=== Sleep ===
{{Main|Sleep}}
{{See also|Circadian rhythm|arousal}}

Many animals alternate between sleeping and waking in a daily cycle. Arousal and alertness are also modulated on a finer time scale by a network of brain areas.<ref name="Kandel 2000" /><!--Ch. 45--> A key component of the sleep system is the [[suprachiasmatic nucleus]] (SCN), a tiny part of the hypothalamus located directly above the point at which the [[optic nerves]] from the two eyes cross. The SCN contains the body's central biological clock. Neurons there show activity levels that rise and fall with a period of about 24 hours, [[circadian rhythm]]s: these activity fluctuations are driven by rhythmic changes in expression of a set of "clock genes". The SCN continues to keep time even if it is excised from the brain and placed in a dish of warm nutrient solution, but it ordinarily receives input from the optic nerves, through the [[retinohypothalamic tract]] (RHT), that allows daily light-dark cycles to calibrate the clock.<ref>{{cite journal |last1=Antle |first1=MC |title=Orchestrating time: arrangements of the brain circadian clock |journal=Trends in Neurosciences |year=2005 |volume=28 |pages=145–151 |url=http://www.columbia.edu/cu/psychology/silver/publications2/149%20antle%20et%20al.pdf |pmid=15749168 |doi=10.1016/j.tins.2005.01.003 |last2=Silver |first2=R |issue=3 |s2cid=10618277 |url-status=dead |archive-url=https://web.archive.org/web/20081031120051/http://www.columbia.edu/cu/psychology/silver/publications2/149%20antle%20et%20al.pdf |archive-date=2008-10-31 }}</ref>

The SCN projects to a set of areas in the hypothalamus, brainstem, and midbrain that are involved in implementing sleep-wake cycles. An important component of the system is the [[reticular formation]], a group of neuron-clusters scattered diffusely through the core of the lower brain. Reticular neurons send signals to the thalamus, which in turn sends activity-level-controlling signals to every part of the cortex. Damage to the reticular formation can produce a permanent state of coma.<ref name="Kandel 2000"/><!--Ch. 45-->

Sleep involves great changes in brain activity.<ref name="Kandel 2000"/><!--Ch. 47--> Until the 1950s it was generally believed that the brain essentially shuts off during sleep,<ref>{{cite book|last=Kleitman|first=Nathaniel|title=Sleep and Wakefulness|publisher=The University of Chicago Press, Midway Reprint|others=Revised and enlarged edition 1963, Reprint edition 1987|orig-date=1939|date=1987|isbn=978-0-226-44073-6|location=Chicago}}</ref> but this is now known to be far from true; activity continues, but patterns become very different. There are two types of sleep: ''[[Rapid eye movement sleep|REM sleep]]'' (with [[dream]]ing) and ''[[Non-rapid eye movement sleep|NREM]]'' (non-REM, usually without dreaming) sleep, which repeat in slightly varying patterns throughout a sleep episode. Three broad types of distinct brain activity patterns can be measured: REM, light NREM and deep NREM. During deep NREM sleep, also called [[slow wave sleep]], activity in the cortex takes the form of large synchronized waves, whereas in the waking state it is noisy and desynchronized. Levels of the neurotransmitters [[norepinephrine]] and [[serotonin]] drop during slow wave sleep, and fall almost to zero during REM sleep; levels of [[acetylcholine]] show the reverse pattern.<ref name="Kandel 2000"/><!--Ch. 47-->

=== Homeostasis ===
[[File:LocationOfHypothalamus.jpg|thumb|right|Cross-section of a human head, showing location of the [[hypothalamus]]]]

For any animal, survival requires maintaining a variety of parameters of bodily state within a limited range of variation: these include temperature, water content, salt concentration in the bloodstream, blood glucose levels, blood oxygen level, and others.<ref name=Dougherty/> The ability of an animal to regulate the internal environment of its body—the [[milieu intérieur]], as the pioneering physiologist [[Claude Bernard]] called it—is known as [[homeostasis]] ([[Ancient Greek|Greek]] for "standing still").<ref>{{cite journal|last=Gross|first=Charles G.|year=1998|title=Claude Bernard and the constancy of the internal environment|url=http://www.princeton.edu/~cggross/Neuroscientist_98_Bernard.pdf|url-status=dead|journal=The Neuroscientist|volume=4|issue=5|pages=380–385|doi=10.1177/107385849800400520|archive-url=https://web.archive.org/web/20181208033601/http://www.princeton.edu/~cggross/Neuroscientist_98_Bernard.pdf|archive-date=2018-12-08 |s2cid=51424670}}</ref> Maintaining homeostasis is a crucial function of the brain. The basic principle that underlies homeostasis is [[negative feedback]]: any time a parameter diverges from its set-point, sensors generate an error signal that evokes a response that causes the parameter to shift back toward its optimum value.<ref name=Dougherty/> (This principle is widely used in engineering, for example in the control of temperature using a [[thermostat]].)

In vertebrates, the part of the brain that plays the greatest role is the [[hypothalamus]], a small region at the base of the forebrain whose size does not reflect its complexity or the importance of its function.<ref name="Dougherty">{{cite web|last=Dougherty|first=Patrick |title=Hypothalamus: structural organization|url=http://neuroscience.uth.tmc.edu/s4/chapter01.html|url-status=dead|archive-url=https://web.archive.org/web/20111117073211/http://neuroscience.uth.tmc.edu/s4/chapter01.html|archive-date=2011-11-17|access-date=2011-10-11|website=Neuroscience Online}}</ref> The hypothalamus is a collection of small nuclei, most of which are involved in basic biological functions. Some of these functions relate to arousal or to social interactions such as sexuality, aggression, or maternal behaviors; but many of them relate to homeostasis. Several hypothalamic nuclei receive input from sensors located in the lining of blood vessels, conveying information about temperature, sodium level, glucose level, blood oxygen level, and other parameters. These hypothalamic nuclei send output signals to motor areas that can generate actions to rectify deficiencies. Some of the outputs also go to the [[pituitary gland]], a tiny gland attached to the brain directly underneath the hypothalamus. The pituitary gland secretes hormones into the bloodstream, where they circulate throughout the body and induce changes in cellular activity.<ref>{{cite web|last=Dougherty|first=Patrick |title=Hypothalamic control of pituitary hormone|url=http://neuroscience.uth.tmc.edu/s4/chapter02.html|url-status=dead|archive-url=https://web.archive.org/web/20111117073249/http://neuroscience.uth.tmc.edu/s4/chapter02.html|archive-date=2011-11-17|access-date=2011-10-11|website=Neuroscience Online}}</ref>

=== Motivation ===
[[File:Basal ganglia.svg|thumb|right|350px|Components of the basal ganglia, shown in two cross-sections of the human brain. Blue: [[caudate nucleus]] and [[putamen]]. Green: [[globus pallidus]]. Red: [[subthalamic nucleus]]. Black: [[substantia nigra]].]]

The individual animals need to express survival-promoting behaviors, such as seeking food, water, shelter, and a mate.<ref>{{cite journal |last1=Chiel |first1=HJ |last2=Beer |first2=RD |title=The brain has a body: adaptive behavior emerges from interactions of nervous system, body, and environment |journal=Trends in Neurosciences |year=1997 |volume=20 |pages=553–557 |doi=10.1016/S0166-2236(97)01149-1 |pmid=9416664 |issue=12|s2cid=5634365 }}</ref> The motivational system in the brain monitors the current state of satisfaction of these goals, and activates behaviors to meet any needs that arise. The motivational system works largely by a reward–punishment mechanism. When a particular behavior is followed by favorable consequences, the [[reward system|reward mechanism]] in the brain is activated, which induces structural changes inside the brain that cause the same behavior to be repeated later, whenever a similar situation arises. Conversely, when a behavior is followed by unfavorable consequences, the brain's punishment mechanism is activated, inducing structural changes that cause the behavior to be suppressed when similar situations arise in the future.<ref>{{cite journal |last=Berridge |first=KC |title=Motivation concepts in behavioral neuroscience |journal=Physiology & Behavior |year=2004 |volume=81 |pages=179–209 |pmid=15159167 |issue=2 |doi=10.1016/j.physbeh.2004.02.004|s2cid=14149019 }}</ref>

Most organisms studied to date use a reward–punishment mechanism: for instance, worms and insects can alter their behavior to seek food sources or to avoid dangers.<ref>{{cite journal |title=An elegant mind: learning and memory in ''Caenorhabditis elegans'' |journal=Learning and Memory |year=2010 |volume=17 |pages=191–201 |last1=Ardiel |first1=EL |last2=Rankin |first2=CH |doi=10.1101/lm.960510 |pmid=20335372 |issue=4|doi-access=free }}</ref> In vertebrates, the reward-punishment system is implemented by a specific set of brain structures, at the heart of which lie the basal ganglia, a set of interconnected areas at the base of the forebrain.<ref name=Grillner2005/> The basal ganglia are the central site at which decisions are made: the basal ganglia exert a sustained inhibitory control over most of the motor systems in the brain; when this inhibition is released, a motor system is permitted to execute the action it is programmed to carry out. Rewards and punishments function by altering the relationship between the inputs that the basal ganglia receive and the decision-signals that are emitted. The reward mechanism is better understood than the punishment mechanism, because its role in drug abuse has caused it to be studied very intensively. Research has shown that the neurotransmitter dopamine plays a central role: addictive drugs such as cocaine, amphetamine, and nicotine either cause dopamine levels to rise or cause the effects of dopamine inside the brain to be enhanced.<ref>{{cite journal |title=Addiction and the brain: the neurobiology of compulsion and its persistence |journal=Nature Reviews Neuroscience |year=2001 |volume=2 |pages=695–703 |last1=Hyman |first1=SE |last2=Malenka |first2=RC |doi=10.1038/35094560 |pmid=11584307 |issue=10|s2cid=3333114 |url=https://zenodo.org/record/1233105 }}</ref>

=== Learning and memory ===
Almost all animals are capable of modifying their behavior as a result of experience—even the most primitive types of worms. Because behavior is driven by brain activity, changes in behavior must somehow correspond to changes inside the brain. Already in the late 19th century theorists like [[Santiago Ramón y Cajal]] argued that the most plausible explanation is that learning and memory are expressed as changes in the synaptic connections between neurons.<ref>{{cite journal |last=Ramón y Cajal |first=S |title=The Croonian Lecture: La Fine Structure des Centres Nerveux |journal=Proceedings of the Royal Society |volume=55 |issue=331–335 |pages=444–468 |year=1894 |doi=10.1098/rspl.1894.0063|doi-access=free |bibcode=1894RSPS...55..444C }}</ref> Until 1970, however, experimental evidence to support the [[synaptic plasticity]] hypothesis was lacking. In 1971 [[Tim Bliss]] and [[Terje Lømo]] published a paper on a phenomenon now called [[long-term potentiation]]: the paper showed clear evidence of activity-induced synaptic changes that lasted for at least several days.<ref>{{cite journal |last=Lømo |first=T |title=The discovery of long-term potentiation |journal=[[Philosophical Transactions of the Royal Society B]] |volume=358 |issue=1432 |year=2003 |pages=617–620 |pmid=12740104 |doi=10.1098/rstb.2002.1226 |pmc=1693150}}</ref> Since then technical advances have made these sorts of experiments much easier to carry out, and thousands of studies have been made that have clarified the mechanism of synaptic change, and uncovered other types of activity-driven synaptic change in a variety of brain areas, including the cerebral cortex, hippocampus, basal ganglia, and cerebellum.<ref>{{cite journal |last1=Malenka |first1=R |last2=Bear |first2=M |title=LTP and LTD: an embarrassment of riches |journal=Neuron |volume=44 |issue=1 |pages=5–21 |year=2004 |pmid=15450156 |doi=10.1016/j.neuron.2004.09.012|s2cid=79844 |doi-access=free }}</ref> Brain-derived neurotrophic factor ([[BDNF]]) and [[physical activity]] appear to play a beneficial role in the process.<ref name="AirpollutionPhysicalactivity">{{cite journal|last1=Bos|first1=I|last2=De Boever|first2=P|last3=Int Panis|first3=L|last4=Meeusen|first4=R|year=2004|title=Physical Activity, Air Pollution and the Brain|url=https://www.researchgate.net/publication/264793941|journal=Sports Medicine|volume=44|issue=11|pages=1505–1518|doi=10.1007/s40279-014-0222-6|pmid=25119155 |s2cid=207493297}}</ref>

Neuroscientists currently distinguish several types of learning and memory that are implemented by the brain in distinct ways:

* '''[[Working memory]]''' is the ability of the brain to maintain a temporary representation of information about the task that an animal is currently engaged in. This sort of dynamic memory is thought to be mediated by the formation of [[Hebbian theory|cell assemblies]]—groups of activated neurons that maintain their activity by constantly stimulating one another.<ref>{{Cite journal |last1=Curtis |first1=CE |last2=D'Esposito |first2=M |title=Persistent activity in the prefrontal cortex during working memory |journal=Trends in Cognitive Sciences |volume=7 |pages=415–423 |year=2003 |pmid=12963473 |doi=10.1016/S1364-6613(03)00197-9 |issue=9 |citeseerx=10.1.1.457.9723|s2cid=15763406 }}</ref>
* '''[[Episodic memory]]''' is the ability to remember the details of specific events. This sort of memory can last for a lifetime. Much evidence implicates the hippocampus in playing a crucial role: people with severe damage to the hippocampus sometimes show [[amnesia]], that is, inability to form new long-lasting episodic memories.<ref>{{cite journal |title=Episodic and declarative memory: role of the hippocampus |journal=Hippocampus |year=1998 |volume=8 |pages=198–204 |pmid=9662134 |last1=Tulving |first1=E |last2=Markowitsch |first2=HJ |doi=10.1002/(SICI)1098-1063(1998)8:3<198::AID-HIPO2>3.0.CO;2-G |issue=3|s2cid=18634842 |doi-access=free }}</ref>
* '''[[Semantic memory]]''' is the ability to learn facts and relationships. This sort of memory is probably stored largely in the cerebral cortex, mediated by changes in connections between cells that represent specific types of information.<ref>{{cite journal |title=Semantic memory and the brain: structures and processes |journal=Current Opinion in Neurobiology |year=2001 |volume=11 |pages=194–201 |pmid=11301239 |last1=Martin |first1=A |last2=Chao |first2=LL |doi=10.1016/S0959-4388(00)00196-3 |issue=2|s2cid=3700874 }}</ref>
* '''[[Operant conditioning|Instrumental learning]]''' is the ability for rewards and punishments to modify behavior. It is implemented by a network of brain areas centered on the basal ganglia.<ref>{{cite journal |title=The integrative function of the basal ganglia in instrumental learning |journal=Behavioural Brain Research |volume=199 |pages=43–52 |year=2009 |pmid=19027797 |last1=Balleine |first1=BW |last2=Liljeholm |first2=Mimi |last3=Ostlund |first3=SB |doi=10.1016/j.bbr.2008.10.034 |issue=1|s2cid=36521958 }}</ref>
* '''[[Motor learning]]''' is the ability to refine patterns of body movement by practicing, or more generally by repetition. A number of brain areas are involved, including the [[premotor cortex]], basal ganglia, and especially the cerebellum, which functions as a large memory bank for microadjustments of the parameters of movement.<ref>{{cite journal |last=Doya |first=K |title=Complementary roles of basal ganglia and cerebellum in learning and motor control |journal=Current Opinion in Neurobiology |year=2000 |volume=10 |pages=732–739 |pmid=11240282 |doi=10.1016/S0959-4388(00)00153-7 |issue=6|s2cid=10962570 }}</ref>