Brain stem structures, reticular formation, pattern generation, and the cerebellum are discussed.

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Part 1.
Brain Anatomy

Brain Structure and Neurons

DNA, the Brain, and Human Behavior

Human Brain Development

Brain Anatomy Diagram

Broca's Limbic Lobe, Papez's Circuit, and MacLean's Limbic System

Brain Evolution—The Triune Brain Theory

  Brain Anatomy—Early Structures and Systems

Subcortical Brain Structures, Stress, Emotions, and Mental Illness

The Brain's Two Hemispheres

The Brain's Cerebral Cortex (Neocortex)

Part 2:
and Emotional Systems

Brain Neurotransmitters—an Introduction

Brain Neurotransmitters and Illness

Emotions are Hard-Wired in the Brain: Introduction to Ancestral Brain Systems


The Brain's SEEKING System

Attention, Learning, and Memory: The VIGILANCE System

Rage: an Innate Brain System

Fear: an Innate Brain system

PANIC/LOSS: an Innate Brain System

PLAY: an Innate Brain System

The MATING System, the Brain, and Gender Determination

CARE: an Innate Brain System Important to Motherhood

Part 3:
Innate Behavior, Grooming, OCD, and Tourette Syndrome

Depression, Obsessions, and Compulsions: Concepts in Ethology and Attachment Theory

Body Dysmorphic Disorder, Trichotillomania, and Skin Picking

OCD and Tourette Syndrome: Causes and Symptoms

OCD, Dopamine, and the Nucleus Accumbens

OCD Treatments Including Antipsychotic Medications

Dopamine neurons in the brain.

Brain Anatomy—Early Structures and Systems

"Below the cortex, the human brain bears a striking resemblance to those of much older species," writes Thomas B. Czerner in What Makes You Tick? The Brain in Plain English (2001). "Just as they do in most animals, neurons in the medulla oblongata and pons located at the base of your brain, where it begins to taper into your spinal cord, steadily and reliably regulate your vegetative functions, automatic bodily activity such as your heartbeat and respiration."

Brain stem structures and the reticular formation:

Human brain, brain stem: midbrain, pons, and medulla oblongata. Author: John A. Beal PhD, Dept of Cellular Biology and Anatomy, Louisiana State University. What is called the brain stem includes the midbrain, the pons, and the medulla oblongata. MacLean designated the brain stem structures part of the protoreptilian formation (see Brain Evolution—The Triune Brain Theory). The structures in the image to the right (links to source) that are outlined in a red box represent the brain stem. John A. Beal, of Louisiana State University, provides this image.

The core of the brain stem is called the reticular formation. The word "reticular" means "net like," so the term reticular formation describes the structural appearance of brain stem tissue. The illustration below of the reticular activating system comes from the HOPES Brain Tutorial at Stanford University and links to source. According to MedlinePlus Dictionary, the reticular activating system is "a part of the reticular formation that extends from the brain stem to the midbrain and thalamus with connections distributed throughout the cerebral cortex and that controls the degree of activity of the central nervous system (as in maintaining sleep and wakefulness and in making transitions between the two states)." Several neurotransmitters are involved in reticular activating system function, including acetylcholine and norepinephrine.

The brain's reticular formation aids in regulation of the sleep-wake cycle as well as the level of arousal when awake. The neurons that manufacture serotonin, called the raphe nuclei, form a ridge or seam in the middle of the reticular formation. Jaak Panksepp, in Affective Neuroscience: The Foundations of Human and Animal Emotions (1998), explains that these neurons are "situated at the very midline (or seam) of the brain indicating that they are very ancient in brain evolution." We will discuss the raphe nuclei as part of our discussion on serotonin in Part 2 of

John Allman, in Evolving Brains (2000), points out that "the network of serotonergic neurons in the brain stem was present in the earliest vertebrates and has retained a remarkably constant anatomical position throughout vertebrate evolution. The serotonergic neurons are so named because they secrete from their axon terminals the neurotransmitter serotonin. … The cell bodies of the serotonergic neurons occupy virtually the same location in the basement of every vertebrate brain and are even in the same spot in the central nervous system of amphioxus, a primitive chordate. Thus the serotonergic system was essentially in place 500 million years ago, and it has been amazingly conserved throughout evolution, yet it participates vitally in the most complex aspects of our thinking and emotions." (For those of us who are not biologists, I'll explain here that chordates have notocords, a simple central nervous system. Chordates include fish and very primitive sea creatures).

Pattern generation in the brain:

Although we rarely stop to think about it, our brains constantly generate patterns of activity, seemingly without effort. Many of these patterns can continue even after consciousness shuts down. The brain stem is our most obvious example of a pattern generator. Neil Shubin, in Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the Human Body (2009), writes: "Our brain can control our breathing without any conscious effort on our part. Most of the work takes place in the brain stem, at the boundary between the brain and the spinal cord. The brain stem sends nerve impulses to our main breathing muscles. Breathing happens in a pattern. Muscles of the chest, diaphragm, and throat contract in a well-defined order. Consequently, this part of the brain stem is known as a 'central pattern generator.' This region can produce rhythmic patterns of nerve and, consequently, muscle activation. A number of such generators in our brain and spinal cord control other rhythmic behaviors, such as swallowing and walking."

In Part 3 of, we will discuss innate fixed-action patterns. It seems that evolution has—over eons of time—conserved and promoted replication of neuron firing patterns that produce behaviors which contribute to reproduction and survival, thereby automating certain movements. These movements—called fixed-action patterns—may have something to do with obsessions and compulsions.

ANS—the autonomic nervous system:

In Why Zebras Don't Get Ulcers: The Acclaimed Guide to Stress, Stress-Related Diseases, and Coping (2004), Robert M. Sapolsky writes: "The principal way in which your brain can tell the rest of the body what to do is to send messages through the nerves that branch from your brain down your spine and out to the periphery of your body." We are most in touch with the voluntary nervous system where, "You decide to move a muscle and it happens," says Sapolsky. He explains that it is another part of the nervous system, however, the autonomic nervous system (ANS), that controls more spontaneous and involuntary events such as blushing, gooseflesh, and orgasm.

MedlinePlus Dictionary defines the ANS as "a part of the vertebrate nervous system that innervates smooth and cardiac muscle and glandular tissues and governs involuntary actions (as secretion, vasoconstriction, or peristalsis)… . The second home edition of The Merck Manual of Medical Information provides a very good summary of the autonomic nervous system. According to the manual, the autonomic nervous system "works automatically (autonomously), without a person's conscious effort" and "supplies the internal organs, including the blood vessels, stomach, intestine, liver, kidneys, bladder, genitals, lungs, pupils and muscles of the eye, heart, and sweat, salivary, and digestive glands."

The sympathetic nervous system trunk, abdominal portion, from Gray's Anatomy. The ANS is made up of two subsystems: the parasympathetic nervous system and the sympathetic nervous system. The abdominal portion of the sympathetic nervous system is depicted in the illustration to the right (image links to source). The sympathetic cables, made of nerve fibers, are colored yellow in the illustration. A Wikipedia entry for "autonomic nervous system" provides a good way to remember the complimentary functions of the these subsystems, explaining that the parasympathetic nervous system function is to promote calm functions such as rest and digest, while the sympathetic nervous system function is to prepare for fight or flight.

Parasympathetic nervous system: Sapolsky explains that para- means "alongside," and refers to the fact that the parasympathetic neural projections run alongside those of the sympathetic nervous system, close to the spinal cord.

The network of parasympathetic nerves is complex; projections originate in the sacral spinal nerves (in the lower portion of the spine), and the third, seventh, ninth, and tenth cranial nerves that emerge directly from the brain. The tenth cranial nerve is the vagus nerve, which we will discuss in greater detail below.

Parasympathetic nerve cells send long projections along the spinal cord towards target organs. Along this pathway, near to or inside internal organs, the projecting axons contact collections of nerve cell bodies called ganglia. The parasympathetic neuronal projections from ganglia are short and release acetylcholine to target structures. Acetylcholine acts to maintain calm, autonomic function in smooth muscle, the heart, salivary glands, and glands in the colon, ureters, bladder and reproductive organs.

The vagus nerve and the parasympathetic nervous system:

Updated 8/31/2011

The vagus nerve arises from the lower brainstem, specifically the medulla, and innervates the viscera—the internal organs of the body including the lungs, heart, liver, and intestine—with autonomic sensory and motor fibers. In an interview with Ravi Dykema of Nexus: Colorado's Healthy-Living Connection, March/April 2006, Stephen W. Porges, Professor and Director of the Brain-Body Center in the College of Medicine at the University of Illinois at Chicago, explains that the vagus nerve—the primary nerve for the parasympathetic nervous system—has two major branches: an ancient unmyelinated branch that we share with reptiles and a more recently evolved myelinated branch unique to mammals that "is linked to the cranial nerves that control facial expression and vocalization."

The vagus nerve often functions to promote rest and digest activities during which we humans are most social. However, in dire circumstances, when a mammal—including humans—cannot escape a threat, Porges proposes that the vagus nerve initiates the freezing response by shutting down body systems. We discuss Porges's "Polyvagal Theory" as part of our discussion of the FEAR system in Part 2 of

Sympathetic nervous system: The Merck Manuals Online Medical Library explains that the "preganglionic cell bodies of the sympathetic system are located in the intermediolateral horn of the spinal cord between [vertebrae labeled] T1 and L2 or L3." The term preganglionic refers to nerve cell bodies that project toward ganglia in the sympathetic nervous system's dual tracts of nerve fibers. The Merck Manual also explains that most of the sympathetic ganglia "are located just outside the spinal cord on both sides of it." Sapolsky illuminates the projection of the sympathetic nervous system in Why Zebras Don't Get Ulcers, explaining that "sympathetic projections exit your spine and branch out to nearly every organ, every blood vessel, and every sweat gland in your body. They even project to the scads of tiny little muscles attached to hairs on your body. If you are truly terrified by something and activate those projections, your hair stands on end; gooseflesh results when the parts of your body are activated where those muscles exist but lack hairs attached to them." More succinctly, in his video course, Sapolsky says that the sympathetic nervous system "governs fear, flight, fight, and sex (the four Fs)."

Hypothalamus, thalamus, and hippocampus brain structures, an NIH illustration.So the sympathetic nervous system kicks into gear in response to dangerous, threatening circumstances. It could be that a hungry predator has you cornered or it could be that your boss just told you the report is due tomorrow instead of Monday. But how do sympathetic nerve fibers that project to muscles and organs know you are in danger? What "turns on" the sympathetic nervous system, therefore preempting your digestion and peristalsis while pumping up the beating of your heart? In the illustration to the left (image links to source), the hypothalamus is about the size of a pearl. Near the hypothalamus lie the thalamus and the hippocampus. (I like to refer to these three structures and other recessed nuclei as subcortical nuclei). The hypothalamus is the key player in the sympathetic nervous system. It is the hypothalamus that turns on the fight-or-flight response.

Hypothalamus sends CRH to the pituitary, which responds by secreting ACTH. ACTH then causes the adrenals to release cortisol into the bloodstream. NIH illustration. In Why Zebras Don't Get Ulcers, Sapolsky explains that "the hypothalamus integrates sensory input and, when necessary, releases powerful hormones." Sapolsky calls these hormones releasing hormones. He explains that the hypothalamus releases these hormones into the "hypothalamic-pituitary circulatory system… . The principal such releaser is called CRH (corticotropin releasing hormone), while a variety of more minor players synergize with CRH. Within fifteen seconds or so, CRH triggers the pituitary to release the hormone ACTH (also known as corticotropin). After ACTH is released into the bloodstream, it reaches the adrenal gland and, within a few minutes, triggers glucocorticoid release. Together, glucocorticoids and the secretions of the sympathetic nervous system (epinephrine and norepinephrine) account for a large percentage of what happens in your body during stress." Regarding the illustration above, the adrenal glands secrete "cortisol," which is a glucocorticoid. Image links to NIH source.

I should note here that to make matters more confusing, epinephrine may also be called adrenaline and norepinephrine may also be called noradrenaline. Regarding norepinephrine, you may be familiar with its role as a neurotransmitter in the brain. Sapolsky explains that norepinephrine's role in the sympathetic nervous system "proves the point about the varied roles played by any given neurotransmitter. In one part of the body (the heart, for example), norepinephrine is a messenger concerning arousal and the Four Fs [Fear, Flight, Fight, Sex], while in a different part of the nervous system, norepinephrine seems to have something to do with the symptoms of depression."

In Part 2 of, we will discuss norepinephrine as a neurotransmitter in the brain. Also, we will more fully discuss how the sympathetic nervous system releases norepinephrine, which is converted to epinephrine in the adrenal glands as part of the fight-or-flight response.

The cerebellum and equilibrium:

Human brain with the cerebellum highlighted in purple. MedlinePlus Dictionary notes that the cerebellum (Latin for little brain) is "situated between the brain stem and the back of the cerebrum and formed in humans of two lateral lobes and a median lobe." In the image to the right (image links to source), the cerebellum is highlighted in purple. Several sources, when defining the cerebellum, refer to its maintenance of bodily equilibrium. Maintaining body balance within the environment is another way to describe this function. Equilibrium is established in part via messages flowing through the spinocerebellar tract, which Wikipedia defines as "a set of axonal fibers originating in the spinal cord and terminating in the ipsilateral cerebellum." This tract conveys information to the cerebellum about limb and joint position, a process called proprioception. This feedback about body position is coordinated with information sent between the many neural connections connecting the cerebellum and the motor cortex, a region of the neocortex. The motor cortex, in turn, sends information to the muscles causing them to move. Thus, the cerebellum participates in maintaining body balance, or bodily equilibrium.

I am including a summation of the cerebellum's three parts from The Merck Manuals Online Medical Library. You will see some familiar prefixes here, including "paleo" and "neo."

Archicerebellum (vestibulocerebellum): It includes the flocculonodular lobe, which is located in the medial zone. It helps maintain equilibrium and coordinate eye, head, and neck movements; it is closely interconnected with the vestibular nuclei.
Midline vermis (paleocerebellum): It helps coordinate trunk and leg movements. Vermis lesions result in abnormalities of stance and gait.
Lateral hemispheres (neocerebellum): They control quick and finely coordinated limb movements, predominantly of the arms.
According to the Merck Manual, "There is growing consensus that, in addition to coordination, the cerebellum controls some aspects of memory, learning, and cognition." The manual explains that ataxia (a reeling, wide-based gait) is the archetypal sign of cerebellar dysfunction, but that many other motor abnormalities may occur with such dysfunction.

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