The primary source of this file is the talk.origins jargon FAQ.  This is a subset of that FAQ, used to define terms I use on my pages.  Some of the differences between this document and that FAQ are that the FAQ details every definition in use on the 'talk.origins' newsgroup by both sides, whereas this document is intended to represent what I consider the words to mean. Other sources include many reference works on critical thinking, and rhetoric.

• Abiogenesis: The development of life from non-living systems via natural mechanisms.  cf. creation.
• Allele: Different versions of the same gene.  For example, humans can have A, B or O blood type alleles.
• Anagenesis: The change of a species over time into another ( not nowadays generally used )
• Analysis: Step Six in the Scientific Method.  Experimental results are gathered.  The experiment should be repeated (replicated) several times to avoid chance error.  The results are subjected to statistical analysis.  Statistical analysis is designed to help minimize false positives and false negatives.   In most statistical procedures in biology, a 5% error rate is allowed to occur and still consider the results viable.  This much error is accepted as "due to chance alone."
• Agnostic: Someone who defers belief or non-belief in a god until the evidence is in. Usually accompanied by the assertion that the evidence is not in. cf. unbelief
• Asexual Reproduction:  (also called Vegetative Reproduction) A form of duplication using only mitosis.  Example, a new plant grows out of the root or a shoot from an existing plant.  This process produces only genetically identical offspring since all divisions are by mitosis.  1.  offspring called clones meaning that each is an exact copy of the original  organism  2. this method of reproduction is rapid and effective allowing the spread of an organism 3.  Since the offspring are identical, the only mechanism for introducing genetic diversity is mutation.
• Athiest: Someone who either states a disbelief in a god or gods ('strong' or 'positive' atheism), or an unbelief in a god or gods ('weak', 'negative' or 'passive' athiesm).  cf. agnostic.
• Belief : The position of affirming the truth of a proposition. Belief, if asserted as true in a debate, bears a burden of proof (as does disbelief). See also: unbelief.
• Biological Species Concept:  A definition of 'species' as "a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature."   BSC applies well to sexually reproducing animals, but not as well to plant life because there is greater gene flow between plant species.  BSC is also difficult if not impossible to apply to the fossil record.   Fossils are divided into species based on taxonomic classification (similarity of physical characteristics).
• Burden of Proof : Also known (especially in legal terminology) as the onus probandi. The burden of proof is something shouldered by anyone who makes an assertion regarding a proposition -- a requirement that they support/substantiate their assertions, if they expect anyone else to accept them. It is important to note, however, that simply having a belief or disbelief on a subject does not require the burden of proof -- one must actually assert that one's position is true.  cf. unbelief.
• Cladistics: A system of classification which places emphasis on specialized or derived characteristics rather than on shared features. Also known as "phylogenetic systematics" and "Hennigian systematics."
• Cladogenesis: The splitting of a daughter species from an ancestral species rather than transformation of the ancestral species in toto. This is a multiplication of species.
• Common descent. This is the theory that every group of organisms descended from a common ancestor, and that all groups of organisms, including animals, plants, and microorganisms, ultimately go back to a single origin of life on earth.
• Creation: The bringing forth of matter from nothing, or the development of life from non-living systems. cf. abiogenesis.
• Creationism: The belief in creation as having a supernatural agent, but usually without limiting the range of mechanisms used by that agent.
• Darwinism:  In 1859 Charles Darwin supplied a mechanism, namely natural selection, that could explain how evolution occurs. Darwin's theory of natural selection helped to convince most people that life has evolved and this point has not been seriously challenged in the past one hundred and forty years. It is important to note that Darwin's book "The Origin of Species by Means of Natural Selection" did two things. It summarized all of the evidence in favor of the idea that all organisms have descended with modification from a common ancestor, and thus built a strong case for evolution. In addition Darwin advocated natural selection as a mechanism of evolution. Biologists no longer question whether evolution has occurred or is occurring. That part of Darwin's book is now considered to be so overwhelmingly demonstrated that is is often referred to as the FACT of evolution. However, the MECHANISM of evolution is still debated.   cf. Modern Synthesis
• Decision:  Step Seven in the Scientific Method:  The estimate of error and the allowance for error are analyzed, and the hypothesis is either "rejected" or "not rejected"   Please notice that the hypothesis is not 'proven'!  The end result of the process is a theory.  A theory is what a hypothesis becomes after it has accumulated supporting experimental data.
• Diploid: Having two alleles for every gene at every locus, one from the mother and one from the father.  Most animals, including humans, are diploid.
• Disbelief: A position which asserts that a proposition is false. This is technically a "positive" position on any matter, and, like belief, must shoulder a burden of proof if it is to be proven. cf. unbelief.
• Evolution: A change in the gene pool of a population over time. The process of evolution can be summarized in three sentences: Genes mutate. Individuals are selected. Populations evolve.
• Evolutionary Mechanism Theory: Any one of several theories in biology dealing explicitly with some aspect of evolution or cumulative evolution.  Examples include Sewall Wright's "shifting-balance theory", Eldredge and Gould's "punctuated equilibrium theory", the theory of common descent, Darwin's "descent with modification", Henry Fairfield Osborn's "orthogenesis", and "Gene Flow". While "evolutionary theory" is equivalent, the point that mechanisms are proposed and tested in evolutionary mechanism theories is worthy of stress and repetition.  Some mechanisms increase genetic variation ( cf. mutation, recombination, gene flow ) and some decrease genetic variation ( cf. natural selection, genetic drift )
• Experiment: Step five in the Scientific Method.  The system is manipulated and the results are compared against a control setting and the prediction.
• Gametes: The specialized cells produced by organisms for sexual reproduction. In isogamous species, the gametes produced by the sexes are of equal size;  in anisogamous species, the gametes are of different sizes (with the producers of smaller gametes considered as male). In most metazoan animals, gametes are produced by meiosis and are haploid.
• Gene:  The fundamental physical and functional unit of heredity which carries information from generation to the next.
• Gene Flow: An evolutionary mechanism theory.  Gene Flow states that new organisms may enter a population by migration from another population. If they mate within the population, they can bring new alleles to the local gene pool.  In some closely related species, fertile hybrids can result from interspecific matings. These hybrids can vector genes from species to species.
• Gene Pool: The set of all genes in a species or population.
• Genetic drift: Evolution due to the fact that the transmission of alleles from one generation to the next is essentially a process of sampling from a finite set.  The actual base pair sequences within the genome of a species may undergo mostly unexpressed variations without the application of natural selection.  Genetic drift underlies the premise of the neutral theory.
• Gradualism. An evolutionary mechanism theory.  According to this theory, evolutionary change takes place through the gradual change of populations and not by the sudden (saltational) production of new individuals that represent a new type.
• Haploid: having only half the normal complement of chromosomes.
• Homozygous: Having two identical alleles at a given locus.
• Heterozygous: Having two different alleles at a given locus.
• Hypothesis: The third step in the scientific method.  A statement which proposes a natural mechanism for a phenomenon, where the mechanism is amenable to test, provides explanatory and predictive power, and is conditionally held on review of further observations and experiment.  cf. theory.
• Isochron dating:  A self-checking method of dating used with several radioisotopes.  This mechanism compares ratios of radioactive isotopes to their decay products.
• Locus: The location of a gene on a chromosome. At any locus there can be many different alleles in a population, more alleles than any single organism can possess. For example, no single human can simultaneously carry the A, B and an O blood-type allele.
• Macroevolution:  Evolution at or above the species level. The boundary between macro- and micro- is fuzzy, as some researchers prefer to include speciation in micro- and others reson that the only macro- process that gives distinctive events is speciation. Speciation events are thus, to many scientists, examples of macroevolution.  Another definition is  evolution too imperceptible to be observed within the lifetime of one researcher .
• Meiosis: A process which converts a diploid cell to a haploid gamete, and cause a change in the genetic information to increase diversity in the offspring.
• Metazoan: A fancy term for "multicellular animals"
• Microevolution:  Evolution within the species level, or a change in allele frequency in a population over time. Note that this connotation is equivalent to evolution. All "Scientific Creationists" so far admit that microevolution is observed. Some Theistic Anti-Evolutionists may not.
• Modern Synthesis: Modern Synthesis is a theory about how evolution works at the level of genes, phenotypes, and populations whereas Darwinism was concerned mainly with organisms, speciation and individuals.   Modern Synthesis differs from Darwinism in three important aspects: 1.  It recognizes several mechanisms of evolution in addition to natural selection. One of these, random genetic drift, may be as important as natural selection.  2. It recognizes that characteristics are inherited as discrete entities called genes. Variation within a population is due to the presence of multiple alleles of a gene.  3.  It postulates that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution.
• Multiplication of species: The theory that species multiply, either by splitting into daughter species or by "budding", that is, by the establishment of geographically isloated founder populations that evolve into new species.  cf. cladogenesis.
• Mutation:  An error in duplication of genetic material which results in a different sequence of and/or a different number of base pairs in the copy than were in  the original. Mutation creates new alleles.
• Natural selection: The differential reproduction and, thereby, transmission of alleles between generations, of individuals in a population, due to heritable variation in a trait or traits which they possess. This is one mechanism by which evolution can occur.
• Observation:  This is the first step in the scientific method.  The scientific method is founded upon direct observation of the world around us. A scientist looks critically and attempts to avoid all sources of bias in this observation. But more than looking, a scientist measures to quantify the observations; this helps in avoiding bias.
• Peripatric speciation: A theory of speciation which states that a population of an ancestral species in a geographically peripheral part of the ancestral range is modified over time until even when the ancestral and daughter populations come into contact, there is reproductive isolation.
• Population: A group of organisms, typically a single species, and typically isolated from other members of its species in some manner.
• Prediction:  Step four in the scientific method.  The prediction is a formal way to put a hypothesis to a test. If you have carefully designed your hypothesis to be sure it is falsifiable, then you know precisely what to predict. The prediction has three parts: 1. If my hypothesis is true...  2. Then _____ should happen ... 3. When _____ is manipulated.  The manipulation is what you knew would likely falsify your hypothesis.
• Proposition: A statement which can be either true or false, as opposed to interrogative, exclamatory, or imperative sentences. See also: belief, unbelief, disbelief.
• Punctuated Equilibria: An evolutionary mechanism theory that contains the following features:  [ Note: This "definition" is from the punctuated equilibria FAQ on the talk.origins archive site.   I don't pretend to understand all of it. :) ]
1. Paleontology should be informed by neontology.
2. Most speciation is cladogenesis rather than anagenesis.
3. Most speciation occurs via peripatric speciation.
4. Large, widespread species usually change slowly, if at all, during their time of residence.
5. Daughter species usually develop in a geographically limited region.
6. Daughter species usually develop in a stratigraphically limited extent, which is small in relation to total residence time of the species.
7. Sampling of the fossil record will reveal a pattern of most species in stasis, with abrupt appearance of newly derived species being a consequence of ecological succession and dispersion.
8. Adaptive change in lineages occurs mostly during periods of speciation.
9. Trends in adaptation occur mostly through the mechanism of species selection.
• Question: The second step in the scientific method is to formulate a question.  The question must be answerable.  "Why am I here?" is not a question that is answerable by science.
• Recombination:  Recombination creates new combinations of alleles.  Recombination primarily occurs through sexual reproduction, where diploid cells form haploid gametes.  The organism inherits one gamete each from the mother and the father, and the gametes  are 'recombined' to form a new diploid chromosome.  Recombination can occur not only between genes, but within genes as well. Recombination within a gene can form a new allele.  (cf. mutation ) Recombination is a mechanism of evolution because it  adds new alleles and combinations of alleles to the gene pool.
• Reproductive Isolation: Isolation of one species or  population from another species or population by differences in reproductive traits or habits.  The two species or populations may or may not share the same environmental range.  An example of two species being reproductivly isolated are similar species of animals that breed at different times of the year.
• Scientific Creationism:  The belief that scientific evidence supports the literal factuality of the first eleven or so chapters of the book of Genesis in the bible, in contradiction to evolutionary mechanism theories. This is derived from early sources of the term; later ones try to dissociate  "scientific creationism" from "biblical creationism" by the expedient course of not actually mentioning the Bible when discussing "scientific creationism".  "Scientific Creationists" are distinguished by two features from the theistic anti-evolutionists:  "Scientific Creationism" is associated only with literal inerrantist interpretations of Genesis, and "scientific creationists" take a proactive stance on pushing their conjectures into secondary school science classrooms as science alongside or in replacement of evolutionary mechanism theories.
• Scientific Method:  Science can be defined as "a methodical approach to the acquisition of knowledge." This distinguishes how a scientist works from how other people learn about the world. Science is an approach that is methodical, and that approach helps acquire knowledge. Science is not the knowledge gained through the approach. Knowledge can be gained through a variety of ways, but science acquires knowledge methodically.   The scientific method can be described as having seven steps: 1. Observation;  2. Question;  3. Hypothesis;  4. Prediction;  5.  Experiment;  6. Analysis;  7.  Decision.  The end result of the scientific method is either a rejected hypothesis, or a supported hypothesis.   A hypothesis that has gathered enough supporting observations and experimental results is a theory.
• Sexual reproduction: Formation of new individual by a combination of two haploid sex cells (gametes).  Sexual reproduction combines the genetic information from two separate cells that have one half the original genetic information.  Gametes for fertilization usually come from separate parents 1. Female: produces an egg  2. Male: produces sperm.   Both gametes are haploid, with a single set of chromosomes. The new individual is called a zygote, with two sets of chromosomes (diploid).  cf. Asexual Reproduction
• Shifting Balance Theory:  Sewall Wright's 'Shifting Balance' theory argues that  populations are often divided into smaller subpopulations. Drift could cause allele frequency differences between subpopulations if gene flow was small enough. If a subpopulation was small enough, the population could even drift through fitness valleys in the adaptive landscape. Then, the subpopulation could climb a larger fitness hill. Gene flow out of this subpopulation could contribute to the population as a whole adapting.
• Species:  Highly controversial term given a variety of definitions by biologists. Currently, the Biological Species Concept (BSC) is widely popular: Groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups (Mayr, 1963, Animal Species and Evolution).
• Speciation: The event of one species dividing into two species. cf. anagenesis, cladogenesis
• Theism: Refers to the position of belief in a God or gods. Some more  narrowly-construed versions of belief in God include: monotheism (belief in one God), polytheism (belief in two or more gods), pantheism (belief that God is everything), and deism (belief in a God which created the universe, but does not "interfere" with it; or, alternatively, is not all-powerful).  cf. atheism, agnosticism
• Theistic Anti-Evolutionist: Any person who expresses opposition to evolutionary mechanism theories when motivated by religious doctrine, as contrasted with those who propose alternative hypotheses and theories within the framework of the scientific method. The  theistic anti-evolutionist  tends to confuse evolution and evolutionary mechanism theories, which typically results in the theistic anti-evolutionist making specific criticisms of a particular evolutionary mechanism theory while asserting that all evolutionary mechanism theories are affected.
• Theory:  A statement which proposes a natural mechanism for a phenomenon, where the mechanism is amenable to test, provides explanatory and predictive power, is conditionally held on review of further observations and experiment, and has accumulated supporting observations and experimental results.  cf. hypothesis, scientific method.
• Unbelief: The position of not believing a proposition. This is distinct from disbelief in that it does not assert that the proposition is false; rather, it merely states that there is no good reason to assert that it is true or false. Unbelief is, in essence, a position of suspension of judgment on a matter, and as such does not bear any burden of proof.  cf. belief
• Vegetative Reproduction: cf. Asexual Reproduction