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

Brain Anatomy


A modern parcellation of the human cortex has been performed yielding180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults.


Link to —  Homunculus (Topographic) Diagram

Link to —  Spinal Cord Diagram

Link to —  Cortical Layers Diagram

Link to —  Sensory Pathways


Brain neurons and their synapses mediate the functions of consciousness. Fortunately, formal Latin names are not used in experts' discussions of consciousness. In addition to the anatomical descriptions incorporated as a part of consciousness literature, I use two major book references for brain anatomy and function:

It is useful to keep in mind the evolutionary development of the vertebrate nervous system as a guide in gaining some understanding of the anatomical and functional modularity of the human central nervous system (CNS). The brain stem, limbic system, and cortex have expanded over vastly different evolutionary time periods for reptiles, mammals and primates. Humans have anatomical vestiges of these ancient biological ancestors. Discrete anatomical modularity in the human brain likely began as tiny cellular assemblies in ancient multicellular creatures. Neural assemblies beneficial in ancient local environments were retained by natural selection. The tiny cellular assemblies expanded during millions of subsequent generations to result in the anatomical features we see today, such as the basal ganglia and thalamus.


evolutionary development from the brain stem, the midbrain, and forebrain.

distinctive anatomical and functional modularities of the brain.

three topological networks that characterize the brain.

Anatomy of the Brain

Brain's gross anatomy shows massive fiber tracts leading from posterior to anterior cortex, from one hemisphere to the other, and from cortex to thalamus and back again. (Baars; Neuronal Mechanisms of Consciousness, 270)

Development of the Human Nervous System. (Pinel; Anatomy of Human Brain, 53)

The radial unit hypothesis posits that the output of proliferative units (at the ventricle) is translated by glial guides to the expanded cortex in the form of ontogenetic columns. (Neocortex Outer Region Subventricular Zone Development)

Gross Anatomy of the Human Brain. (Pinel; Anatomy of Human Brain, 71)

Major Structures of the Brainstem. (Pinel; Anatomy of Human Brain, 91)

Major Structures of the Cerebral Hemispheres. (Pinel; Anatomy of Human Brain, 109)

Sensory Systems of the Central Nervous System. (Pinel; Anatomy of Human Brain, 133)

Sensorimotor Pathways of the Central Nervous System. (Pinel; Anatomy of Human Brain, 153)

Memory and Brain Structures. (Pinel; Anatomy of Human Brain, 171)

Motivational Systems of the Brain. (Pinel; Anatomy of Human Brain, 187)

Language and Thinking. (Pinel; Anatomy of Human Brain, 207)


Evolutionary classification

Brain evolution can be conceptualized in three stages: (1) reptilian brain represented by the brain stem, (2) mammalian brain represented mainly by the limbic system, (3) primate and human brain represented mainly by the cortex.

Modularity classification

Brain modularity in subcortical areas including the brain stem consists of many nuclei intricately related. Brain modularity in the cortex consists of many functional areas interrelated with subcortical nuclei.

Three-topological-networks classification

(1) Thalamocortical


(2) Basal ganglia loop

Two functions of the basal ganglia. Restraint on FAPs of movement. Participate with cortex in synthesizing plans of movement. Reality emulator. Working memory decides on an action plan and channels the resulting plan to the premotor and motor cortices for action. Motor cortex signals unlatch the basal ganglia restraints on FAPs, which produce action.

Basal ganglia generate a continuous offering of stereotyped movement sequences that are normally constrained until unlatched.

Basal ganglia functionality is compromised in Parkinson's disease, which is characterized by tremors at rest and difficulty initiating movement.  Presumably, the tremors at rest are an unintended release of the ongoing stereotyped movement sequences being generated, and the difficulty in initiating movement is a manifestation of an inability to unlatch the stereotyped movement sequences.

Huntington's disease is characterized by rapid, involuntary, jerky motions: choreiform movements. Basal ganglia are affected by a profound but selective atrophy of the caudate and putamen, with some associated degeneration of the frontal and temporal cortices.  (Neuroscience, 426) Presumably, the choreiform movements are an unintended release of ongoing stereotyped movement sequences

(3) Widespread hair-like fibers


Anatomical classification

The neuroanatomy book, Hirsch: Neuroanatomy, classifies brain structures into three groups: (1) brain stem structures together with cerebellum, (2) diencephalon including thalamus and hypothalamus, (3) telencephalon including cortex, basal ganglia, and limbic system.  I think it is helpful to keep this classification in mind, although I'll use a functional classification that I think is more pertinent to consciousness.


Functional classification

(1) Cognitive brain


(2) Emotional brain


(3) Movement brain

FAPs, brain stem, reflexes


Midbrain and reticular formation neurons release neuromodulators

Clusters of neurons in the midbrain and rostral pontine reticular formation participate in the modulation of conscious states. (Purves; Neuroscience, 398)

Reticular formation: Forebrain projections of noradrenergic neurons in the locus coeruleus and serotogenergic neurons in the raphe nuclei. (Purves; Neuroscience, 398)

Biogenic amine neurotransmitters function as neuromodulators that alter the membrane potential and firing patterns of thalamocortical and cortical neurons. (Purves; Neuroscience, 398)

Reticular formation neurons in the caudal pons and medulla oblongata; integrate feedback sensory signals with executive commands from upper motor neurons and deep cerebellar nuclei; organize the efferent activities of motor neurons in the brainstem and spinal cord. (Purves; Neuroscience, 398)

Reticular formation neurons organize mastication, facial expressions, reflexive orofacial behaviors such as sneezing, hiccuping, yawning, swallowing. (Purves; Neuroscience, 398)

Some clusters of the reticular formation organize complex activities that require the coordination of both somatic motor and visceral motor outflow, such as gagging and vomiting, and even laughing and crying. (Purves; Neuroscience, 399)

Reticular formation, heterogeneous collection of distinct neuronal clusters in the brainstem tegmentum; modulate the excitability of distant neurons in the forebrain and spinal cord; coordinate the firing pattern of neurons engaged in reflexive or stereotypical somatic motor and visceral motor behavior. (Purves; Neuroscience, 399)


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. inhibitory (LeDoux 57)



Amygdala is a complex structure, consisting of about 10 distinct nuclei. (Kandel; Principles of Neural Science, 990)

Association cortices

Association cortices do not process any one type of sensory information; rather, they receive inputs from a number of primary and secondary sensory cortices and associated thalamic nuclei. (Purves; Neuroscience, 418)

Basal ganglia

The basal ganglia influence our conscious motor actions: from basal ganglia to thalamus to motor cortex.  (Edelman)  Edelman also proposes that our thoughts may also be influenced by the sub-cortical basal ganglia.  For one thing, the striatum, the first input level of the basal ganglia, has reciprocal connections with many of the cortical areas that give this first input to the basal ganglia.  Perhaps this increases activation of these cortical areas, which might be experienced as heightened environmental perception (posterior lobe), memory recall (temporal lobe), generalized environmental mapping and calculations (parietal lobe), and goal-directed intentionality (frontal lobes).  (Liss)


It is also possible that the thalamic patterns, created by the basal ganglia output (from the substantia negra and globus pallidus), can also influence cortical patterns outside of the motor cortex.  Thus, our thinking and other aspects of our mental life, once again, may be influenced by the sub-cortical basal ganglia.  For example, it is possible that the sequencing patterns of the basal ganglia motor routine can then return to the cortex, via the thalamus, to create sequencing of thoughts, both verbal thoughts and non-verbal thoughts. (Liss)


Cingulate gyrus


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


Gap junctions

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


The insula and anterior cingulate are closely interlocked regions, the two being joined by mutual connections. (Damasio; Self Comes to Mind, 118)


Neocortex (Cerebral Cortex)

Cerebral cortex with its gyri and sulci is shown in (Neuroanatomy, 206ff)

Fully mature cerebral cortex, mean surface area, 2200 cm2. Two-thirds of the cortex is hidden in sulci, or fissures. (Changeux 45)

Within Brodmann's  classic cortical map, the insula is considered to be the fifth and smallest lobe of the brain, comprising Brodmann's areas 13--16. The insula lies within the the convergence of the frontal, temporal, and parietal lobes, and can be seen only when these lobes are retracted. (Miller; Human Frontal Lobes, 62)

The cortex consists of two separate sheets of nerve cells, one on each side of the head. The sheet varies somewhat in thickness but is typically 2 to 5 millimeters thick. About 100,000 neurons per square millimeter in the cortex. (Crick 82)

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)

Cortical Columns

About 148,000 neurons beneath a square millimeter of cortical surface; organized into minicolumns of about 100 neurons each, which are sometimes organized into macrocolumns of about 300 minicolumns. (Calvin; Neil's Brain, 92)

The anatomy of local connections between nearby pyramidal cells and local inhibitory neurons may provide a network basis for understanding the columnar architecture of the neocortex, for it implies that local recurrent connectivity on this scale is a feature of the cortical computation. (Rolls; Memory, Attention, and Decision-Making, 27)



Mammalian neocortex is made up of gray and white matter. Neocortex presents a stratified structure with six parallel layers. Pyramidal cells, predominant type, outnumber all others. (Changeux; Neuronal Man, 46)

Three major cytoarchitectural divisions of the neocortex. (1) granular cortex of the sensory areas, contains small, densely packed neurons in the middle layers; (2) agranular cortex of the motor and premotor cortical areas, (3) varying populations of granule cells, mostly 'association cortex'. Within each of these areas there are many subdivisions, both functional and anatomical., (Shepherd, Synaptic Organization of the Brain; Douglas; Neocortex, 459)


V1 has about twice the density of neurons per unit surface area as the rest of neocortex. (Van Essen; Dynamic Routing Strategies, 285)


It would take an expert to distinguish rat frontal cortex from sheep parietal cortex, or cat auditory cortex from monkey somatosensory cortex. (Koch; Large-Scale Neuronal Theories of the Brain; Ullman; Sequence Seeking Counterstreams, 257)

Pyramidal cell axons, major output, or efferent, pathway from the cerebral cortex. (Changeux, Neuronal Man, 46)

Pyramidal cell axons form the main output of the cortex. (Changeux, Neuronal Man, 56)

Stellate cells, interneurons, communication between pyramidal cells. Pyramidal and stellate cells are not distributed uniformly throughout the cortical thickness. Layer I, no pyramidal neurons. Layers II, III, V, VI, lots of pyramidal cells. Layer IV, stellate cells sandwiched in. (Changeux, Neuronal Man, 48)

Cerebral cortex is made up of a small number of cellular elements repeated many times. (Changeux, Neuronal Man, 50)

General principles of wiring are the same throughout the cortex, regardless of the functional specialization. The network consists of the same cell categories and of similar numbers of cells in each category. (Changeux, Neuronal Man, 57)

Cortex is not equally thick everywhere, and the density of cells and the distribution of different neuron categories through the six layers vary from one area to another. The thin primary visual projection area (Brodmann's area 17) contains abundant stellate cells. The remarkably thick mortor cortex (area 4) has many large pyramidal cells. Total number of cells under a given surface area does not vary in the course of mammalian evolution. (Changeux, Neuronal Man, 50)

146,000 neurons per square millimeter of cortical surface in all mammalian species. (Changeux, Neuronal Man, 51)

Frontal cortex and limbic system are richly connected. Forebrain constricts the limbic to socially acceptable behavior.



Major input to thalamus originates among layer 6 pyramidal cells of the cortex.  There seems to be at least an order of magnitude more corticothalamic axons than thalamocortical ones. (Shepherd; Synaptic Organization of the Brain, 295)

Each cortical axon innervates many thalamic neurons. (Shepherd; Synaptic Organization of the Brain, 295)

Strong reciprocity exists in thalamocortical connections. (Shepherd; Synaptic Organization of the Brain, 295)

Corticothalamic pathway faithfully adheres to the map established in the thalamic nucleus. (Shepherd; Synaptic Organization of the Brain, 296)

Roughly 25% of the cells in most thalamic nuclei are local interneurons. (Shepherd; Synaptic Organization of the Brain, 299)


Thalamus is regarded as the functional and morphological gate to the forebrain. With the exception of the olfactory system, all sensory messages reach the cerebral cortex through the thalamus. (Koch; Large-Scale Neuronal Theories of the Brain; Llinás; Perception as Oneiric-like, 113)




(Llinas 44)

 (Crick 82)

(Crick 84)

(Crick 88)

(Crick 137)

(Crick 250)



(Neuroscience, 372)

(Neuroscience, 403)

(Neuroscience, 403)

(Neil’s, 89)

(Neil’s, 90)

(Neil’s, 92)


Dorsal and Ventral Pathways  (Quest 127)


Neuroscience – an excellent textbook with lots of illustrations and lots of informative discussion of all the traditional neuroscience topics other than consciousness.

Neuroanatomy – this book includes a computer CD that provides rotatable figures on the screen showing all the major brain anatomical structures in various combinations. The computer display contains all 173 illustrations in the book as rotatable 3D models, which you view with anaglyph glasses to get the 3D effect. (I bought an extra pair of anaglyph glasses on the internet.) It is very informative, for example, to have a rotatable display of the Ventricular system alone, or the Ventricular system with the Thalamus, or the Ventricular system with the Basal Ganglia, etc. The ventricular system, which starts forming very early in the embryo, serves as a spatial reference anchor for many midbrain structures around the brain stem. This computer CD display is an excellent adjunct to the illustrations in the Neuroscience book above.

The internet provides many diagrams with discussions of brain structures. Here are a few examples of links:

Whole Brain Atlas (Harvard Medical School) – I can’t interpret the brain scan images.

Simple discussion of brain and evolution – brief, high-school-level description of brain areas and evolution

Discussion of brain and CNS (John Kimball) -- an excellent discussion.

Hippocampus discussion from Wikipedia

Lecture notes

Anatomy of the Brain – high-school level


General features

Human brain -  ~100 billion neurons. (Edelman, 38)

Cerebral cortex -  ~30 billion neurons and 1 million billion (1015) synapses. (Edelman, 38)

Number of different types of neurons in the brain -  ~50. (Edelman, 38)

Lengths and branching patterns of dendrites and axons from a given type of neuron fall with certain ranges of variation, but even with a given type, no two cells are alike. (Edelman, 38)

Brain is the most metabolically active organ in the body. (Edelman, 40)

Human brain average 1330 gm, wide variation, 1000-2000 gm (Changeux 39)

Absolute weight of brain is of no significance (Changeux 40)

Three main neuroanatomical motifs in the brain: (1) thalamocortical, (2) polysynaptic loop structure, (3) diffuse ascending projections of the different value systems. (Wider 26)

Front of the cortex is concerned with contemplating, planning, and executing voluntary motor outputs. (Quest 244)

Between the brain's five main sensory input sectors and three main output sectors lie the (1) association cortices, (2) basal ganglia, (3) thalamus, (4) limbic system cortices, (5) brain stem, (6) cerebellum. (Damasio; Descartes' Error, 93)

Cortex is an interconnected six-layer sheet of about ten billion neurons with about a million billion (1015) connections. (Edelman; Bright Air, 104)

Cortex is arranged in functionally segregated maps that are reentrantly connected that subserve all the different sensory modalities and motor responses. (Edelman; Bright Air, 104)

Diencephalon -- the part of the central nervous system between the two hemispheres. Includes the thalamus and hypothalamus. (Afifi; Functional Neuroanatomy, 235)




Nature 445, 168-176 (11 January 2007)

Genome-wide atlas of gene expression in the adult mouse brain

Dozens of authors with the following affiliations:

Allen Institute for Brain Science, Seattle, Washington 98103, USA

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA

Department of Genes and Behavior, Max Planck Institute of Biophysical Chemistry, 37077 Goettingen, Germany

Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approx20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.


Representative cell-type-specific genes and corresponding molecular functions

Near ubiquitous – Cellular metabolism; Cell-cell signaling; Protein metabolism; Macromolecule biosynthesis; Cytoskeleton organization and biosynthesis

Neuron-enriched – Synaptic transmission; Nervous system development; Neuron differentiation; Regulation of synaptic plasticity; Regulation of synapse structure and function

Oligodendrocyte-enriched – Nerve ensheathment, Lipid biosynthesis, Neuron differentiation, Nervous system development, Myelination

Astrocyte-enriched – Ion homeostasis, Lipid catabolism, Cell-cell signaling, Response to reactive oxygen species, Blood vessel development

Choroid-plexus-enriched – Ion transport, Vitamin metabolism, Lipid transport, Proteolysis, Eye morphogenesis

Not expressed – Immune response, Chemotaxis, Meiotic cell cycle, Blood coagulation, Sensory organ development



   Link to — Consciousness Subject Outline

   Further discussion — Covington Theory of Consciousness