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.

2nd Law of thermodynamics

All physical systems tend to establish an equilibrium in energy levels, a status said to be maximum entropy.

Hot coffee cools to ambient temperature, never the reverse. Rocks roll downhill, never uphill

Energy for biological systems is derived from sunlight processed by plants to produce carbohydrates and oxygen, which are then consumed by animals for their metabolism.


Amblyopia -- nonparallel eyes, cross eye or walleye. (Hubel: Eye, Brain, and Vision, 204)

Discordant vision through the two eyes during an early critical period results in the enduring loss of visual acuity (amblyopia) that reflects aberrant circuit remodeling within primary visual cortex (V1).



Amnesia is a condition in which memory is disturbed or lost. In anterograde amnesia, the ability to memorize new things is impaired or lost. In retrograde amnesia, a person's pre-existing memories are lost to conscious recollection, beyond an ordinary degree of forgetfulness. (Wikipedia)

(Squire & Kandel; Memory, 91)


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

Amygdala diagram

The amygdalae are almond-shaped groups of nuclei located deep within the medial temporal lobes of the brain in complex vertebrates, including humans. The amygdalae have a primary role in the processing and memory of emotional reactions and are considered part of the limbic system. (Wikipedia)

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 cingulate gyrus has strong connections with a variety of other neural areas and plays a critical role in attention and what is meant by consciousness, and relates both to awareness and to voluntary control. (Posner; Constructing Neuronal Theories, 188)

Among the signals collected by the prefrontal system are those from the anterior cingulate cortex, which monitors success or failure of past actions.  (Fuster; Prefrontal Cortex, 381)  [Bayesian inference]

The ACC has a fundamental role in relating actions to their outcomes and consequences, and thus guides decisions and choices about actions. (Posner; Cognitive Neuroscience of Attention, 313)

Cingulate gyrus diagram

Anterior medial prefrontal cortex

(Pinel; Anatomy of Human Brain, 216)

Medial prefrontal cortex diagram

Anteriorgrade amnesia

.In anterograde amnesia, the ability to memorize new things is impaired or lost. (Wikipedia)

Association cortex

(Pinel; Anatomy of Human Brain, 118)

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

The association cortex surrounding primary areas and occupying the vast intervening areas is functionally involved with the more complex aspects of motor and sensory integrations and of higher functions generally. (Libet; Brain Stimulation Conscious Experiences, 559)


Auditory cortex

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

The primary auditory cortex is located in the temporal lobe and is about the same as Brodmann areas 41 and 42. Additional areas of the neocortex involved in processing sound, are in the frontal and parietal lobes. The auditory cortex is involved in functions such as identifying and segregating auditory "objects" and identifying the location of a sound in space. (Wikipedia)

Autobiographical self


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

Bayesian inference

A statistical inference technique (Bayesian inference) 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 system for recursive updating of an a priori model. This technique is also the consistent with Llinas’s hypothesis of "dreams modulated by reality" (Llinás & Paré; Brain Modulated by Senses, 6) The mechanism is also consistent with Susan Greenfield's hypothesis (Greenfield; Centers of Mind, 99ff) of neuronal assembly gestalts.


("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)

Binocular Rivalry Studies

The general procedure for binocular rivalry studies is to present different images simultaneously to the two eyes  At different times, one or the other eye will be dominant. This subject will be aware of the image presented to one eye, while being unaware of the image presented to the suppressed eye. (Shevrin; Psychological Unconscious, 551)

BOLD signal

Blood Oxygen Level Dependent signal in fMRI studies.

Brain Stem (or Brainstem)

The brain stem is usually described as including the medulla oblongata (myelencephalon), pons (part of metencephalon), and midbrain (mesencephalon). Less frequently, parts of the diencephalon are included. (Wikipedia)

The brain stem plays an important role in the regulation of cardiac and respiratory function. It also regulates the central nervous system, and is pivotal in maintaining consciousness and regulating the sleep cycle. (Wikipedia)

Pons and medulla include the tegmentum, locus coeruleus, raphe nuclei, pendulo-pontine nuclei, all involved in neuromodulator production; (

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.  


(Squire & Kandel; Memory, 183)


(Pinel; Anatomy of Human Brain, 124)


(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)

Cerebral Cortex

Typical cerebral cortex has a surface area of 2200 cm2 and a thickness between 1.5 and 4.5 mm in humans. (Science, “From the Connectome to the Synaptome,” 26 Nov 2010, vol. 330 no. 6008, p.1200)

Cingulate Cortex

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

Cingulate cortex diagram

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)


Thin sheet of neurons next to lower cortical layers, project very widely over the cortex. (Crick; Astonishing Hypothesis


Cocaine Addiction

When a person takes cocaine, the drug is picked up by the nucleus 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 subcortical centers send their activating (or deactivating) inputs to the basal ganglia via the nucleus 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.  Reentry 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.) (

 Cochlea nuclei

(Pinel; Anatomy of Human Brain, 138)



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)

Animals without true linguistic abilities, such as chimpanzees, have concepts. (Edelman; Remembered Present, 140)

Frontal, prefrontal, and temporal cortex and the basal ganglia; together are good candidates to mediate the formation of concepts. (Edelman; Remembered Present, 143)

Concept formation is not the same as thinking, deducing, or inducing. (Edelman; Remembered Present, 147)

Concept formation essential for primary consciousness. (Edelman; Remembered Present, 146)



Concussions are the mildest form of brain injury.

(Squire & Kandel; Memory, 130)


Memory consolidation, believed to be enhanced by sleep and dreaming, converts long-term memories involving the hippocampus, into long-term memories independent of the hippocampus.

(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 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; Neuronal Man, 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; Neuronal Man, 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; Neuronal Man, 57)

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

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

Corticocortical fibers

(Edelman; Universe of Consciousness, 42)

Declarative (explicit) memory

(Squire & Kandel; Memory, 110)

(Squire & Kandel; Memory, 118)


Degeneracy, Redundancy, Fault Tolerance — No one neuron is essential and critical for the operation and functioning of the neural network.


Dementia -- a chronic syndrome of heterogeneous aetiology characterized by multiple cognitive deficits that include severe memory impairment. (Dudai; Memory from A to Z, 77)


(Pinel; Anatomy of Human Brain, 32, 38-41)

Dentate gyrus

(Pinel; Anatomy of Human Brain, 172)


(Pinel; Anatomy of Human Brain, 98-101)


Differentiation among a repertoire of possibilities constitutes information, in the 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 "dynamic core," in order to emphasize both its integration and its constantly changing activity patterns.

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

Medial Temporal Lobe

Medial temporal lobe is a large region of the brain; it includes the amygdala, the hippocampus, and surrounding cortex. (Squire & Kandel; Memory, 93)


Electroencephalography (EEG) is the recording of electrical activity along the scalp produced by the firing of neurons within the brain. In clinical contexts, EEG refers to the recording of the brain's spontaneous electrical activity over a short period of time, usually 20–40 minutes, as recorded from multiple electrodes placed on the scalp. In neurology, the main diagnostic application of EEG is in the case of epilepsy, as epileptic activity can create clear abnormalities on a standard EEG study. A secondary clinical use of EEG is in the diagnosis of coma, encephalopathies, and brain death. EEG used to be a first-line method for the diagnosis of tumors, stroke and other focal brain disorders, but this use has decreased with the advent of anatomical imaging techniques such as MRI and CT. (Wikipedia)

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.

Emergent property

Consciousness is an emergent property arising from the self-organization of concurrently active but spatially distributed regions of the brain; there is no central organizer and no unique location where it comes into existence.

The liquidity of water is an emergent property. Nothing in the equations of atomic physics even hints at such a property. (Waldrop; Complexity, 82)

Life is an emergent property, the product of DNA molecules and protein molecules and myriad other kinds of molecules, all obeying the laws of chemistry. (Waldrop; Complexity, 82)

The mind is an emergent property, the product of billions of neurons obeying the biological laws of the living cell. (Waldrop; Complexity, 82)


Emotional learning

(Squire & Kandel; Memory, 167)


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)

The entorhinal cortex (EC) is the main interface between the hippocampus and neocortex. The EC is located in the medial temporal lobe and functions as a hub in a widespread network for memory and navigation. The EC-hippocampus system plays an important role in autobiographical/declarative/episodic memories and in particular spatial memories including memory formation, memory consolid,ation and memory optimization in sleep. (Wikipedia)


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 structuresEnzymes 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)

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.

Extended consciousness

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


(Squire & Kandel; Memory, 111)

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.


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 (fMRI) uses the radio frequency (RF) electromagnetic waves emitted by the nuclei of hydrogen atoms with single-proton nuclei to construct detailed images of the brain and other organs.

Changes in local neural activity cause a change in local blood flow and result is an increase in blood oxygenation when blood flow increases and a decrease in blood oxygenation when blood flow decreases.

fMRI studies of human cognition rely on blood oxygenation level dependent (BOLD) changes in the intensity of the magnetic resonance (MR) signal. MR imaging of BOLD changes is based on a difference in the magnetic property of oxygenated versus deoxygenated hemoglobin.


The forebrain, the largest part of the brain, is composed mostly of the cerebrum. Other important forebrain structures include the thalamus, hypothalamus and limbic system. The cerebrum is comprised of two cerebral hemispheres connected by the corpus callosum. Each hemisphere is divided into four lobes, frontal, parietal, occipital and temporal.

Forebrain includes Telencephalon and Diencephalon. (Pinel; Anatomy of Human Brain, 61)


(Squire & Kandel; Memory, 75)


(Pinel; Anatomy of Human Brain, 122)

Fornix diagram

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)

Fornix is one of two major efferent pathways from the hippocampus. (Squire; Memory and Brain, 196)

Fornix -- fiber bundle that carries part of the outflow of the hippocampus. (Kandel; Principles of Neural Science, 987)

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)


GABA (an amino acid) is a neurotransmitter of inhibitory neurons. (LeDoux; Synaptic Self, 53)

Glutamate and GABA are fast-acting; they cause an electrical change in the postsynaptic cell within milliseconds of being released from the presynaptic terminal, and their effect is over in a matter of milliseconds. (LeDoux; Synaptic Self, 57)

Two common fast-acting neurotransmitters: excitatory (ACh) and inhibitory (GABA) (Shepherd; Synaptic Organization of the Brain, 32)

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)

Genome-Editing with Rationally Engineered Cas9 Nucleases

Structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9).


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 cortex 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 is the most common neurotransmitter in the brain.

“Groove” in music

The word is often used to describe the aspect of certain music that makes one want to move, dance, or 'groove'. (Wikipedia)

Musicologists and other scholars began to analyze the concept of "groove" in the 1990s. They have argued that a "groove" is an "understanding of rhythmic patterning" or "feel" and "an intuitive sense" of "a cycle in motion" that emerges from "carefully aligned concurrent rhythmic patterns" that sets in motion dancing or foot-tapping on the part of listeners. (Wikipedia)

Gyri of Cerebral Hemispheres

(Pinel; Anatomy of Human Brain, 114)


(Squire & Kandel; Memory, 178)


Habituationsimplest case of nondeclarative memory. (Squire & Kandel; Memory, 26)

Hebb rule

Hebbian plasticity

Hebbian plasticity binds simultaneously active cells together so that the next time the same or similar stimulus occurs, the same cells and connections will be activated. (LeDoux; Synaptic Self, 308)

Highly differentiated

Differentiation among a repertoire of possibilities constitutes information, in the specific sense of reduction of uncertainty.


(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 (Hirsch; Neuroanatomy, 180, 184, 188)

     Section of Hippocampus  (

Hippocampus diagram


Hypothalamus senses and controls the internal milieu.

Autonomic nervous system. Sympathetic, Parasympathetic

Human-type consciousness

Human-type consciousness, a term I use to refer to what Antonio Damasio calls “extended consciousness”  (Damasio; Feeling of What Happens, 202) and Gerald Edelman calls “higher-order consciousness” (Edelman; Universe of Consciousness, 194). Terminology can become confusing when different researchers use their own ad hoc terms to refer to 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 has critical involvement in basic life-supporting functions such as growth, reproduction and metabolism.

(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)

Hypothalamus acts on the autonomic nervous system by modulating visceral reflex circuitry that is basically organized at the level of the brainstem. (Kandel; Principles of Neural Science, 986)

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)


Research Study — Hypothalamus involved in Systemic Ageing and Lifespan Control


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.

Infantile amnesia -- no one is capable of remembering distinctly the experiences of early infancy, especially those before the age of 30 months. (Fuster; Memory in Cerebral Cortex, 212)

Childhood amnesia, also known as infantile amnesia, is the common inability of adults to remember the earliest years of their childhood. The amnesia generally covers events from birth until around four years old. (Wikipedia)

It has been suggested that the average age of the first memories is three years, six months, with the vast majority of subjects dating their first recollection somewhere between ages 2 and 5 years. (Wikipedia)

Childhood amnesia may be due to the lack of neurological development of the infant brain, preventing the creation of long term or autobiographical memories. Two key structures in the neuroanatomy of memory, the hippocampus and prefrontal cortex, do not develop into mature structures until the age of three or four years. These structures are known to be associated with the formation of autobiographical memories of the type notably missing from adult recollection of early childhood. (Wikipedia)

Inferior parietal cortex

(Pinel; Anatomy of Human Brain,  212)

Inferotemporal cortex

(Pinel; Anatomy of Human Brain, 136)

The inferior temporal gyrus is one of the higher levels of the ventral stream of visual processing, associated with the representation of complex object features, such as global shape. It may also be involved in face perception. (Wikipedia)

The inferior temporal cortex (IT) of primates is thought to be the final visual area in the ventral stream of cortical areas responsible for object recognition. Consistent with this hypothesis, single IT neurons respond selectively to highly complex visual stimuli such as faces. (Nature 442, 692-695, 10 August 2006)


Information and Energy in Biology

All of biology can be characterized in terms of information and energyInformation 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 actionsEnergy is required to perform information processing, protein synthesis and maintenance operationsEnergy is derived from glucose molecules and oxygen after its conversion into ATP molecules by mitochondria in eukaryotic cells for use in cellular metabolism.


Interneurons link their short axons to nearby neurons, often projection neurons, and are involved in information processing. (LeDoux; Synaptic Self, 49)


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. (Reber, Implicit Learning and Tacit Knowledge, 603)

Dorsolateral prefrontal cortex, crucial for working memory - substrate of volition and of planning, while the medial and orbitofrontal regions appear to mediate social judgment and insight. (Hobson; Dream Drugstore, 63)

Phineas P. Gage, 1848, 25 years old, railroad foreman in Vermont, drilled hole, explosive powder, iron rod went through his skull and front of the brain, survived, personality changed. (Damasio; Descartes' Error, 3)

Kinesthetic Perception

Consists of Vestibular Perception and Proprioception.

Knockout mice

(Squire & Kandel; Memory, 119)

A knockout mouse is a genetically engineered mouse in which one or more genes have been turned off through a targeted mutation. (Wikipedia)

Knockout mice are important animal models for studying the role of genes which have been sequenced but whose functions have not been determined. By causing a specific gene to be inactive in the mouse, and observing any differences from normal behaviour or condition, researchers can infer its probable function. (Wikipedia)

Mice are currently the most closely related laboratory animal species to humans for which the knockout technique can easily be applied. (Wikipedia)

The first knockout mouse was created by Mario R. Capecchi, Martin Evans and Oliver Smithies in 1989, for which they were awarded the Nobel Prize for Medicine in 2007. (Wikipedia)


(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

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; Neuroscience of Memory, 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; Neuroscience of Memory, 346)

Magnetic Resonance Imaging (MRI)

Magnocellular Basal Nucleus of the Amygdala

Magnocellular basal nucleus of the amygdala returns projections to every level of the visual information-processing hierarchy of the temporal & occipital cortex. Recordings of individual neurons in the amygdala have found neurons that respond specifically to auditory, taste, smell or somatosensory as well as visual stimuli, but the visual neurons are the most plentiful. Some amygdala neurons respond primarily to faces. (

 Mammilary bodies

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


(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. (Purves; 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 Forebrain Bundle

There are several areas of the brain whose activation can have gratifying effects, but it is the stimulation of one particular pathway that produces the most intense pleasure. This is the medial forebrain bundle (MFB), which runs between the ventral tegmental area (VTA) and the lateral hypothalamus. (

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)

Mediating circuits

Two types of circuits in the brain.   (1) mediating circuits produce behaviors, (2) modulatory circuits act on the mediating circuits, regulating the strength of their synaptic connections. (Kandel; Search of Memory, 224)

Mediating neurotransmitters: glutamate excitatory, GABA inhibitory


(Edelman; Universe of Consciousness, 98).

Memory trace

A memory trace pattern is a pattern of high synaptic efficacies  engraved in the neural network synapses as a result of prior network activity, which may be the result of sensory inputs, internally generated signals such as pain, or internal cognitive activity, i.e. thinking.

Upon encoding, the hippocampus rapidly fuses the different features of an experience into a coherent memory trace. (Long-Term Memory Formation)

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)

All the first-order maps -- those of the object and those of the organism  reacting to the object -- are the source of mental images whose flow constitutes the thought process. (Damasio; Neurobiology for Consciousness, 117)

Activation state of memory -- a memory trace (subnetwork) is active or inactive. (Fuster; Memory in Cerebral Cortex, 12)

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


Major Structures of the Mesencephalon (midbrain) -- Superior colliculi, Inferior colliculi, Red nuclei, Periaqueductal gray, Substantia nigra.  (Pinel; Anatomy of Human Brain, 96)

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.

Modulator Neurotransmitter

Modulatory circuits

Two types of circuits in the brain.   (1) mediating circuits produce behaviors, (2) modulatory circuits act on the mediating circuits, regulating the strength of their synaptic connections. (Kandel; Search of Memory, 224)

Major modulatory systems of the brain. (1) noradrenergic, (2) adrenergic, (3) dopaminergic, (4) serotonergic, (5) cholinergic, (6) histaminergic. (Kandel; Principles of Neural Science, 890)

Mossy fiber pathway

(Squire & Kandel; Memory, 112)


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)


(Pinel; Anatomy of Human Brain, 116)

Neural complexity

Complex systems involve nonlinear interactions between simple elements. Consciousness is an emergent property arising from the self-organization of concurrently active but spatially distributed regions of the brain; there is no central organizer and no unique location where it comes into existence.

Life is a major source of complexity, and evolution is the major principle or driving force behind life.

Neural integration

Integration of distributed neuronal populations through reentrant interactions is required for conscious experience.

Neural map

(Damasio; Feeling of What Happens, 317)


Neurons and synapses

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

Connected in a neural network


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)


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 subcortex (amygdala).  Its major ouput is to the action-producing Basal Ganglia.  Therefore, the N. Accumbens influences our “readiness” to actDopamine 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. (

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 subcortical 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.  Reentry 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.)


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

Orbitofrontal cortex is the cortex of the ventral aspect of the frontal lobe.  It comprises mainly Brodmann areas 11 and 13. (Fuster; Prefrontal Cortex, 198)

Orbital and mediolateral portions of the prefrontal lobe are functionally correlated with emotional alterations and disinhibition of behavior. (Edelman; Remembered Present, 160)

Orbitofrontal patients may show by their behavior a blatant disregard for even the most elementary ethical principles. (Fuster; Prefrontal Cortex, 199)

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

Orbitofrontal cortex diagram



Pallidum connects with movement-control regions in the cortex and brain stem. (LeDoux; Synaptic Self, 249)


( 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.

Papez Loop

Route from the hippocampus via mammillary bodies and thalamus to the cingulate gyrus makes up the outer loop of the limbic system, sometimes called the Papez loop. (Edelman; Remembered Present, 128)

Paradoxical sleep

Parietal Lobe

The parietal lobe integrates sensory information from different modalities, particularly determining spatial sense and navigation. (Wikipedia)

The parietal lobe plays important roles in integrating sensory information from various parts of the body, knowledge of numbers and their relations, in the manipulation of objects, and in visuospatial processing. Although multisensory in nature, the posterior parietal cortex contains the dorsal stream of vision (as opposed to the ventral stream in the temporal lobe). Dorsal stream of vision is called the 'where' stream (as in spatial vision). (Wikipedia)


(Edelman; Remembered Present, 49)

Perception-Action Cycle

Perception-action cycle is a circular cybernetic flow of information processing between the organism and its environment in a sequence of goal-directed actions.  (Fuster; Prefrontal Cortex, 382) [Bayesian inference]  [Recursion]

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)

Perirhinal cortex

(Pinel; Anatomy of Human Brain, 174)

PET scan

Pial surface

The outer brain surface (the pia is a membrane that covers the brain underneath the skull).

 Pituitary gland

(Pinel; Anatomy of Human Brain, 102)

‘Place’ cells in mouse hippocampus

(Squire & Kandel; Memory, 125)

Pleasure centers


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)


(Squire & Kandel; Memory, 160)

Problem of self

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

Procedural (implicit) memory

Projection neurons



Prosody, the distinctly human ability to modulate the voice, adding emphasis and emotional tones that help convey meaning. (Ratey; User's Guide to Brain, 258)

Protein synthesis

(Squire & Kandel; Memory, 135)


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, 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)


(Pinel; Anatomy of Human Brain, 122)


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)


(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.


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.

Read nuclei

(Pinel; Anatomy of Human Brain,  158)


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.

Reentry and recursion are fundamental operations in Bayesian inference and in Fuster’s Perception Action Cycle.


Degeneracy, Redundancy, Fault Tolerance — No one neuron is essential and critical for the operation and functioning of the neural network.

Reentrant pathways


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)

Reentry and recursion are fundamental operations in Bayesian inference.

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.


(Edelman; Universe of Consciousness, 108)

Schaffer collateral pathway

(Squire & Kandel; Memory, 113)


Organized semantic networks, clusters of related information, capable of supporting conscious recall. (Corkin, Permanent Present Tense, 256)


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.

Second messenger

(Squire & Kandel; Memory, 50)

Second problem of consciousness

Second-order maps

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



A person' s individuality as a person is represented in the neurons and synapses, thus forming the molecular signature, or "the self," of the person.

Self-Organizing System

Consciousness is an emergent property arising from the self-organization of concurrently active but spatially distributed regions of the brain; there is no central organizer and no unique location where it comes into existence.

Brain is an example of a self-organizing system. Precise point-to-point wiring cannot occur; the variation is too great for the information stored in the genome. (Edelman; Bright Air, 25)

Semantic memory

(Squire & Kandel; Memory, 106)

Sense of Self

Consciousness at any instant is simply the integrated product of the information represented in the activated thalamocortical networks at that instant. That includes sense of self; awareness of body; and awareness of the world, be it real or fictive.  (Hobson; Consciousness, 141)   [Edelman's dynamic core]


(Squire & Kandel; Memory, 48)

(Squire & Kandel; Memory, 143)

Sensory system

Detect the external and internal environment


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)


(Squire & Kandel; Memory, 134)

Sexual Orientation

Most homosexuals have known all their lives: sexual orientation is neither a choice  nor something in the way people are brought up. It's something influenced by genes and perhaps prenatal factors, and people are born that way. (Horstman; Love, Sex, and the Brain, 72)

Short-term memory

(Squire & Kandel; Memory, 84)


(Squire & Kandel; Memory, 176)

Somatosensory cortex

(Pinel; Anatomy of Human Brain,  144)


(Pinel; Anatomy of Human Brain, 4)


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

Caudate and Putamen; terminal all the dopaminergic nigrostriatal pathway.


The subiculum is the most inferior component of the hippocampal formation. It lies between the entorhinal cortex and the CA1 subfield of the hippocampus proper. It receives input from CA1 and entorhinal cortical layer III pyramidal neurons and is the main output of the hippocampus. (Wikipedia)

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)


(Squire & Kandel; Memory, 144)


(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)

Temporal lobe diagram

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.


(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)


Thought - the building of conceptual theories about the world. (Edelman; Remembered Present, 148)

All the first-order maps -- those of the object and those of the organism  reacting to the object -- are the source of mental images whose flow constitutes the thought process. (Damasio; Neurobiology for Consciousness, 117)


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.


The valence of a stimulus: whether it is rewarding (pleasant) or punishing (aversive). (Zald & Rauch; Orbitofrontal Cortex, 268)

Value system

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

(Edelman; Universe of Consciousness,  105)

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”.

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)

Vestibular Perception

Visual system — from eye to cortex

(Pinel; Anatomy of Human Brain, 134)

VTA (Ventral Tegmental Area)

(Pinel; Anatomy of Human Brain, 192)


Wernicke’s area

(Pinel; Anatomy of Human Brain, 208)

Working memory

(Squire & Kandel; Memory, 84)



Link to — Consciousness Subject Outline

Further discussion — Covington Theory of Consciousness