Online Book Glossary

Online Book Glossary

3 March 2012: ONLINE BOOK AVAILABLE ON AMAZON: The sites online book 'Consciousness, Biology and Fundamental Physics' is now available on Amazon both as a paperback and as a kindle book. New paperbacks currently priced from £9.05 and kindle books from £2.63. Text remains free on this site.

GLOSSARY

Algorithm: A procedure or rules for performing a calculation.

Amino acids: Molecules formed from carbon, hydrogen, oxygen and nitrogen. These are grouped in an amine group, a carboxylic acid group and a side chain that is different for each amino acid. Genes code for 20 amino acid and chains of amino acids form the proteins that are basic to life.

AMPA and NMDA receptors: Excitatory receptors for glutamate on post-synaptic dendritic spines of neurons.

Anthropic principle: Concept that we would not be able to observe the universe if the laws of physics did not permit the existence of intelligent life forms, and that this therefore explains why the laws of physics are to an improbable degree set just right for the existence of such life.

Artificial intelligence: Computer basis for robotics P. Association cortex: Occipital, parietal and temporal cortex involved in sensory input and perception. Mainly towards the rear of the brain.

Axon: Long extension from the main body of a neuron or brain cell. Electrical signals pass down these to synapses, which communicate with other neurons. P. Axon spike: Fluctuation in electrical potential in the cell membrane of the axon transmitting a signal to the synapse.

Axon terminal: The end of the axon from which neurotransmitters are sent across the intermediate synapse to the next neuron. This is the basis for information transfer in the brain.

Ca2+ channel: Ion channel in the cell membrane that selects for calcium ions. P. Cartesians: Those following or deemed to be influenced by the 17^th century philosopher Descartes.

Classical computers: Includes all normal existing computers, and means those computers not utilising entangled quantum states.

Classical physics: Physics before quantum theory was developed in the early 20^th century and still the main way of describing the behaviour of macroscopic objects or anything much above the scale of the atom.

Coherence: (See quantum coherence) P. Conformation of protein or folding of protein: Changes in the shape of proteins, which is crucial to biological processes. P. Conservation of energy: First law of thermodynamics stating that energy in the universe cannot be created or destroyed.

Copenhagen theory: Early and for a long time orthodox interpretation of quantum theory, given this name because it derives from Neils Bohr based in Copenhagen. Seeks to overcome the problems of the theory by proposing that the quanta are only mathematical abstractions until observed or measured.

Cortex: Upper and outer layers of the brain, particularly associated with processing incoming sensory signals, cognitive and some emotional processing and consciousness. P. Covalent bond: Chemical bonding in which atoms share a pair of electrons. A basic bond in chemistry and the formation of molecules.

Delocalisation: Delocalised electrons are spread over several adjacent atoms rather than a single atom or the covalent bond between two atoms. A notable example is the delocalisation of the six pi electrons in aromatic molecules such as benzene and tryptophan.

Dephasing: Process by which the coherence or in-phase oscillation of the quanta breaks down and creates the classical state.

Dipole and dipole attraction: Refers to a molecule that carries opposite electric charges. Biomolecules and water are both important here.

Donor and acceptor states: Atoms providing or obtaining electrons

Dorsal and ventral stream: The dorsal stream stretches from the primary visual cortex in the occipital lobe to the parietal lobe and is involved with spatial location of objects and related actions. The extent to which it is separate from the ventral stream running from the primary visual area to the temporal lobe and responsible for visual perception is still controversial. Studies have suggested that only the processing of the ventral stream enters consciousness.

Electron cloud: Electrons around an atom are conceived as quantum waves not having a definite position, and the electrons as a whole are therefore viewed as a cloud. This is consider a more accurate view than the easier to understand 'Bohr atom' with the electrons like planets orbiting the solar system.

Electron or quantum tunnelling: As quantum waves, electrons can extend through barriers that would be impenetrable to them as particles. Such quantum tunnelling in biological matter.

Entropy: Measure of disorder. A gas concentrated in one corner of a container has low entropy. A gas dispersed evenly in a container has high entropy.

Exciton: An exciton is formed when an electron is excited out of its valence band leaving behind a positively charges whole. The exciton can transport energy through matter without transporting net electrical charge.

Femtosecond: 10^-15 seconds or one quadrillionth of a second P. fMRI : Functional magnetic resonance imaging used to measure changes in blood flow related to neural activity. The predominant form of brain imaging since the 1990s.

GABA: Inhibitory neurotransmitter widespread in the brain.

Gamma oscillation or synchrony: Process by which electrical signalling in substantial areas of the brain oscillates in phase. Known for its correlation with conscious processing.

Gap junction (or electrical synapse): Allows direct passage of current and smaller molecules between the interiors of separate cells including neurons.

Gephyrin: Protein in the postsynaptic network of inhibitory synapses

Glutamate: The main excitatory neurotransmitter in the brain.

Gödel theorem: Theorem proposing that with any system of axioms there would be a proposition that was obviously true but could not be proved by the axioms.

Golgi apparatus: Organelle found in cells and responsible for modifying and organising macromolecules within the cell.

GTP hydrolysis: Hydrolysis or the reduction of GTP to GDP is involved in the development of microtubules. Each of the dimers of the tubulin protein carry two GTP molecules. When these hydrolysis into GDP the microtubule can depolymerise. While the GTP remains it serves as a cap to the end of a microtubule to prevent depolymerisation.

Inferior temporal region: Part of the temporal lobe associated with object recognition.

Interference pattern: When waves intersect they form a pattern of peaks and troughs, or with light waves, light and dark bands. The appearance of this in the two slit experiment indicates the wave form of the quanta.

Ion channel: Ion channels are formed by proteins in the membranes of cells, allowing the flow of ions across the membrane. This process drives the fluctuation in electrical potential across the membrane, which is the basis of neural signalling. This refers to voltage-gated ion channels. Other ion channels respond to the binding of particular ligand molecules.

K+ channel: Also potassium channel. Ion channel selecting for potassium ions. P. Lateral geniculate nucleus: Region of the thalamus relaying signals from the retina to the primary visual cortex.

Light cone: In special relativity there are both past and future light cones. The past light cone is formed by light rays converging on the observer and is the limit of the observer's knowledge of the past. The future light cone marks out the region that can be influenced by the observer. P. Limbic system: Areas of the brain associated with emotional processing. Definition of these seems to have varied over time. At present hippocampus, entorhinal cortex, amygdala, orbitofrontal cortex, piriform cortex and nucleus accumbens are included.

Localisation: When a state goes from being quantum to classical the quanta become localised in a particular position. This is the condition of classical physics. P, Masking: Experimental process by which an initial image is blocked from consciousness by another image. P. Medial temporal region: Area of the temporal lobe around the hippocampus involved in the formation of long-term memories.

Membrane lipids: The membrane of cells including neurons are formed out of lipid layers. P. Membrane proteins: Ion channels and receptors inserted through the membrane of cells including neurons.

Midbrain: Viewed as part of the brainstem, and includes the substantia nigra, which is a dopamine producing area that interacts with the basal ganglia.

Mitochondria: Mitochondria are organelles within cells including neurons that provide the cells with energy. They convert oxygen and other nutrients into ATP. ATP releases energy via the removal of one of its phosphate oxygen groups.

Neuronal assembly: Large number of neurons acting together in neural processing. P. Neuronal columns: Neurons arranged vertically through the layers of the cortex which function together.

Neurons spiking or firing: Instance when an electrical signal passes down the axon of a neuron in order to communicate with other neurons.

Neurotransmitter: Amino acid conveying messages between synapsis and dendritic receptors. Part of the basic information processing of the brain.

NMDA receptor: (see AMPA and NMDA receptors)

Non-algorithmic: Process not based on rules for making a calculation.

Non-locality: Ability of quantum entangled particles to effect one anothers quantum properties despite being out-of-range of a signal travelling at the speed of light. The effect is considered instantaneous over any distance.

Occipital cortex: Area of primary visual cortex situated at the rear of the brain.

Orchestrated objective reduction: Theory of consciousness based on the collaboration of Roger Penrose and Stuart Hameroff.

Orch OR (see orchestrated objective reduction)

Parietal cortex: Area of the cortex handling sensory input related to spatial location and navigation.

Picosecond: 10^-12 seconds or a trillionth of a second.

Planck length: 10-35 metres, considered to be the scale at which the continuity of spacetime breaks up. In Penrose's objective reduction the separation of superpositions of quanta become unstable and collapse above this level.

Pons structure: A part of the brain stem involved in communication between the two hemispheres of the brain.

Post-synaptic density protein (PSD): This contains hundreds of proteins including scaffold proteins and acts to ensure that membrane receptors are close to presynaptic neurotransmitters.

Primary visual cortex (V1): Located in occipital lobe at the rear of the brain, and responsible for processing signals sent from the retina via the thalamus.

Quantum coherence: The wave form of the quanta. All the possible states of the quanta oscillate in phase. Decoherence describes the process of this in-phase oscillation breaking down and giving way to a classical state.

Quantum vacuum: The vacuum as understood by quantum theory, which involves space being filled by virtual photons jumping in and out of existence, because uncertainty principle does not allow the non-existence of particles to be specified.

Receptor: Protein inserted through the neuron membrane to which neurotransmitters can bind.

Rubin vase-face: Well known ambiguous image that can be read either of a face in profile or the outline of a vase.

Schrödinger wave: Describes the development of the quantum wave. This ceases when the wave function collapses to a classical state.

Second law of thermodynamics: Entropy of a closed system including the universe can never diminish, but only either remain the same or increase.

Sensory cortex: Those areas of the cortex handling sensory input such as vision, hearing and touch. P. Superior colliculus: A part of the midbrain involved in directing the eyes.

Synapses: Gap between neurons over which neurotransmitters are sent as a part of the brain's basic information processing.

Synaptic plasticity: Ability of the strength of synaptic connections to wax and wain in response to their usage.

Synaptic vesicle: Synaptic vesicles store neurotransmitters within the axon terminal for transmission across the synaptic cleft.

Thalamus: Brain region handling most incoming signals before they pass on to specific regions of the cortex.

Thermal equilibrium: Even distribution of temperature, which also indicates a high degree of entropy. Living systems are far from thermal equilibrium.

Turing machine: Refers to Alan Turing who developed the mathematical principles for computing.

Van der Waal forces: The force between dipoles on different molecules. This can be between two permanent dipoles, between a permanent dipole and an induced dipole (Debye force) or between induced dipoles (London forces).

Ventral stream: (See dorsal and ventral stream)

Ventral striatum: A part of the basal ganglia strongly connected to the limbic areas.

Virtual photon: Uncertainty principle means that the vacuum is filled by virtual photons that jump in and out of existence. Energy can convert the virtual photons into real photons as demonstrated in a recent experiment.