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Critique of Intelligent Design

Evolution vs. Creationism

The Art of ID Stuntmen

Faith vs Reason

Anthropic Principle

Autopsy of the Bible code

Science and Religion

Historical Notes


Serious Notions with a Smile


Letter Serial Correlation

Mark Perakh's Web Site

29+ Evidences for Macroevolution


Copyright 1999-2003 by Douglas Theobald, Ph.D.

abiogenesis Not to be confused with "spontaneous generation," it is the theory that life originally arose from non-living matter, given the proper conditions during the early earth.

analogy The case of similar function despite different structures; the opposite of parahomology. Similar to the evolutionary concept of convergence.

character A feature or trait of an organism. Characters have a specific structure and function.

cladistics A method for constructing phylogenies based on shared derived characters of species, originally rigorously detailed by Willi Hennig in 1950.

convergence Convergence is an amorphous evolutionary term that is used in somewhat different senses by different authors (or even by the same people at different times). It generally refers to similarities between organisms that evolved independently, i.e. similarities not directly inherited from a common ancestor. Convergent similarities can involve structure, form, and function. Strict convergence of both function and structure is very rare, except in trivial cases. Convergence of form and function is common, and is a direct prediction of the theory of natural selection. In a sense, convergence is the opposite of homology.

derived characters Among a given group of organisms, the shared derived characters are generally the less common characters. The evolutionary interpretation is that these characters of organisms are more recently evolved. They are contrasted with primitive characters. Shared derived characters should have the same structure and function.

function The function concept is complex. Functions are not simply anything that appears "useful"; this is a subjective teleological notion. An objective definition of function is any identifiable process performed by a biological entity that is necessary for the successful reproduction of that entity. A function of a certain structure is a particular consequence of that structure responsible for that structure's continued existence in terms of reproductive success. Functions are relative; some similar structures function better than others. If structure A results in better reproductive success than another similar structure B, then structure A is more functional than B. Thus, function depends on context; gills have no function on land and lungs do not function underwater. Also, sometimes it is necessary to infer the function of a character based on its form (e.g. pterodactyl wings were used for flight) (Wright 1973; Cummins 1975; Millikan 1989; Reeve and Sherman 1993). In general the functionality of a given structure can be experimentally measured and quantified (a common practice in genetics).

homology In this essay, since we are not assuming the truth of common descent, "homology" simply refers to similar structures, regardless of function. In evolutionary biology, structures are homologous only if they were derived from the same structure in a common ancestor. "Homology" in evolutionary practice is thus a hypothesis which can be tested, and which can garner various levels of evidential support (primarily taking into account all available phylogenetic evidence). Importantly, there exist multiple levels of homology in biology. What is evolutionarily homologous at one level may not be so at a lower level or at a higher level (Dickinson 1995). The causal chain in biology is discontinuous, including genes, genetic networks and pathways, cells, cell types, developmental pathways, organs, and organisms. Though each level is dependent upon the preceding level, functions at one level can be redundant (due to the stochastic and opportunistic nature of evolution), and thus functions are occasionally free to shift, resulting in uncoupling between levels of homology. This fact has caused some confusion in practice for the precise application and delineation of the homology concept. For example, the genes which control the development of eyes are homologous between vertebrates and invertebrates, yet the organs (the eyes themselves) are not (i.e. they evolved convergently into very different structures having somewhat similar functions). Also see parahomology, analogy, and convergence.

intermediate form A fossil or modern species that displays characters definitive of two or more different taxa or that displays characters morphologically intermediate between two different taxa. The existence of intermediate forms is a prediction of common descent. An intermediate is not necessarily a common ancestor or even an actual ancestor of a modern species. For example, the intermediate species Archaeopteryx displays characters definitive of two different taxa (e.g. dromaeosaur dinosaurs and birds), yet Archaeopteryx is probably not an ancestor of modern birds.

macroevolution Evolution on the grand scale resulting in the origin of higher taxa. In evolutionary theory it thus entails common ancestry, descent with modification, the genealogical relatedness of all life, transformation of species, large scale functional and structural changes, etc.

microevolution Change within species; relatively minor change in the composition of a species' gene pool with time.

ontogeny The development of an individual organism, especially the process studied in the science of embryology.

parahomology In non-evolutionary terms, similarity of structure despite difference of function; the opposite of analogy. The proper evolutionary interpretation of parahomology would refer to only homologous characters (at a specified biological level) which had diverged in function. Nota Bene: In this essay, I use the nonstandard term "parahomology"; it is a term I invented. This is necessary for two reasons. First, the standard homology argument for evolution is primarily based upon structures that are similar between organisms but have different functions. In contrast, the evolutionary concept of homology includes all corresponding structures inherited from a common ancestor, regardless of whether they have the same or different functions. To clarify the homology argument, then, a new and specific term is needed that refers to the subset of homologous structures that have different functions. Second, the standard homology argument can be criticized as being circular. Now that common descent is accepted as scientific fact, it is only logical to redefine homology in terms of common descent, as opposed to the original definition of homology that had no evolutionary basis. Modern evolutionary biologists define homology in this way (even though they use independent methods to infer homology). Thus it is fallacious to use the redefined evolutionary homology concept as evidence for common descent. In contrast, the parahomology concept, as used here, is defined independent of common descent and can be recognized in organisms regardless of whether one accepts evolutionary theory or not. Of course one could define homology similarly, but using a different term avoids the confusion of multiple definitions.

phenotype The morphological, physiological, biochemical, behavioral, and other properties of an organism, manifested throughout its life.

phylogeny A genealogy of species; the history of descent of taxa from common ancestors, including the relative times at which species branched or diverged from each other.

primitive characters Contrasting with derived characters, they are the more common shared characters of a given group of organisms. Like derived characters, they also have the same structure and function. The evolutionary interpretation is that these characters evolved earlier than derived characters.

species As usually used within this article, a species is a reproductively isolated group of organisms capable of interbreeding in the wild and producing viable, fertile offspring. This is known as the Biological Species Concept (BSC). An alternative statement of the BSC defines a species as the most inclusive group of sexual and cross-fertilizing individuals which share a common gene pool. However, this concept breaks down for asexual species, fossil species, and even sexual species in many cases. In reality there are only degrees of reproductive and genetic isolation, so species are not absolute entities. Joseph Boxhorn has given a more detailed analysis of the species concept in the "Observed Instances of Speciation" FAQ. Note, the BSC has interesting implications for the nature of the last universal common ancestor of all life, especially if horizontal genetic transfer was extensive then (as it is today between the different unicellular "species" of bacteria, archaea, and eukaryotes).

structure Relative position and shape of an organism's various parts; the pattern underlying its form. Similar structures have similar positions and shapes of parts; however, relative size can vary considerably. Should not be confused with "form." A bat and insect wing both have similar forms (e.g. they are both elongated and flat and can be flapped), but they have very different underlying structures.

transitional form See intermediate form.

vestigial characters A vestigial character is reduced and rudimentary compared to the same complex structure in other organisms. Vestigial characters, if functional, perform relatively simple, minor, or inessential functions using structures that were clearly designed for other complex purposes. The most extreme test for vestigiality is to remove the character and observe the organism's viability and reproductive success. If these remain unchanged, the character is definitively vestigial. However, vestigial characters can certainly have functions; non-functionality is not a requirement.


Cummins, R. (1975) "Functional Analysis." Journal of Philosophy 72: 741-765.

Dickinson, W. J. (1995) "Molecules and morphology: where's the homology?" Trends Genet. 11: 119-121. [PubMed]

Millikan, R. (1989) "In defence of proper functions." Philosophy of Science 56: 288-302.

Reeve, H. K. and Sherman, P. W. (1993) "Adaptation and the goals of evolutionary success." Quarterly Review of Biology 68: 1-32.

Wright, L. (1973) "Functions." Philosophical Review 82: 139- 168.

Full references