|A book by|
William H. Calvin
UNIVERSITY OF WASHINGTON
SEATTLE, WASHINGTON 98195-1800 USA
THE CEREBRAL CODE|
Thinking a Thought in the Mosaics of the Mind
Available from MIT Press and amazon.com.
copyright ©1996 by William H. Calvin
Many neuroscientists can trace their scientific roots back to the pioneers via only several generations of mentors. Mine go back to Donald Hebb via Steve Glickman, now professor of psychology at Berkeley, who, when I was a physics undergraduate at Northwestern in the late 1950s and he was the closest thing to a neuroscientist on campus, told me about how Hebb posed the important problems and arranged for me to visit Montreal. My relevant roots also go back to Keffer Hartline and the lateral inhibition problem via his student Chuck Stevens, with whom I subsequently did my Ph.D. thesis a few years later in Seattle.
So, I was in possession of most of the essential components of the problem long before a solution finally coalesced in 1991, all thanks to the way others had formulated the problems they studied, even when they couldn't solve them. The missing key was the "dog that didn't bark in the night," those silent sidestepping gaps that pattern the recurrent excitation, that Jenny Lund told me about in 1991. No wonder that everything fell together so rapidly thereafter.
Page references are to the MIT Press edition.
allele Alternate forms of a gene. Perhaps 20 percent of your expressed genes have a different allele on the other chromosome, that is, you are heterozygous for that gene and might switch to using it under some conditions. One reason that hybrids don't breed true to type is that parents are often passing on their less-used allele. Inbred strains have less heterozygosity. [18, 103, 140]
area When capitalized, it's a Brodmann Area, a subdivision of cerebral cortex based on the relative thickness of the six layers. Area 17 is better known as primary visual cortex; it seems to be a functional unit but Area 19 comprises at least six major functional units. A territory or work space is an area occupied temporarily by active patterns of cloned hexagons.
attractor If you plot one variable against another for a series of times, the successive points may seem to move along a trajectory, often a cyclical one. This phase portrait may well look like an oddly-shaped orbit around an imaginary gravitational attractor, from whence the name. All of my chaotic illustrations are in such a phase space. There are four general classes of attractors: point (say, the neuron's resting state), periodic (as in pacemaker cells), quasi-periodic, and chaotic. The magnets in my loopy illustrations serve as a stand-in for a quasi-periodic attractor, as would an organ pipe. Whereas pipes have well-defined harmonics, chaotic attractors have overtones everywhere, in the manner of white noise. Chaotic systems are highly sensitive to initial conditions; while somewhat predictable in the short run, they may do surprising things in the long run. 
automatic gain control (AGC) A process that reduces gain (loudness, in a typical auditory application) as input levels increase. It tends to make the output levels about the same for faint and loud inputs -- unless the faint one occurs soon after the loud one, as it takes time for the gain to be raised again. The nineteenth-century speed governor for engines was an example of an AGC, and modern tape recorders use them. 
axon The neuron's "wire," a long (0.1 - 2,000 mm), spiderthread-thin portion of the neuron that carries voltages between the neuron's input sites (concentrated on cell body and dendritic tree) and the neuron's outputs, its many-branched axon terminals that make synapses onto downstream neurons. It's typically a one-way street, messages flowing from the dendrites and cell body to the far end of the axon where synapses are made. [26, 31, 34]
basin of attraction If one thinks of the attractor as the low point of a washbowl, then starting points on the counter top lie
outside the basin of attraction. Starting anywhere within the basin results in a trajectory that circles
around the attractor. Basins can be discontinuous, as seen in pinball games. A bifurcation is a change
from one basin of attraction to another, in the manner of changing gaits. |
binding In linguistics, binding is the part of the grammar which determines the reference of such words as he, himself, each other. In cognitive neuroscience, binding is the notion that some process must maintain links between the various features of a perceived object during cognitive processing, given the dispersal of object features to those what specialists in temporal lobe and to the where aspects specialists up in parietal areas. One simple proposal is that the involved neurons in these dispersed areas actually become synchronized, and that this is what recouples red with the top light on the traffic signal (another object's features -- say, those characterizing the approaching pedestrian -- synchronize at different times). This proposed use of synchrony is, of course, on a much grander scale than I propose for the triangular arrays, which might span a few millimeters. Binding may not be needed except for very complex sensory scenes, such as the streaming encountered when brachiating through the trees or driving a car; some suspect that the perceived need for binding to reassemble specialists is a remnant of the cartesian theater reasoning that Dennett critiques. 
bottleneck An evolutionary event that greatly narrows the variability in a population. 
cell-assembly Donald O. Hebb's 1949 coinage for a group of cortical neurons that subserves and sustains the active
memory trace that follows perception. |
central nervous system (CNS) The brain, spinal cord, and the retina (all the rest is the peripheral nervous system).
cerebral cortex The outer 2 mm (that's two thin coins worth) of the brain's cerebral hemispheres with a layered structure. It isn't required for performing a lot of simple actions but seems essential for creating new episodic memories, the fancier associations, and many new movement programs. Paleocortex (archicortex) such as hippocampus has a simpler structure and earlier evolutionary appearance than the six-plus-layered neocortex. 
chaos Complicated patterns that are not truly random. Chaos is a cryptic form of order, what a random-number generator produces. There is, as the phrase goes, "a sensitive dependence on initial conditions." Because chaos was defined in a paradoxical way ("It may look random, but it's merely chaotic"), it is a term often misused or misunderstood. See attractor, basin of attraction, itinerancy.
chunking Collapsing multiple-word phrases into a single word, in the manner of acronyms.
cipher A disguising transformation of a message without using chunking, such as a simple substitution cipher.
code In cryptography, a disguising transformation that also chunks -- and thereby shortens -- the message, as when a number stands for a standard five-word phrase. More generally, as in genetic code, it refers to the transformation of a representation's short form into its long-form implementation. As such, it is analogous to a matrix. It may also simply refer to the short form itself, such as a DNA base-pair sequence capable of generating a particular protein.
columns A minicolumn is a cylindrical group of about 100 neurons extending through all the layers of neocortex and about 0.030 mm in diameter, usually organized around a dendritic bundle; the orientation column is an example. Macrocolumns are a hundred times larger in area (and about 0.5 mm across) and often more like curtain folds than cylinders; they are typically identified by common inputs, e.g., the ocular dominance columns of visual cortex. 
corticocortical connection An axon or axon bundle connecting one patch of cerebral cortex to another. Some remain local, within the superficial layers of cortex, while others go through the white matter to distant targets -- some, via the corpus callosum, to the other cerebral hemisphere. See photograph, p. 131.
Darwin Machine My 1987 coinage, on the Turing Machine analogy, for any full-fledged darwinian process incorporating
the six essentials for the darwinian algorithm. Species evolution, the immune response, some genetic
algorithms, and the hexagonal work space competitions are all examples.|
deme A geographic subpopulation, mostly inbreeding but with occasional gene flow via migrants from the larger metapopulation.
dendrite Neurons have branches. There is a single thin axon that initiates and propagates impulses to distant destinations, and there are somewhat thicker dendritic branches that receive synapses from other neurons's axon terminals. Pyramidal neurons have a tall-tree-like apical dendrite plus some rootlike basal dendrites. At least in neocortex, dendrites are the receiving branches of the neuron and the axon is the sending branch. Elsewhere, some dendrites can also act like axon terminals, releasing neurotransmitter in response to impulses and local voltage changes. [26, 31]
efference copy The notion that, in generating movement commands, the nervous system also generates an expected set of
sensory inputs that will result from the movement, the comparison of expected and actual serving to
warn of problems in the execution of the movement.|
gene A unit of heredity, essentially that segment of a DNA molecule comprising the code for a particular
peptide or protein. We also talk loosely of "a gene for blue eyes" and so forth, but many a DNA gene is
pleiotropic: it has multiple (and sometimes very different) effects on its body. As for what's a unit, here's
Helena Cronin's answer:|
The answer must be: When it's a unit that selection can work on . . . a gene and the ramifying tree of all its phenotypic effects (in comparison with alternative forms of the gene, its alleles). If it should turn out that the bone of a toe and the shape of an eyebrow are pleiotropic effects of the same gene, then that bizarre combination is a respectable adaptive unit. Natural selection works on genetic differences in populations. If a genetic change that lengthens the bone also curves the eyebrow, then our adaptive explanation should recognize that; we should be interested in the genetic differences that give rise not merely to differences in toe-length but to differences in toe-length-plus-eyebrow-shape, even if eyebrow shape should turn out to be selectively neutral. This is an answer that would not have been obvious to the organism-centered view of classical Darwinism but comes readily to a theory that is gene-centered.gene repertoires When alternative forms of a gene are expressed at different stages of development, e.g., fetal hemoglobin is replaced by the adult version.
genetic code A table with 43 (64) entries that tells you which of the 20 amino acids will result from a particular triplet of the four types of RNA nucleotides, e.g., CAU yields histidine (as does CAC).
genotype The full set of genes carried by an individual, whether expressed or silent alleles. Similar to genome. Compare to phenotype. What makes living matter so different from other self-organizing systems is that a cell has an information center, the genes, concerned with orchestrating the many different processes going on within the cell, and in such a manner that copies of the cell tend to survive.
grammar, universal Each of the languages of the world has a corresponding mental grammar, constructed as we learn the language. Though they differ in many ways, the human brain seems to have a highly specific menu of possibilities for grammatical organization, known as Universal Grammar, or UG, that structures language learning even when the input itself is lacking in structure (pidgins, home sign, and so on). See Jackendoff (1993).
hash A hash is a unique short-form identifier, a "fingerprint" of something more complicated. One simple
application is to create a file name that isn't already in use -- and also isn't unnecessarily long, since you
want a low-dimensional search space that can be scanned rapidly. Using the seconds and minutes fields
of file modification time stamps often suffices for a hash; a document can also be hashed by using the
least significant bits of a checksum. |
Hebbian synapse Hebb proposed that a successful synapse is strengthened: "When an axon of cell A is near enough [the synaptic cleft hadn't yet been seen in 1949] to excite cell B and repeatedly or persistently takes part in firing it, some growth process or metabolic change takes place in one or both cells such that A's efficiency, as one of the cells firing B, is increased."
immune response Following infection with an antigen, a process begins that gradually destroys the foreign molecules --
but, in the process lasting days to weeks, the initially inefficient antibodies evolve into much better fits to
the antigen. Because they linger in the body for some time, immunity to further infection is achieved.|
impulse Action potential and spike are synonyms; it's the regenerative change in the voltage across the neuron's membrane used for long-distance (more than a millimeter) signaling in the nervous system. It is brief (1/1000 sec, quicker than any other signal in the brain but a million times slower than computers) and large (only 1/10 volt but bigger than any other voltage in the brain). Its threshold property can also be used as a simple decision making mechanism. See also axon, myelin, sodium channel.
in vitro "In glass" is used to designate experiments carried out in a dish on cells that have been removed from their natural setting. 
in situ "as situated" is (along with in vivo) the opposite of in vitro. 
inheritance principle Darwin's great but often misunderstood insight, that variation is not truly random. Rather than variations being done from some ideal or average type, small undirected variations are preferentially done from the more successful individuals of the current generation, exploring the solution space nearby (not jumping randomly to somewhere truly unrelated) in the next generation. [21, 101]
interneuron An "insider neuron." Most CNS neurons are interneurons; the only ones which aren't are the sensory neurons and the motor neurons that drive the muscles. An interneuron receives input from about 2,000-10,000 "upstream" neurons and transmits its output to a similar number of "downstream" neurons -- occasionally even one of its own input neurons, creating a loop (see figure, p. 32).
ion An atom or small free-floating molecule with a net electrical charge. When NaCl dissolves in water, most of its weak chemical bonds break, but the Cl carries away one of the Na's electrons, and so they become the ions Cl- and Na+. The major players in the extracellular space outside the neuron's membrane are Ca++, Cl- and Na+, with much of the K+ concentrated inside cells. The Ca++ inside cells tends to be tightly regulated ("buffered") by various mechanisms because it too can serve a signal function (a "second messenger," the first being the neurotransmitter) for the slower processes that follow synaptic transmission.
island biogeography The peculiarities of animal and plant species when largely isolated, with just occasional interbreeding. An "island" can also be a deep ocean basin, a high mountain valley, or a patch in a patchy resource distribution that prevents migration. Islands often have a reduced number of species, so traditional predators or parasites may be lacking. Species often arrive in small numbers, so bottlenecks are a standard feature of island populations.
itinerancy Like the seasonal progress of a peddler revisiting towns that have changed somewhat since the last visit, chaotic itinerancy emphasizes the recurrence of similar, rather than identical, states. 
limit cycle A type of nonlinear oscillator, such as a threshold device with reset (cisterns that automatically flush
linkage In genetics, an association between the expression of two gene alleles that is greater than could be expected from random assortment. For example, two adjacent genes may tend to move together during meiosis.
long-term potentiation (LTP) A sustained (minutes to days) change in connection strength, largely synaptic, that follows some priming events -- such as a barrage of impulses. Originally seen via conditioning and testing in the same pathway, it has also been seen to cross over from separate conditioning and test pathways. LTP is thought to provide the physiological scaffolding for slowly making (during memory consolidation) the anatomical changes that more permanently increase the synaptic strength. 
meiosis The cell division used for making sperm and ova (as compared to ordinary mitosis), notable for the
crossing-over of chromosomes that results in a shuffling of the grandparents' genes and for the reduction
of diploid to haploid.|
meme Richard Dawkins's 1976 coinage, on the analogy to gene (with a little aid from mime and mimic), for a cultural copying unit, such as the word or melody that is mimicked by others.
membrane All cells are a bag of components, separated from the extracellular fluid and other cells by a limiting membrane. There are transport systems within this membrane, little pumps throwing sodium ions out of the cell while bringing potassium ions into the cell. There are ion channels through the membrane, pores that allow certain sizes of ions (and therefore certain types) to move inside and out. A channel may be controlled by a receptor-guarded gate on the external surface (the typical neurotransmitter-activated route for producing current flows), by the electrical field across the membrane (the typical voltage-gated channels that produce the impulse), or sometimes both (see NMDA).
memory, episodic One-trial learning involving distinct episodes, such as being an eyewitness to an accident. Such memories are notoriously malleable, influenced by subsequent events and the mistakes made in recall attempts.
message digest The fingerprintlike result of a computation (see hash) that reduces a long document to a number that serves to uniquely characterize it; were any changes to be made in the document -- even adding an extra space -- a different message digest would result. Although you cannot reconstruct the document from the message digest, nor does it serve as an abstract, you can use it for recognition ("I've seen exactly this before"). 
metapopulation A population with dispersed demes that replenish one another with migrants.
myelin Some of the longer axon branches are insulated with myelin (whose fat content is what gives the white matter its characteristic color), flat layers of which are wrapped around the axon in the manner of a bandage roll. This reduces the electrical capacitance that the impulse must charge up (the old capacitors-in-series trick), thereby speeding impulse propagation. The sodium channels that open during the upstroke of an impulse are confined to unwrapped axon regions, little exposed gaps called nodes of Ranvier, thereby reducing the metabolic cleanup costs by confining them to the small percentage of unwrapped axon cylinder. Without myelin, the impulse slowly spreads in the manner of a burning fuse; with myelin, the impulse seemingly jumps from one node to the next (saltatory conduction), achieving conduction speeds a hundred-fold greater than seen in unmyelinated conduction, top speeds being about 150 mm/msec.
neocortex All of cerebral cortex except for archicortex (olfactory cortex, hippocampus), the simpler layered structure
that lacks the patterned recurrent excitatory connections and columnar structures which make the six-layered neocortex so interesting. |
nervous system The whole works, both central nervous system (CNS: brain, spinal cord, and retinas) and peripheral nervous system (most sensory and muscle connections, plus the clusters of neurons called ganglia).
neuromodulator A molecule traversing the synaptic cleft to bind at a postsynaptic receptor site is acting as a neurotransmitter but it can also act as a neuromodulator (affecting the responsiveness to other neurotransmitters), typically by affecting internal processes in the downstream neuron over a longer time scale; it need not travel via the synaptic cleft, but might diffuse like a local hormone from release sites in the neighborhood. The major diffusely broadcasting systems for norepinephrine, acetylcholine, dopamine, and serotonin from subcortical regions surely involve profound neuromodulator actions in neocortex, quite in addition to their more immediate neurotransmitter effects.
neuron The nerve cell, whether sensory neuron, interneuron, or motor neuron. There are about 1012 neurons in the human brain and spinal cord; the neocortex alone is said to have 1011. The cell body of the neuron is the widest section (see figure, p. 26), thanks to containing the cell nucleus, and there are many processes branching off, receiving inputs and distributing outputs. See dendrite, axon.
neurotransmitter A molecule such as glutamate or acetylcholine that is released from an axon terminal (often by the arrival of an impulse), diffuses across a narrow extracellular space, and binds with a receptor on the surface of the postsynaptic cell. Many dozens of neurotransmitters have been identified over the years, and a given axon terminal may release more than one kind.
niche The "outward projection of the needs of an organism" such as food resources, camouflage from predators, suitable housing and sites for effective reproduction.
NMDA The NMDA channel at glutamate synapses was, unfortunately, named after N-methyl-d-aspartate because that molecule, rather than glutamate, is what opens the postsynaptic channel in the lowest doses. But glutamate opens it almost as well, and that's what is usually released as a neurotransmitter. The real significance of an NMDA synapse is that the current state of the dendrite's voltage, at the time the neurotransmitter arrives, is also important: Mg++ tends to plug the channels through the membrane, blocking Na+ and Ca++ inflows, but an antecedent rise in dendritic voltage (whether from the same synapse or neighbors) will unplug some such channels, allowing a much larger response. This is a major source of dendritic amplification of synaptic currents, along with the persistent sodium channels in the apical dendrites, and an example of what Hebb predicted in 1949 (see Hebbian synapse).
node The theoretical term for an intersection in one of my triangular arrays. In the anatomy, it corresponds to a single superficial pyramidal neuron (or perhaps to a minicolumn of act-alike neurons). 
parcellation Fragmentation; breaking apart a population into smaller, isolated units ("parcels"). Rising sea level
converts a hilly island into an archipelago.|
phenotype Usually "body" but actually the entire constitution of an individual (anatomical, physiological, behavioral) resulting from the interaction of the genes with the environment. As Dawkins emphasized in The Extended Phenotype, it can even grade into things such as bird nests.
postsynaptic The postsynaptic neuron's dendrite receives neurotransmitter, rather in the manner of sniffing perfume, and changes the permeability of its membrane to certain ions, usually Na+, K+, Cl-, or Ca++ in some combination. The ion flows through the membrane in turn produce the voltage change known as the postsynaptic potential (PSP). If excitatory, it is called the EPSP; if inhibitory, the IPSP.
pyramidal neurons The excitatory neurons of neocortex. They typically have a tall apical dendrite (an exception is the spiny stellate neuron) and a triangular-shaped cell body (from whence the name), from which their axon leaves. The neurons contributing to the pyramidal tract (alias the corticospinal tract, named for the triangular shape of the axon bundle as it traverses the medulla) are themselves pyramidal neurons, but most pyramidal neurons send axons elsewhere. 
receptive field A map of the inputs to a single neuron, e.g., those parts of the skin of the hand that produce excitation or
inhibition of a cortical neuron (antagonistic surrounds are especially common). The limited view of the
world as seen by a single neuron. |
recombination There are several connotations: (1) The shuffling of genetic material between an individual's two chromosome pairs that occurs just prior to the production of ova or sperm (the crossing-over phase of meiosis) and (2) the production of a new individual through the union of a sperm and an ovum from two parents at fertilization.
recruitment In neurophysiology, this means getting other neurons to join the action, much as the expert choir "recruits" the audience in the Hallelujah Chorus.
resonance A relationship between two periodically moving bodies (say, two pendulum clocks on a shelf) in which their cycles eventually become locked together ("in sync," though often one cycle is some multiple of the other). More abstractly, a moving body may resonate with the stationary bumps in the road, or two chemical processes may resonate with one another and thereby synchronize their cycles. 
sodium channel A pore through the membrane of a size to admit hydrated Na+ but not most other ions, controlled by
gating mechanisms near the outer surface that open when the transmembrane voltage is becoming less
negative. This admits even more Na+, making the inside even less negative. When these currents exceed
those of counterbalancing outward potassium currents (this occurs at a voltage called the threshold), you
get a regenerative cycle continuing for a hundred millivolt rise, known as the impulse. More sluggish
mechanisms on the inner surface tend to close the channel opening, and thereby help (along with
potassium entry through other voltage-sensitive channels) to terminate the impulse and create a refractory
period of several milliseconds in which it is more difficult to initiate another impulse.|
schema As in "schematic outline," it's a mental item more abstract than a rich mental image of an object. In some cognitive contexts, it is used more narrowly for those things like more, less, bigger, inside -- things grounded in our everyday experiences, often making reference to our own body moving through our daily world. Movements need something similar, and schema is often used to refer to standard movement programs. 
spine, dendritic A small protrusion, like a thorn, on the shaft of a dendrite that receives several synaptic contacts from presynaptic axons. See figure on p. 26.
stellate neurons The nonpyramidal neurons in the neocortex, on the basis of anatomy. Physiologically, most of them have inhibitory actions, an exception being the spiny stellate neurons.
synapse The synapse is the junction between neurons across which communications flow, usually in the form of neurotransmitter molecules secreted by the presynaptic axon terminal that diffuse a short distance across the extracellular space (the synaptic cleft) to the postsynaptic neuron, on whose membrane are some receptor molecules to which the neurotransmitter molecules reversibly bind. While they are bound, they open up an ion channel through the postsynaptic membrane, producing postsynaptic current flow. Most drugs affecting the CNS operate by interfering with synaptic transmission. See also dendrite, Hebbian synapse, neuromodulator, neurotransmitter, NMDA, postsynaptic, spine. 
threshold The word has two connotations in neurophysiology, one of which has a lot of imprecise reciprocals. As used in describing the sodium channel, the threshold is the transmembrane voltage (say, -56 mV) at which the inward and outward currents are in unstable equilibrium and above which the inward current becomes regenerative (the upstroke of the impulse). But a "high threshold" is also used in the same way as saying "low excitability," that you've got, say, 20 mV to go from -76 mV before triggering an impulse. The phrase doesn't imply that the threshold voltage has risen to, say, -40 mV. My sea level metaphor for the AGC is based on this latter use: increased sea level is a stand-in for lower gain which would decrease the chances of exceeding threshold.
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