Scientific Understanding of Consciousness
Consciousness as an Emergent Property of Thalamocortical Activity

Esoteric Terms and Concepts

This list includes terms and concepts with connotations specific to or closely allied with consciousness. Researchers often have their own ad hoc terms for similar concepts. In a few cases I have assigned a new name for these similar concepts, especially in cases where the multiple terms in use can be confusing. In most cases I will adopt one of the terms even if different terms may be used by other researchers.

In a number of cases you will notice that a common word has a technical meaning in consciousness connotations.

Laws of thermodynamics

The laws of thermodynamics were firmly established both experimentally and theoretically in the 19th century.

1st law of thermodynamics

Conservation of energy. Energy can be neither created nor destroyed. Cannot make a perpetual motion machine. Energy for biological systems derives from sunlight processed by plants to produce carbohydrates and oxygen, which are then consumed by animals for their metabolism.

2nd Law of thermodynamics

All physical systems tend to establish an equilibrium in energy levels, a status said to be maximum entropy. Rocks roll downhill, never uphill. Water flows in cascades and waterfalls downhill to result in lakes, marshy flats, and oceans. Chemical processes cause silver to tarnish, iron to rust, biological organisms to age and decay.

Amnesia

(Squire & Kandel; Memory, 91)

Amygdala

(Pinel; Anatomy of Human Brain, 122,124, 193, 194)

A clear understanding of the spatial relationship of the amygdala with the hippocampus and limbic system can be seen in (Hirsch; Neuroanatomy, 188)

Anterior cingulate cortex (ACC)

Anterior medial prefrontal cortex

(Pinel; Anatomy of Human Brain, 216)

Anteriorgrade amnesia

Association cortex

(Pinel; Anatomy of Human Brain, 118)

All the neocortex except for the primary sensory and motor areas. (Calvin; Neil's Brain, 226)

Attention

Auditory cortex

(Pinel; Anatomy of Human Brain, 120, 138)

Autobiographical self

(Damasio)

Basal consciousness

I use this term to refer to

Basal Ganglia

(Pinel; Anatomy of Human Brain, 124, 162)

(Edelman - Universe, 42, 45, 184)

Large subcortical structures that include the striatum and the globus pallidus. These ancient regions mediate purposive movements, sequences of motor actions or thoughts, and motor learning. (Koch; Quest for Consciousness, 130)

The computer CD supplied with the Neuroanatomy book provides excellent visualization of the anatomy of the basal ganglia, either alone or together with a number of combinations of ventricle system, limbic system, thalamus, cerebellum, etc. (Hirsch; Neuroanatomy, )

A good reference for basal ganglia. (Purves, Neuroscience, 417)

Basal Ganglia website

Bayes inference

A statistical inference technique in which sensory data is used to update an a priori model of the real world. This technique is consistent with Edelman's reentry pathways in the thalamocortical systems for recursive updating of an a priori model. This technique is also the consistent with Llinas’s hypothesis of "dreams modulated by reality." The mechanism is also consistent with Susan Greenfield's hypothesis of neuronal assembly gestalts.

Benzodiazepines

("benzos") a class of minor tranquilizers

Binding problem

Binding must take place among the brain’s distributed neural maps, each of which is functionally segregated or specialized. For example, binding assures the integration of the neuronal responses to a particular object contour with its color, position, and direction of movement. (Edelman; Universe of Consciousness,106, 107, 114)

BOLD signal

Blood Oxygen Level Dependent signal in fMRI studies.

Brain Stem

(meaning the pons and medulla): tegmentum, locus coeruleus, raphe nuclei, pendulo-pontine nuclei, all involved in neuromodulator production; (http://biosistemica.org/basal_ganglia.htm)

Broca’s area

(Pinel; Anatomy of Human Brain, 208)

Brodmann Areas

Korbinian Brodmann early in the 20th century defined 52 cortical areas based upon neuron size and relative thickness of the cortical layers. (Calvin; Neil's Brain, 93)

Chart of Brodmann areas.

CA₁, CA₂, CA₃, CA₄

Four regions of the hippocampus.

Caudate

(Pinel; Anatomy of Human Brain, 124)

Cerebellum

(Pinel; Anatomy of Human Brain, 162)

A good reference for cerebellum. (Purves, Neuroscience, 435)

The cerebellum influences movements by modifying activity patterns of the upper motor neurons. (Neuroscience, 435)

Primary function of the cerebellum is to detect the difference, or motor error, between an intended movement and the actual movement, and through its projections to the upper motor neurons, to reduce the error. (Neuroscience, 435)

Like the basal ganglia, the cerebellum is part of a vast loop that receives projections from and sends projections back to the cerebral cortex and brainstem. (Neuroscience, 435)

Cerebellum is concerned with the regulation of highly skilled movements, especially the planning and execution of complex spatial and temporal sequences of movement, including speech. (Neuroscience, 435)

Traditionally, the cerebellum is considered to be concerned with the coordination and synchrony of motion. (Edelman; Universe of Consciousness, 45)

Cerebellum - overall organization and subdivisions - (diagram) (Neuroscience, 436)

(Squire & Kandel; Memory, 188)

Cingulate Cortex

(Pinel; Anatomy of Human Brain, 122, 193)

Link to — Cingulate Cortex

Cingulate motor areas

(Pinel; Anatomy of Human Brain, 154)

Classical conditioning

(Squire & Kandel; Memory, 57)

(Squire & Kandel; Memory, 186)

Classical conditioning as Hebbian plasticity - (diagram) (LeDoux; Synaptic Self, 160)

Claustrum

Thin sheet of neurons next to lower cortical layers, project very widely over the cortex. (Crick 250)

Cochlea nuclei

(Pinel; Anatomy of Human Brain, 138)

Cognition

Concepts

The adoption of common words for use as technical terms can be confusing. This use of the word “concepts” refers to the ability of the brain to combine different perceptual categorizations into an abstraction of some common features. Concepts arise as a result of the mapping by the brain of activity in the brain’s different areas and regions. For example, forward motion is a concept. (Edelman; Universe of Consciousness, 104)

Concept is a memory object that contains only a small sensory component, because it is the result of neuronal activity in association areas such as the frontal lobe (where multiple sensory or motor modalities are mixed) or in a large number of areas in different regions of the brain. (Changeux; Neuronal Man, 138)

Concussion

(Squire & Kandel; Memory, 130)

Consolidation

(Edelman; Universe of Consciousness, 45)

Convergence Zone

A convergence zone is an ensemble of neurons within which many feedforward/ feedback loops make contact. (Domasio; Convergence Zone, 71)

There are in the order of thousands of convergence zones, which are all microscopic neuron ensembles, located within the macroscopic convergence regions that have been cytoarchitectonically defined and that number about one hundred. (Domasio; Convergence Zone, 71)

Core consciousness

Antonio Damasio discusses “core consciousness” (Damasio; Feeling of What Happens, 82)

Gerald Edelman calls a similar concept “primary consciousness” (Edelman; Universe of Consciousness, 106). Terminology can be confusing with different researchers using their own ad hoc terms to refer to similar concepts. At some time in the future, neuroscience may converge on widely accepted terminology.

Core self

(Damasio; Feeling of What Happens, 169)

Cortex

Cortex input

Main entries to the cortex are the axons coming from the neurons of the thalamus. Some fibers leave the cortex and return to the thalamus. Feedback circuits.

Thalamic fibers stop in well-defined layers, particularly layer IV and part of layer III. Layer IV can be considered the main gateway to the cortex. (Changeux 56)

Cortex output

First output of the cortex is back to the cortex itself, either on the same side or opposite side; association connections; other outgoing (efferent axons) end outside the cortex to subcortical levels. It seems the function of many cortical signals is to feed back information to the cortex itself. Three major outputs from the cortex: (1) cortex itself, (2) thalamus, (3) outputs of motor commands, which are expressed as behavior. (Changeux 56)

Pyramidal cells that send axons to the thalamus are located in the deepest layer of the cortex (layer VI) or in the lower part of Layer V. (Changeux 57)

Pyramidal cells sending axons to nonthalamic subcortical centers are situated in layer V. (Changeux 57)

Axons that project back to the cortex come from layers II and III. (Changeux 57)

Corticocortical fibers

(Edelman – Universe, 42)

Declarative (explicit) memory

(Squire & Kandel; Memory, 110)

(Squire & Kandel; Memory, 118)

Differentiated

Differentiationamong a repertoire of possibilities constitutes information, inthe specific sense of reduction of uncertainty.

Dorsolateral prefrontal cortex

(Pinel; Anatomy of Human Brain, 154, 214)

Dynamic Core

Edelman proposes that a large cluster of neuronal groups that together constitute, on a time scale of hundreds of milliseconds,a unified neural process of high complexity, be termed the "dynamiccore," in order to emphasize both its integration and its constantlychanging activity patterns.

(Edelman; Universe of Consciousness, 111, 139, 144, 179)

EEG

Electroencephalography

Emergent property

Emotion

Engram

Engram is a term referring to the neural representation of a memory. It can be conceived of as a widely distributed pattern of synaptic strengths formed as a result of a perception and subsequent rehearsals until molecular changes have been consolidated into the synapses. (LeDoux; Synaptic Self, 98)

Entorhinal cortex

(Pinel; Anatomy of Human Brain, 174)

Enzymes

Enzymes are proteins that have a catalytic function in cells of greatly increasing the probability of very specific chemical interactions. Enzymes are often involved in information signaling operations on intricate intracellular pathways, each step of which is energized via an ATP molecule. Enzymes provide their function at low temperature, thus avoiding damage to protein structures. Enzymes that energize specific molecules in the signaling pathways are often call kinases.

Ephaptic interactions

Ephaptic interactions refer to interactions between neurons based largely upon their close physical proximity.

Episodic memory

(Squire & Kandel; Memory, 107)

Extended consciousness

term used by Antonio Damasio to refer to what I have called human-type consciousness

Facilitation

(Squire & Kandel; Memory, 111)

Feelings

the conscious experiences of emotions. (LeDoux; Emotional Brain, 82)

First problem of consciousness

How neural patterns in any map become mental patterns or images. (Damasio; Feeling of What Happens, 170)

First-order maps

(Damasio; Feeling of What Happens, 169)

Fissures of Cerebral Hemispheres

(Pinel; Anatomy of Human Brain, 110)

fMRI scan

Functional Magnetic Resonance Imaging

Forebrain

Fornix

Fornix is a great track with more than a million fibers. It is the main efferent pathway from the hippocampus and circles around under the corpus callosum to end in the septal nuclei, the hypothalamus, and the mammalliary bodies. (Eccles; Evolution of Brain, 98)

Major efferents of the hippocampal formation travel in a massive fiber bundle, the fornix. Another portion of the fornix contains fibers traveling to the mammillary bodies, which in turn connect to the anterior ventral nucleus of the thalamus, then to the cingulate gyrus, and other regions of the limbic such as the entorhinal cortex itself. Route from the hippocampus via mammillary bodies and thalamus to the cingulate gyrus makes up the Papez loop. (Edelman; Remembered Present, 128)

Functional cluster

subset of elements within a neural system that strongly interact among themselves but interact much less strongly with the rest of the system. (Edelman; Universe of Consciousness, 120)

Embryonic development

Overall synopsis. Neural structures form in the early embryo (genetics influence begins). Hox genes. Neurons form, migrate, axons form, growth cones, chemitaxis guided by structure, non-precise contact, synapses form, neural activity (environmental influence begins), “use it or loose it” begins in early fetus and continues postnatal.

As an example, hippocampus memory provide long-term memory. Most people cannot remember earlier than age three. Critical time for language.

Emotional learning

(Squire & Kandel; Memory, 167)

Evolution of brain

Evolution via natural selection has produced a brain to compete in an ever more complex environment. A creature’s body is a container to protect the genetic information from the hazards of the external world and pass the genetic information of successful creatures along to subsequent generations. The Second Law of thermodynamics produces degradation of the body with time and mutation errors in genetic material. (Any physical process has an associated increase in entropy. Mere existence is a physical process, and even an idle state will experience an increase in entropy).

Brain stem (reptilian), Limbic (mammalian), cortical (primate and human).

Evolution via natural selection has produced a brain to process sensory data and generate command signals for movement.

Forgetting

(Squire & Kandel; Memory, 75)

Fornix

(Pinel; Anatomy of Human Brain, 122)

GABA

inhibitory neurotransmitter GABA plays the most important role in the basal ganglia.

Gap junctions

Gap junctions, synchronizing hippocampal GABA cells (LeDoux; Synaptic Self, 61)

Gene expression

(Squire & Kandel; Memory, 135)

Gestalts

A neuronal gestalt is a highly variable aggregation of neurons which is temporarily recruited around a triggering epicenter. The gestalt comprising momentary consciousness is the “dynamic core” of Edelman.

Global mapping

(Edelman - Remembered, 54) (Edelman; Universe of Consciousness, 96) – Global mappings are activated when the core links, through its ports, a series of unconscious routines implemented by cortical appendages. (Edelman; Universe of Consciousness, 187)

Globus pallidus

(Pinel; Anatomy of Human Brain, 124)

Glutamate

glutamate is the most common neurotransmitter in the brain.

Gyri of Cerebral Hemispheres

(Pinel; Anatomy of Human Brain, 114)

Habit

(Squire & Kandel; Memory, 178)

Habituation

Habituation: simplest case of nondeclarative memory. (Squire & Kandel; Memory, 26)

Hebb rule

Hebbian plasticity

Highly differentiated

Hippocampus

(Pinel; Anatomy of Human Brain, 122, 172)

(Squire & Kandel; Memory, 111)

A clear understanding of the spatial relationship of the hippocampus with the amygdala and the limbic system can be seen in (Neuroanatomy, 180, 184, 188)

Section of Hippocampus

Homeostasis

Hypothalamus senses and controls the internal milieu.

Autonomic nervous system. Sympathetic, Parasympathetic

Human-type consciousness

a term I use to refer to what Antonio Damasio calls “extended consciousness” and Gerald Edelman calls “higher-order consciousness” (Edelman; Universe of Consciousness, 194). Terminology can become confusing with different researchers using their own ad hoc terms to refer the similar concepts.

Huntington's disease

Huntington's is characterized by loss of memory and odd jerking movements called chorea ("dance"). It is a hereditary disease (with a dominant gene) involving cell death in the caudate nucleus. It usually starts in a person's 30s, but may start at any age. There is no cure, but there are treatments that can reduce the symptoms. It is fatal, although it is complications of the disease that usually cause death, rather than the disease itself. Many Huntington's sufferers commit suicide.

Hypothalamus

(Pinel; Anatomy of Human Brain, 100, 194)

Hypothalamus, brain stem and the limbic system intervene in body regulation and in all neural processes on which mind phenomena are based (perception, learning, recall, emotion, feeling, reasoning, creativity). (Damasio; Descartes' Error, 123)

A clear understanding of the spatial relationship of the hypothalamus with the thalamus in the diencephalon can be seen in (Hirsch; Neuroanatomy, 132)

The hypothalamus has many small subregions whose functions are to regulate hunger, thirst, temperature, sexual behavior, and similar body operations. (Crick; Astonishing Hypothesis, 88)

The hypothalamus is critical for life. Surgeons must be especially careful not to damage it.

Limbic system and hypothalamus are richly connected.

Hypothalamus is connected to all levels of the nervous system, including the neocortex. (LeDoux; Emotional Brain, 100)

Immediate memory

(Squire & Kandel; Memory, 84)

Immediate memory refers to the information that occupies our current stream of thought. Immediate memory can be extended to last minutes or more by rehearsal. (Squire & Kandel; Memory, 131)

Infantile amnesia

Infantile (childhood) amnesia refers to the lack of declarative memory before about 3 years of age. The hippocampus and its associated circuitry have not developed sufficiently to form declarative memories.

Inferior parietal cortex

(Pinel; Anatomy of Human Brain, 212)

Information and Energy in Biology

All of biology can be characterized in terms of information and energy. Information is stored in DNA molecules, which is then transmitted via messenger RNA molecules to ribosomes in the cytoplasm where amino acid molecules are translated into proteins for use by cells. Organisms successful in the environment survive to reproduce and pass along information in their DNA for use by subsequent generations. Cells evolved early in evolution with the function of concentrating molecules, thereby increasing the probability of molecular actions. Energy is required to perform information processing, protein synthesis and maintenance operations. Energy is derived from glucose molecules and oxygen after its conversion into ATP molecules by mitochondria in eukaryotic cells for use in cellular metabolism.

Inferotemporal cortex

(Pinel; Anatomy of Human Brain, 136)

Interneurons

Intuition

An individual has a sense of what is right or wrong, a sense of what is the appropriate or inappropriate response to make in a given set of circumstances, but is largely ignorant of the reasons for that mental state. Intuition is a perfectly normal and common mental state that is the end product of an implicit learning experience. (38 Reber, Implicit Learning and Tacit Knowledge, 625)

Knockout mice

(Squire & Kandel; Memory, 119)

Language

(Edelman; Universe of Consciousness, 193)

Lateral Geniculate Nucleus (LGN)

(Pinel; Anatomy of Human Brain, 134)

Limbic system

(Pinel; Anatomy of Human Brain, 122)

Limbic System and Emotion

Value judgments for decisions on movement control

Fear ---- Pleasure

Much of human motivation and action is based upon perceptions ranging from fear to pleasure. Activity in the amygdala and its connections is associated with fear. Activity in the nucleus accumbens and its connections is associated with anticipation of pleasure.

Amygdala, Nucleus Accumbens

Limbic system and hypothalamus are richly connected.

Forebrain and limbic system determine behavior. Prefrontal cortex, motor cortex, basal ganglia, FAPs, cerebellum, PNS.

Lobes of Cerebral Hemispheres

(Pinel; Anatomy of Human Brain, 112)

Locus coeruleus

(Pinel; Anatomy of Human Brain, 196)

Locus coeruleus consists of only a few thousand neurons in the brainstem that give rise to a vast meshwork of axons that blanket the cortex, hippocampus, basal ganglia, cerebellum, and spinal cord, potentially influencing transmission of billions of synapses over all levels of the central nervous system. (Edelman; Universe of Consciousness, 89)

Long-term depression (LTD)

long-lasting decrease in synaptic transmission; a permanent decrement in synaptic efficacy, resulting from lack of coincident presynaptic activation and generation of postsynaptic action potential. (Eichenbaum, 346)

Long-term memory

(Squire & Kandel; Memory, 87)

(Squire & Kandel; Memory, 132)

Long-term potentiation (LTP)

(Squire & Kandel; Memory, 111)

long-lasting facilitation of synaptic transmission; a permanent increase in synaptic efficacy, resulting from repeated activation of a presynaptic element and its firing the postsynaptic neuron. (Eichenbaum, 346)

Magnetic Resonance Imaging (MRI)

Mammilary bodies

Major terminals of the fornix. (Pinel; Anatomy of Human Brain, 122, 178)

Map

(image, mapping, mental image, neural image, neural map, neural pattern, object, representation, etc.) -- Various terms are used to connote neural representations in the brain. Frequently these terms have implied connotations from the context of the discussion.

The term map derives from the existence of topographic neural maps in the brain (and other parts of the central nervous system) corresponding to sensory areas on the periphery of the body. For example, sensory areas on the hands, legs, face, lips, etc. have a corresponding topographic mapping on the cortex of the brain. In the somatic sensory, visual, and motor systems, neuronal connections in the periphery are arranged as similarly adjacent patterns in the central nervous system. In the early 1960s, Roger Sperry articulated the chemoaffinity hypothesis for map formation. (Neuroscience, 537)

The map terminology for sensory areas carries over to neural maps hypothesized for consciousness entities. Damasio states that the neural aspect of a mental pattern is a neural pattern or map. (Damasio; Feeling of What Happens, 317) Damasio further states that both organism (the self) and object are mapped as neural patterns in the first-order maps; all of these neural patterns can become images. Second-order maps represent the relationship of object and organism. Neural patterns transiently formed in second-order maps can become mental images. (Damasio; Feeling of What Happens, 169) Body surface is represented on the surface of the brain as a sensory map. (Squire; Mind, 197)

Medial orbitofrontal cortex

(Pinel; Anatomy of Human Brain, 216)

Medial prefrontal cortex

(Pinel; Anatomy of Human Brain, 214)

Medial Temporal Lobe

(Squire & Kandel; Memory, 99)

Medial temporal lobe (MTL), a structure composed of the hippocampus and adjacent perirhinal, entorhinal, and parahippocampal cortices. (Science 3 July 2009: Vol. 325. no. 5936, pp. 87 - 89)

Memory

(Edelman; Universe of Consciousness, 98).

Mental Image

Mental pattern in any of the sensory modalities (Damasio; Feeling of What Happens, 9)

Images arise from neural patterns (neural maps) formed in populations of neurons that constitute networks. (Damasio; Feeling of What Happens, 322)

Mental image is closely associated with the concept of a gestalt.

Mossy fiber pathway

(Squire & Kandel; Memory, 112)

Motivation

Modular brain

Modularity is probably a result of evolutionary changes.

Cortex is functionally modular. Subcortical area is physically and functionally modular for emotion generation and processing, movement controls, and homeostasis. Hypothalamus and brain stem are heavily involved in homeostasis.

(paraphrase of Eichenbaum, Cognitive Neuroscience of Memory, 315ff)

The assignment of the central executive function to the prefrontal cortex is supported by substantial anatomical data. The phenomenal expansion, of the prefrontal area in primates and especially humans is impressively associated with the evolution of cognitive capacities. The prefrontal cortex in humans is a diverse area, composed of several distinct subdivisions. There is considerable consensus on correspondences in monkeys with identified areas in the human prefrontal cortex. Although several anatomical areas have been characterized based on morphological appearance, most of the functional evidence has been related to four general regions. These include the medial, dorsolateral, ventrolateral, and orbital areas. Most of the attention with regard to working memory functions in monkeys and humans has focused on the dorsolateral and ventrolateral areas, and these areas are partially distinct in their connections with more posterior parts of the cerebral cortex. Each of the subdivisions receives input from a diverse set of rostral and causal cortical areas, and each has a distinctive input pattern.

Prefrontal areas are characterized by considerable associative connections with other prefrontal areas. The dorsolateral prefrontal area receives inputs mainly from medially and dorsolaterally located cortical areas that preferentially represent somatosensory and visuospatial information. Conversely, the lateral prefrontal areas receive inputs mainly from ventrolateral and ventromedial cortical areas that represent auditory and visual pattern information.

Motivational Systems of the Brain

(Pinel; Anatomy of Human Brain, 187)

Motor cortex

(Pinel; Anatomy of Human Brain, 156)

Motor homunculus

(Pinel; Anatomy of Human Brain, 156)

Movement control

The reason why brains exist.

FAPs. Basal ganglia, cerebellum, motor cortex, thalamus.

Cortex is connected to three structures Edelman calls the organs of succession. Structures involved in the output of the brain: (1) Cerebellum, (2) Hippocampus, (3) Basal Ganglia. Cerebellum, surrounding the upper brain stem; timing and smoothing of successions of movements. Concept formation requires reentrant connections from the higher cortical areas to: (1) other cortical areas, (2) hippocampus, (3) basal ganglia. (Edelman; Bright Air, 104-109)

Neocortex

(Pinel; Anatomy of Human Brain, 116)

Neural complexity

Neural integration --

Neural map

(Damasio; Feeling of What Happens, 317)

Neuromodulator

Neurons and synapses

Many source reference descriptions of neurons and synapses. (Pinel; Anatomy of Human Brain, 32-36)

Connected in a neural network

Neurotransmitter

Nigrostriatal pathway

(Pinel; Anatomy of Human Brain, 164)

Nitric oxide messenger

(Squire & Kandel; Memory, 117)

NMDA receptors and Ca²⁺ influx

(Squire & Kandel; Memory, 117)

Nondeclarative memory

(Squire & Kandel; Memory, 173)

Norepinephrine

Nucleus Accumbens

(Pinel; Anatomy of Human Brain, 192)

Stimulation of the nucleus accumbens in humans elicits smiling, laughter, pleasurable feelings, happiness, even euphoria. (Cardoso; Hardwired for Happiness, 173)

Nucleus accumbens -- part of a network of structures involved in feelings of pleasure and reward, whether it is through eating, having sex, or listening to pleasurable music. (Levitin; Your Brain on Music, 89)

The Nucleus Accumbens receives inputs from cortical regions (Frontal Lobe, Cingular Gyrus) and from the sub-cortex (amygdala). Its major ouput is to the action-producing Basal Ganglia. Therefore, the N. Accumbens influences our “readiness” to act. Dopamine increases in the N. Accumbens (coming from the ventral tegmentum, a brain stem source of activating neuromodulators) is connected to the feeling of reward. The organism acts, feels good and is oriented. (http://biosistemica.org/basal_ganglia.htm)

This same region is involved in the pathology of cocaine addiction. When a person takes cocaine, the drug is picked up by the N. Accumbens and the person feels “high”, powerful, with thinking accelerated (although superficial) and ready to act. How does this end up in pathology? The cocaine substitutes for dopamine and the dopamine becomes depleted. The lowered dopamine level is associated with the inhibition of thinking, a painful mood, and inhibited action. The amygdala, as well as other sub-cortical centers send their activating (or deactivating) inputs to the basal ganglia via the N. Accumbens (at least, partially). Thus the cocaine addict, in the withdrawal phase, cannot renew his dopamine charge; consequently, his basal ganglia cannot be activated in a normal way. Re-entry also means that the cortical and subcortical mechanisms (the amygdala as well as the central gray matter, which give connections to emotional and physical pain perception) will receive messages from the Nucleus Accumbens – Basal Ganglia complex. The unfortunate outcome is that the addict is in for a long period of painful withdrawal before his dopamine metabolism can be restored. (One cocaine dose can throw off the Nucleus Accumbens for months.)

Object

Neural pattern representation of an object. An object can include entities as diverse as a person, a place, a melody, a toothache, a state of bliss. For example a visual object is represented in appropriate neural patterns in a variety of regions of visual cortices, working in a concerted fashion to map the varied aspects of the object in visual terms. Binding of these features yields the neural map. (Damasio; Feeling of What Happens, 134)

Olfactory bulb (system) (Pinel; Anatomy of Human Brain, 64, 120)

Optic chiasm

(Pinel; Anatomy of Human Brain, 134)

Optic nerves

(Pinel; Anatomy of Human Brain, 134)

Optic radiations

(Pinel; Anatomy of Human Brain, 134)

Optic tracts

(Pinel; Anatomy of Human Brain, 134)

Orbitofrontal cortex

(Pinel; Anatomy of Human Brain, 194, 214)

Organism

Pallidum

PAP

( or Athymhormic) syndrome -- PAP is characterized by an unusual lack of motivation. A dramatic case was that of Mr. M, who, while drowning, simply failed to try to save himself, even though a good swimmer. Damage to the caudate nucleus means that nothing carries any emotional significance anymore. Drowning? Don't be concerned. People with PAP also ignore the usual social and moral motivations we all take for granted. They don't quite "get" that their lack of action could have significant consequences. Without the motivating influence of the basal ganglia, the frontal lobe simply stops planning for the future. Oddly, they can still respond to external motivation, such as a loved one's request or an authority's command.

Paradoxical sleep

Perirhinal cortex

(Pinel; Anatomy of Human Brain, 174)

Putamen

(Pinel; Anatomy of Human Brain, 122)

Perception

(Remembered 49)

Perceptual categorization

Ability carve up the world of sensory input into categories useful for a given species in its environment. Along with control of movement, perceptual categorization is the most fundamental process of the vertebrate nervous system. (Edelman; Universe of Consciousness, 104)

Perceptual learning

(Squire & Kandel; Memory, 164)

Periaqueductal gray

(Pinel; Anatomy of Human Brain, 146, 200)

PET scan

Pituitary gland

(Pinel; Anatomy of Human Brain, 102)

‘Place’ cells in mouse hippocampus

(Squire & Kandel; Memory, 125)

Pleasure centers

Pleiotropism

genetics term used to designate the multiplicity of effects of a single mutation. (Changeux; Neuronal Man, 173)

Pontaine reticular formation

(Pinel; Anatomy of Human Brain, 196)

Positron Emission Tomography (PET scan)

Posterior frontal cortex

(Pinel; Anatomy of Human Brain, 212)

Posterior medial prefrontal cortex

(Pinel; Anatomy of Human Brain, 216)

Posterior parietal cortex

(Pinel; Anatomy of Human Brain, 136)

Prefrontal cortex

Large region of the cerebral cortex that lies anterior to the primary motor cortex, composed of many subdivisions including premotor cortex, dorsolateral, medial, and orbital subdivisions. (Eichenbaum, 348), (diagram) (Koch; Quest for Consciousness, 128)

Connections within the prefrontal cortex, both within and between layers, are far more numerous than the connections coming in from other areas, such as sensory processing areas. (LeDoux; Synaptic Self, 188)

Premotor cortex

(Pinel; Anatomy of Human Brain, 154)

a zone of the cerebral cortex that lies just anterior to the primary motor cortex and is involved in motor learning. (Eichenbaum, 348)

Prestriate cortex

(Pinel; Anatomy of Human Brain, 136)

Primary consciousness

(Edelman; Universe of Consciousness, 107) -- refers to what I have called basal consciousness.

Primary motor cortex

(Pinel; Anatomy of Human Brain, 156)

Primary visual cortex

(Pinel; Anatomy of Human Brain, 136)

Priming

(Squire & Kandel; Memory, 160)

Procedural (implicit) memory

Projection neurons

Protein synthesis

(Squire & Kandel; Memory, 135)

Proto-self

ensemble of brain devices, which continuously and unconsciously maintain the body state with the narrow range required for survival. Brain stem, hypothalamus, basal forebrain. Non-conscious forerunner for the core self and the autobiographical self.

Pulvinar

Pulvinar, a subcortical nucleus of the thalamus, makes reciprocal connections with all of the visual processing cortical areas. (Van Essen; Dynamic Routing Strategies, 285)

Purkinje cell

(Squire & Kandel; Memory, 188)

Putamen

The putamen lies just under and behind the front of the caudate. It appears to be involved in coordinating automatic behaviors such as riding a bike, driving a car, or working on an assembly line. Problems with the putamen may account for the symptoms of Tourette's syndrome.

Pyramidal cells

(Pinel; Anatomy of Human Brain, 116)

Pyramids

(Pinel; Anatomy of Human Brain, 158)

Two bulges on the ventral surface of the medulla, which are created by the axons of the dorsolateral corticospinal tracts.

Qualia

the sensory qualities to be found in such things as the blueness of the sky or the tone of sound produced by a cello. (Damasio; Feeling of What Happens, 9) (Edelman; Universe of Consciousness, 157)

Raphe nuclei

(Pinel; Anatomy of Human Brain, 146, 194, 196)

a subgroup of the reticular nuclei of the brainstem, found in narrow longitudinal sheets along the raphae of the medulla oblongata, pons, and mesencephalon; they include many neurons that synthesize serotonin.

Receptors

Recursive functionality

Recursive functionality in a neuronal network is characterized by continual updating of the status of a mental image as fresh data is included and as further cognitive activity enhances the quality of the mental image. Recursion involves dynamic, momentarily-active reentrant pathways. Reentry is not simple feedback; it involves vast quantities of neuronal circuitry momentarily and precisely back-connected to input circuitry, thereby providing input for successive and improved estimates of a mental image.

Read nuclei

(Pinel; Anatomy of Human Brain, 158)

Reentrant pathways

Reentry

An ongoing, recursive interchange of parallel signals between reciprocally connected areas of the brain, an interchange that continually coordinates the activities of neural maps in space and time. (Edelman; Universe of Consciousness, 48); A process of ongoing recursive signaling between separate brain maps along massively parallel anatomical connections, most of which are reciprocal. Reentry is the most important integrative mechanism in higher brains. (Edelman; Universe of Consciousness, 105); Antonio Damasio is describing reentry when he describes core consciousness: Core consciousness is created in pulses triggered by each object that we interact with or that we recall. The proto-self modified by the first object then becomes the inaugural proto-self for the new object. A new pulse of core consciousness begins. (Damasio; Feeling of What Happens, 176)

REM sleep

(Rapid Eye Movement)

Reticular formation

in brain stem (Pinel; Anatomy of Human Brain, 92-95)

The reticular formation is a tangled, densely packed cluster of nerve cells containing mostly gray matter interlaced with fibers of white matter. It is an anatomical region about the size of a little finger, extending through the central core of the brainstem, from the upper spinal cord, through the medulla oblongata and pons, into the midbrain. For the most part, the reticular formation is not distinctly identifiable as a discrete system of CNS nuclei. Rather, it communicates, via networks of interneurons with (1) afferent sensory pathways that course through this anatomical region, (2) sensory nuclei and motoneuronal cell groups located in the brainstem, and (3) neural pathways that operate through the autonomic nervous system. In addition, the reticular formation has elaborate connections with the thalamus and hypothalamus. (Schneck & Berger; Music Effect, 84ff)

The interneurons of the reticular formation are very short, allowing messages to be relayed quickly from one nerve cell to the next. This allows it to function as sieve, continuously sifting through the mass of incoming data. Only those sensory inputs that the neural hardwiring construes to be essential, unusual, possibly dangerous, and/or in some sense "action-provoking" are passed along for further processing and forwarding to the higher levels of the brain.

In summary, the reticular formation is best viewed as a heterogeneous collection of distinct neuronal clusters in the brainstem tegmentum that either modulate the excitability of distant neurons in the forebrain and spinal cord, or coordinate the firing patterns of more local lower motor neuronal pools engaged in reflexive or stereotypical somatic motor and visceral motor behavior. (Purves; Neuroscience, 399)

Reverberative circuits

A term sometimes used to refer to reentry circuits and recursive functionality. These terms are described on this webpage.

Schaffer collateral pathway

(Squire & Kandel; Memory, 113)

Schizophrenia

Schizophrenia is a severe mental disorder with a lifetime risk of about 1%, characterized by hallucinations, delusions and cognitive deficits, with heritability estimated at up to 80%. Research on pathogenesis has traditionally focused on neurotransmitter systems in the brain, particularly those involving dopamine. A research study indicates that schizophrenia is significantly associated with single nucleotide polymorphisms (SNPs) in the extended major histocompatibility complex region on chromosome 6.

Scene

(Edelman; Universe of Consciousness, 108)

Second messenger

(Squire & Kandel; Memory, 50)

Second problem of consciousness

Problem of self

(Damasio; Feeling of What Happens, 9, 170)

Second-order maps

represent the relationship of object and organism (Damasio; Feeling of What Happens, 169)

Seizures

Self

Self-assembly

Semantic memory

(Squire & Kandel; Memory, 106)

Sense of Self

Sensitization

(Squire & Kandel; Memory, 48)

(Squire & Kandel; Memory, 143)

Sensory system

Detect the external and internal environment

Septum

Limbic nucleus that is located on the midline at the anterior tip of the cingulate cortex; a major terminal of the fornix.(Pinel; Anatomy of Human Brain, 122, 193)

Serotonin

(Squire & Kandel; Memory, 134)

Short-term memory

(Squire & Kandel; Memory, 84)

Skills

(Squire & Kandel; Memory, 176)

Somatosensory cortex

(Pinel; Anatomy of Human Brain, 144)

Spine

(Pinel; Anatomy of Human Brain, 4)

Striatum

(Pinel; Anatomy of Human Brain, 164, 193)

Caudate and Putamen; terminal all the dopaminergic nigrostriatal pathway.

Substantia nigra

(Pinel; Anatomy of Human Brain, 96, 164, 192)

Superior temporal cortex

(Pinel; Anatomy of Human Brain, 212)

Supplementary motor area

(Pinel; Anatomy of Human Brain, 154)

Suprachiasmatic nuclei

(Pinel; Anatomy of Human Brain, 198)

Synapses

(Squire & Kandel; Memory, 144)

Synchronization

(Edelman - Universe, 48)

Talairach coordinate system

Talairach and Tournoux (1988), the most commonly used standard space, originally created for stereotactically based neurosurgery. (Miller; Human Frontal Lobes, 170)

Talairach coordinate system is defined by making two points, the anterior commissure and posterior commissure, lie on a straight horizontal line. Since these two points lie on the midsagittal plane, the coordinate system is completely defined by requiring this plane to be vertical. Distances in Talairach coordinates are measured from the anterior commissure as origin.

As Talairach coordinates should be, they are in the LPI convention (so that the right hemisphere has positive X values, the anterior part has positive Y values, and the superior part has positive Z values; with AC being at coordinate 0,0,0)

Spatially warp an individual brain image obtained through Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET) and other imaging methods to this 'standard Talairach space'.

Temporal cortex

(diagram) (Koch; Quest for Consciousness, 128)

Thalamocortical system

Conscious experience is associated with the activity of populations of neurons that are widely distributed in the thalamocortical system. The distributed groups of neurons must engage in strong and rapid reentrant interactions.

Thalamus

(Pinel; Anatomy of Human Brain, 98)

The thalamus is divided into about two dozen regions, each of which is concerned with some particular subdivision of the neocortex. Each thalamic area also receives massive connections from the cortical areas to which it sends information. These neocortical areas can also connect directly to other parts of the brain. (Crick; Astonishing Hypothesis, 84)

Theory of Mind

Humans have an innate ability to understand that other humans have minds. First called Theory of Mind (TOM) by David Premack. (Gazzaniga; Human, 48-49)

Twins

Identical twins do not have identical neural connections.

Unconscious FAPs produce movement

Reflexes – brain not involved.

Procedural memory in brain – innate and learned. Sneeze, hiccup, walking, ride bicycle.

Voluntary movement.

Unconscious processing

(Edelman; Universe of Consciousness, 179)

Much activity of the brain is unconscious. The autonomic nervous system provides much functionality for the sense of self.

Value-category memory

memories established during a lifetime. The memories that endure are those that have an emotional or novelty context. Emotions can regulate the modulator neurotransmitters produced by the brain stem nuclei and limbic system. Edelman calls the modulator neurotransmitter system the “value system”.

Value system

Edelman calls the modulator neurotransmitter system the “value system”.

(Edelman; Universe of Consciousness, 105)

Ventricular system

The ventricular system is a good place to start to get spatial orientation of brain anatomy.

Ventricular system of the human brain. - (diagram). (Purves; Neuroscience, 771)

Ventricular system (Neuroanatomy, 222)

Neural migration - Cortex of the brain is formed by migration of neurons from a 'germinal zone' close to the ventricles deep in the brain. Migration is guided by glial cells, which extend radial fibers along the route. - (diagram) (Zeman, 202)

Esoteric Terms and Concepts

Laws of thermodynamics

1st law of thermodynamics

2nd Law of thermodynamics

Amnesia

Amygdala

Anterior cingulate cortex (ACC)

Anterior medial prefrontal cortex

Anteriorgrade amnesia

Association cortex

Attention

Auditory cortex

Autobiographical self

Basal consciousness

Basal Ganglia

Bayes inference

Benzodiazepines

Binding problem

BOLD signal

Brain Stem

Broca’s area

Brodmann Areas

CA1, CA2, CA3, CA4

Categories

Caudate

Cerebellum

Cingulate Cortex

Cingulate motor areas

Classical conditioning

Claustrum

Cochlea nuclei

Cognition

Concepts

Concussion

Consolidation

Convergence Zone

Core consciousness

Core self

Cortex

Cortex input

Cortex output

Corticocortical fibers

Declarative (explicit) memory

Dendrite

Dentate gyrus

Diencephalon

Differentiated

Dorsolateral prefrontal cortex

Dynamic Core

EEG

Emergent property

Emotion

Engram

Entorhinal cortex

Enzymes

Ephaptic interactions

Episodic memory

Extended consciousness

Facilitation

Feelings

First problem of consciousness

First-order maps

Fissures of Cerebral Hemispheres

fMRI scan

Forebrain

Fornix

Functional cluster

Embryonic development

Emotional learning

Evolution of brain

Forgetting

Fornix

GABA

Gap junctions

Gene expression

Gestalts

Global mapping

Globus pallidus

Glutamate

Gyri of Cerebral Hemispheres

CA₁, CA₂, CA₃, CA₄

NMDA receptors and Ca²⁺ influx