Glossary

A to C** D to F** G to I** J to L** M to O** P to S** T to V** W to Z

Letters A to C

A23187
One of a group of agents called calcium ionophores that dissolve in cell membranes, making them permeable to calcium ions. It disrupts the cell's control over calcium permeability and would be expected to interfere with the production of calcium waves. It is observed to inhibit capping and particle movement.

Academic
The normal meaning of academic is the activities and people of educational institutions. In philosophy and logic, the word has a different meaning. An idea is academic if no possible course of action or perception is affected, whether or not it is true. It is an irrelevant idea.

Academic Freedom
The right of a worker in academic institutions to research and teach their beliefs without their livelihood being placed in jeopardy by those who disagree.

Actin
A protein, along with myosin, the main component of muscle. Molecules of actin come together (polymerise) to form long filaments. In muscle the filaments are very regularly aligned. Muscle exerts force as a result of myosin filaments sliding along filaments of actin in a way that is driven (or fuelled) by energy produced by the hydrolysis of ATP. This sliding is a one way process and causes the muscle to become shorter. The muscle can be "reset" by being lengthened again as another muscle contracts, hence muscles always work in pairs so that they reset one another.
Actin and myosin are present in the great majority of non-muscle cells and form filaments, called microfilaments. They are much less regularly arranged than in muscle. The meshwork they form is called the cytoskeleton. Variations on this name are used e.g. the acto-myosin cytoskeleton, to distinguish the network from the microtubular cytoskeleton, based on different proteins.

Advocacy
A way of advancing a particular point of view. It is characterised by a lawyer in a court room who presents arguments purely to sway the judge or jury in favour of his client. As far as possible, facts failing to conform to his side's case are ignored. It is the job of the opposing lawyer to raise such points. An advocate, doing his job properly, will, without actually lying, try to use any legal technicalities to keep inconvenient evidence away from the jury and may seek to give a false impression.
Advocacy is different from rationalist debate which seeks to approach truth. On the spectrum of debating styles, advocacy lies between rationalist debate and propaganda. Advocacy does not result in valid conclusions unless all sides are heard, hence the rules of legal process.

Aequorin
A luminescent protein, which when exposed to calcium ions (Ca2+) and ATP, gives off light. It is has been used to demonstrate calcium waves in cells. A cell is injected with aequorin and examined under a microscope. Light is emitted in waves, revealing waves of cytoplasmic Ca2+. Similar results are obtained with a group of dyes whose colour depends on Ca2+ concentration.

Amoeba
A single-celled organism, many species of which live in free in water. A few are pathogens, amoebic dysentery is caused by an amoeba that parasitises the gut. Their overall shape and pattern of movement is similar in character to the way many animal cells behave, although the latter are usually much smaller. Such cells are often referred to as amoeboid.

ATP
Adenosine triphosphate, is a major energy storing compound. When ATP breaks down into ADP (adenosine diphosphate) and phosphate, it releases energy used to fuel many biochemical processes, such as muscle contraction, nerve action, protein synthesis etc. ATP is made, mostly in mitochondria, from ADP and phosphate. Food is "burned" under controlled conditions, by reacting it with oxygen from air, and the energy so produced harnessed to make ATP.

Axonal Transport
Nerve cells are very large, deriving much of their size from the very long protuberances, nerve axons. These are very thin but can be centimetres or even metres long. The membranes of the axons transmit electrical waves which are the messages the nervous system sends around the body. These very fast electrical waves are associated with voltage dependant changes in the permeability of the membrane to sodium and potassium ions, the mechanism is well understood. Calcium ions are under similar permeability control in nerves, as in other cells, and produce similar waves, in some species of the axon. These are examples of fast calcium waves.
Cellular material is carried moved Inside and along the length of the axon moving in both directions. This process is known as axonal transport. Objects in contact with the surface of an axon will also move. All these movements are much slower than the electrical wave of nerve impulses but are comparable with the speed of slow calcium waves. The mechanisms of these movements is not established but the general supposition is that whatever causes capping and particle movement also causes axonal transport.

Belousov-Zhabotinsky reaction
The reaction between malonic acid and bromate ions in the presence of a catalyst. One of the few chemical reactions known to produce spontaneous oscillations and wave patterns, it has been studied extensively. Although rare, the properties that cause the oscillations are well understood. It arises as a result of autocatalysis and inhibition. The product of one stage of the reaction catalyses its own formation while inhibiting the other stages and the resulting patterns of feedback cause oscillations and waves.
Many biochemical reaction pathways have this sort of feedback as part of the control used to switch them on or off. Consequently, oscillation is much more common in biochemical pathways than in simple chemistry.

Brownian Motion
Named after the Scottish botanist Robert Brown who discovered it among pollen grains on water during his studies of plant sexual behaviour. Tiny particles suspended in fluid, such as dust in cigarette smoke or Brown's pollen grains, when and seen through microscope, are in a constant state of random motion. The phenomenon occurs because the particles are so small that they visibly move on collision with molecules of fluid. This is evidence that molecules themselves are in constant random motion.

Calcium
Calcium, Ca, is element number 20 in the periodic table. It is a metal but, in living tissue, occurs only in its reacted form, as an electrically charged ion Ca2+. The cell actively transports it across the outer membrane and this ion plays a role in determining the electrical voltage difference between the inside and outside of the cell. It also has a role in controlling muscle contraction.

Capping
The property of motile amoeboid cells that causes them to accumulate polymerised surface receptors at the rear of the cell. Described in detail in Chapter 3.

Cell
Almost all living tissue is made of cells. Throughout biology all cells work on similar chemical principles containing DNA, RNA, & proteins. RNA is made using DNA as a template and the information in the RNA guides the production of protein. Everything else the cell makes is the product of enzymes which are proteins. These processes are universal and common to all cells of all species.
Other processes are also common from one cell to another. The more closely related the species from which the cells come, the more closely related is their biochemistry.

Cell Wall
Bacteria and plant cells are rigid. Their shape is maintained by a cell wall which, in plants, is made largely from cellulose, from which paper and cotton are made.

Centripetal
This means simply "towards the centre." Most commonly it is encountered in mechanics. A centripetal force is the force attracting an object to the centre during circular motion. The opposite to centripetal is centrifugal. On cells, centripetal waves travel toward the nucleus. As the nucleus is toward the rear of a cell, such waves move, approximately, from front to back.

Citation Analysis
The process whereby the impact or "quality" of a piece of science is assessed by counting the number of times other scientists mention it in their work.

Cilia
Small hair like structures located on the surface of some cells but rooted in its underlying cytoplasm. Cilia occur only on eukaryotic cells and are always similar. Their structure and mode of action has been well conserved throughout biology. When they occur, cilia are often abundant, covering either the whole cell surface or a large proportion of it.
Cilia are motile organelles, helping the cell to move. For example, they cover the cell surface of paramecium and beat in waves to enable swimming. This is how cilia usually function. In the mucociliary escalator of the lung lining, the cell itself is stationary but the cilial beating drives the mixture of particulate debris and mucous adherent to its surface upward and out of the lung.

Contractile
Muscles power the body by contraction. The proteins that enable the muscle to produce force on this contraction are actin and myosin. Accordingly these proteins are known as contractile proteins.

Cytoplasm
A general name for the jelly-like material that makes up the interior of a cell and is bounded by the cell membrane.

Cytosinew
A word suggested here to more aptly describing the function of the cytoskeleton.

Cytoskeleton
The framework of protein filaments in a cell. Cytoskeleton is a poor name as it is not rigid. The proteins comprising the main structure of the cytoskeleton are muscle proteins and changing the name from cytoskeleton to cytosinew would be better.
At least two cytoskeletons are recognised, one based on microfilaments containing actin and myosin (the muscle proteins) and another based on microtubules, containing another protein, tubulin. Both have a role in motility but capping and particle movement seem particularly linked to the microfilamentous cytoskeleton. Generally, drugs disrupting microfilaments stop capping, while it is somewhat less sensitive to agents disrupting the microtubular cytoskeleton.

Letters D to F

Demarcation Criterion
A term used by philosophers of science for a criterion used to distinguish scientific from non-scientific hypotheses. An important one was proposed by Popper who argued that a hypothesis was only scientific if it could, in principle, be falsified by experiment. Thus the hypothesis must be able to predict the result of attainable experiments or observations.

Dictyostelium
One of an unusual class of organisms known as slime moulds. At one stage in their life cycle they produce small amoeboid cells which seem much like any other. Most amoeboid cells are produced by diploid eukaryotic organisms. However, dictyostelium is haploid having just one copy of each gene. Haploidy makes genetics much easier as any gene defect is immediately reflected in the properties of the cell. Scientists have chosen this organism for genetic studies of motility, with the results summarised in the text.

Diffuse, diffusion
If an area contains a high concentration of molecules, then purely on statistical grounds, they will spread out, much as children in a playground fill the whole ground rather than remain at one end of it. Diffusion causes molecules in regions of high concentration to spread into regions of low concentration. Such spread is called diffusion and the molecules are said to diffuse.

Diploid
An organism is diploid if it possesses two copies of each chromosome and hence two copies of each gene. The alternative to diploid is haploid which means the possession of just one copy per gene.
The distinction between haploid and diploid is important in genetics. Mutant haploid organisms always display the effects of a mutation but not so the diploids. When a mutant diploid occurs, the mutation is often masked by the remaining good copy of the gene. Hence, many mutations are silent, or recessive. Its effects are not seen unless the particular animal possesses two copies of that mutation. A few dominant mutations show their effect with only one copy.

Dissonance
Sometimes cognitive dissonance. The sense of discomfort people experience when confronted by contradictory ideas.

DNA
Deoxyribonucleic acid. This chemical contains genetic information and forms the famous double helix structure.

Empirical
Experimental or observational.

Endocytosis
The process whereby amoeboid cells takes in particles or liquid from the surrounding medium. The cell membrane folds inwards to produce a sack whose connection to the external medium finally pinches off, leaving a vesicle inside the cell.

Entrain, Entrainment
When an object becomes caught up with a wave train (a series of waves) it can be said to become entrained with them, just as a passenger becomes associated with a real train. The term can be used to describe a class of models for capping and particle movement in which the moving object is associated either with a cell wave train, or other ongoing cellular process.
The alternative is a recognition-response model, where the cell recognises the particle and then responds in some preprogrammed way, see section 4.2.

Enzymes
Enzymes are proteins that serve as biological catalysts. "Biological" washing powders contain enzymes to break down stain materials. They are very specific catalysts and one enzyme catalyses only one, or a small range of, reactions.

Epithelial Tissue
The layers of cells forming the boundary of organs or tissue.

Eukaryotic
The living world is divided into two classes of organism. Eukaryotic and, much simpler, prokaryotic organisms such as bacteria. Generally eukaryotes are diploid and their cells have internal organelles, such as nuclei. Prokaryotes are haploid with much simpler cells.

Excitable
The potential of a structure to produce waves. Even if no waves are present, the potential to produce them makes the structure excitable. A liquid surface with wind blowing over it is excitable, it is capable of producing waves. The surface structures of eukaryotic cells are also excitable.

Exocytosis
See endocytosis

Focal Contacts
The points of contact between a moving amoeboid cell and the surface over which it moves. c.f. points d'appuis

Foraminifer
A group of large shelled protozoa. They send out long thin shoots (reticulopods) through holes in their shell. The whole organism can be as much as a centimetre across. Foraminifers are quite abundant and have occupied the earth for millions of years. Many chalk deposits are the shells of now dead organisms of this class, an example is the White Cliffs of Dover.

Letters G to I

Gatekeeper
A sociological concept. All groups have gatekeepers, people to decide (wholly or partly) who or what forms part of a given subculture. Thus, prospective gang members are checked out by existing leaders. Possible university students have an interviewer who decides whether or not to "open the gate". In the same way, gatekeepers decide who is a scientist, by controlling access to jobs, to research money and to publication in journals. By those decisions they determine what subjects are considered to be science.

Gödel's Theorem
see Heisenberg

Haploid
See diploid

Heisenberg's Uncertainty Principle
The principle in physics which states that no value can be measured with complete certainty. There are equivalent principles in all fields of knowledge. A sociologist recording behaviour, must be aware that his very presence alters what is being observed. Even in mathematics, Gödel's theorem states that their are always some results which, though true, cannot actually be proven.

Heuristic
The first meaning is any discovery process based on experience.
The second meaning is the pre- programmed strategies problems-solving of the human mind. These strategies arose from natural selected and, because they arise from evolutionary experience, they are called heuristics. Plotkin (1994) used heuristic in a third sense, as a level in a hierarchy of evolutions.

Hydrocarbon
A class of chemicals made entirely from hydrogen and carbon. Petroleum oil is a mixture of hydrocarbons. The tail part of a lipid is usually a large hydrocarbon grouping.

Hypothesis (Hypothetico-deductive Method)
An idea advanced to explain a set of observations. Ideally, any problem can be interpreted by several possible hypotheses. The idea of the hypothetico-deductive method is that a critical experiment can be devised whose outcome should be different for each hypothesis. The actual outcome then eliminates those hypotheses failing to predict it. See section 2.3 etc.
A hypothesis is a similar concept to a model. The distinction is that the hypothesis makes a proposal about reality while a model proposes only that the collection of axioms it represents have properties analogous to reality.

Insulin
The hormone that controls blood sugar level. It is used to treat diabetes.

Intracellular
This word means "inside the cell". The opposite is extracellular.

Letters J to L

Lamellipodium
When amoeboid cells move they put out protuberances commonly called pseudopodia, (literally "false feet,") in the direction of movement. On a surface amoeboid cells become flattened, so that rather than being a foot, the protuberance is a sheet or lamella. Hence lamellipodium.

Ligand
A ligand is any chemical which binds to, forms a chemical link with, some larger molecule or receptor. On cells the binding is to the outer part of the cell surface. If a ligand can bind to two sites at once, it is called a divalent ligand, if three, trivalent, and if many sites can be attacked at once polyvalent.

Lipid
Lipids are soluble in non- aqueous solvents such as white spirit or dry cleaning fluid. Lipids tend to associate with one another, just as oil forms droplets in water. Many lipids have head groups which like water but leg groups which are oily. (see Fig 3.4) Different head groups define several classes of lipid. The leg groups, are much the same for each class, a mixture of hydrocarbon chains. Lipids can form back to back sheets in water, forming the basis for membranes.

Logic
The rules whereby valid conclusions may be derived from a given set of axioms. Also the rules for dialogue, section 15.11.

Logic in Use
A term used by Kaplan (1964) to describe the reasoning actually used by scientists during their work, as distinct from Reconstructed Logic, a term used for the subsequent description of their reasoning.

Luminescent
Emitting light. Luminescent material is visible by the light it generates.

Letters M to O

Membrane
The surface of a cell is a cell membrane. Many of the internal organelles of the cell are themselves surrounded by membranes which are very similar to the outer surface.

Merton's Principles
The ethical norms of scientific dialogue, see section 12.3.

Metabolism, Metabolizing
Living things are sustained by a complex series of biochemical reactions serving to break down food, generate energy, make proteins, reproduce and excrete waste products. Collectively, these reactions are known as metabolism and are stopped by low temperature or poisons that inhibit energy production. Higher organisms then die but many simpler species lie dormant.

Metaphysics
The branch of philosophy asking "what exists?" What entities form this universe? Metaphysical studies can concern difficult, perhaps unanswerable, questions bordering theology. Ayer, (1971) used the term "transcendent metaphysics" for proposals of existence beyond the observable universe. Like Kant, he denied them a part in logic. As used here, metaphysics includes any suggestion that something, not immediately obvious, does exist.
Metaphysics is different from science, which deals with the properties and workings of things known to exist. In logic, proving non- existence is extremely difficult, much more so than contradicting a theory by comparison with observation. Thus, the hypothetico-deductive method as normally considered, seems unable to deal with metaphysical postulates and failing to refute one is insufficient grounds for belief. Thus scientific logic differs from metaphysical logic where ideas need positive support to be accepted. Despite this, the scientific logic is the pre-eminent one. The hypothetico-deductive method does apply to metaphysical ideas, but it applies to the negative of the statements as normally made. One is negating the negative of a metaphysical postulate.
Thus the metaphysical suggestion, "I believe there is life on Mars," cannot be disproved, and is therefore not scientific, but its inverse, "I believe there is no life on Mars," can be disproved by the discovery of Martian roses and therefore is scientific. The upshot is that, in science, the verb to be, has no ultimate meaning except to negate its own negative, a point noted by philosophers. Scientists, of course, generally abandon this double negative for the less tortuous concept of positive evidence, or "proof," but this switch can result in some confusion.

Mitochondrion
An organelle found inside the cell, the mitochondrion is the cell's powerhouse. All living things need to convert food to energy which many do by respiration, a process akin to controlled burning. The resulting energy is used to produce large amounts of ATP, a substance used as a fuel by many other processes.

Model
see hypothesis

Motility
The ability of a cell to move under its own power.

MRC
The Medical Research Council. The agency of the British government charged with the distribution of funds intended for scientific research relevant to medicine. Besides funding the research of independent organisations, such as universities, it also channels a large proportion of its funds into its own research institutions.

Mucociliary Escalator
A mechanism whereby the lungs of mammals rid themselves of small particles that would otherwise become lodged there. The particles become adherent to mucous on the surface of the cell and the mixture of mucous and particles is driven upwards and out of the lungs by coordinated waves of cilial beating. See section 7.2.

Multicellular
An adjective meaning many cells.

Myosin
One of the major proteins of muscle. Myosin can slide along filaments of actin, generating force as it does so and using ATP as its motive energy source.

Nematode
A microscopic free living worm. Many species live by predating bacteria. Nematode sperm cells are very unusual in being large crawling cells.

Norm
A way of behaving or believing that is normal for a group or culture. All societies have their norms, they are simply what most people do. Deviants break norms. Some norms are enshrined in law and society punishes those who deviate from them. Breaches of unwritten norms are unofficially punished. This is important to science, because innovation is a form of deviancy science formally encourages. (Section 15.8.)

Normlessness
A culture or society having no, or only weak norms. Anomie means normlessness and anarchy is the resulting state.

Nucleus
The largest and most obvious organelle inside a eukaryotic cell. The nucleus contains almost all the DNA of the cell.

Organelle
A structure in a cell. Examples are the nucleus, chromosomes, mitochondria, cytoskeleton and vesicles. There are many others.

ORI
The Office of Research Integrity. A US government agency charged with maintaining ethical standards in US research. Previously OSI, Office of Scientific Integrity.

Letters P to S

Paradigm
An overarching model. A concept that is either so widely accepted, or applicable to so many different areas, that it can be used to build sub-models to describe particular areas of interest.

Paramecium
A free living unicellular animal, a protozoan. The surface of paramecium is covered in cilia, that beat in wave patterns to power swimming. (section 7.2)

Peristalsis
The process whereby an undulating surface takes up a fluid near the surface and drives it with the wave. Many aquatic organisms swim by such mechanisms.

Polymerisation and Depolymerisation
Polymerisation is the joining together of many small molecules to form a large one, a polymer. Commercial polymers are very important, they are plastics and man-made fibres. Polymerisation as used in this work describes the joining of many single molecules of actin to form an actin fibre. Depolymerisation is the reverse.

Points d'appuis
The points of contact between a moving invertebrate and the surface upon which its moves. c.f. focal contacts.

Propaganda
A way of presenting a belief that seeks to generate acceptance without regard to facts or the right of others to be heard. Propaganda often presents the same argument repeatedly, in the simplest terms and ignores all rebuttal or counter-argument. It is essentially self- interested and often associated with authoritarian regimes. Propaganda is often used to convey official descriptions of reality, when it may be allied with bureaucratic control of media, censorship of opposing opinions and deliberate misinformation.

Protein
Any of a group of large molecules made by the cell. Any one cell is able to make tens of thousands of different proteins, many of them enzymes.

Protozoan
A member of the large group of single celled animals, the protozoa.

Pseudopod
See Lamellipodium

Refractive Index
The refractive index is a number given to materials that indicates the speed at which light travels through it. Microscopes can be set up to visualise objects on the basis of variations of refractive index.

Recognition-response
see entrainment

Reconstructed Logic
See logic in use.

Ribosomes
The cell organelle on which protein is made.

Saltatory
A saltatory motion is a stop start motion. The movements associated with many cellular processes are saltatory which is consistent with wave-driving.

Sarcoplasmic Reticulum
Membrane structures in muscle involved in the control of calcium concentration and hence muscle contraction.

Satisfice
A word invented by evolutionary theorists, it is a bowdlerisation of satisfy and suffice and implies the meaning of both.

Slime Moulds
A group of organisms, e.g. dictyostelium, that are haploid but produce amoeboid cells like those of eukaryotes.

Subtext
Information in statement which is not contained in its text but is nonetheless inferred by the reader.

Letters T to V

Teleology
A doctrine or idea based on final purposes that Darwinism does not permit. In biology, a teleological idea is one which presupposes a purpose about the ways in which living things behave. The idea is very closely related to vitalism, the idea that living things contain a spirit which imbues them with purpose.

Territorialism
A pattern of animal (and also human) behaviour in which individuals mark out a territory and defend, excluding other animals of the same species.

Trypanosome
A pathogenic protozoan, it causes sleeping sickness. Its principle motile organ is the "undulating membrane".

Unicellular
Possessing only a single cell. As distinguished from an organism possessing many cells, multicellular.

Vacuous
A term used by philosophers of science to describe a theory that fails to compete with alternatives. For example, it is vacuous to hypothesise that a tossed dice will fall with a number uppermost.

Vesicles
Small hollow balls of membrane or lipid. Amoeboid cells contain many vesicles which exchange with membrane due to endocytosis and exocytosis. Vesicles can also be made in the test tube.

Letters W to Z

 

This is Appendix 2 to "A Habit of Lies - How Scientists Cheat" by John A. Hewitt

© Copyright John A Hewitt.
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Last Modified 21 October 2005