The concept of homology, or morphological correspondence, was the central tenet of philosophical anatomy. It was used to define structural similarity. Homologies, which are now defined in terms of evolution, were formerly interpreted in a transcendental sense. Whereas homologous parts are now considered to have descended from a common ancestor, in the pre-Darwinian era they were usually looked upon as evidence of an ideal pattern imposed on nature, or a blueprint in the mind of the creator.
At stake in the question of homology is the idea of a "rational morphology" that would provide a systematic unification of diversity. Homology is a systematic similarity -- when two parts occupy the same positions in distinct but otherwise isomorphic systems of relations, in their relative positions and in the connection of the parts. This conceptual reduction to schematic identity enables comparisons between organisms in terms of their similarities and difference. It can be extended into embryological studies and forms the basis for taxonomic grouping.
For Geoffroy St Hilaire and other philosophical anatomists, homologous parts were those parts in different animals which were essentially " the same" -- even though the parts might have different shapes and be employed for different purposes. (In this sense, homology works like geometrical similarity -- see scientific space). Geoffroy was particularly acute in his insistence that it was plan, rather than function, that identified both organisms and their parts. (We can give this claim the slogan "function follows form".) Geoffroy intended homologies to be interpreted in ideal rather than real and physical terms. He focussed his efforts on the skeletal system, and the connections of the parts, considering them in abstraction as "materials of organization." (see Toby A. Appel, The Cuvier-Geoffroy Debate) Geoffroy fought for the idea of a "rational unity," declaring all distinctions into class and species to be nothing but fiction. He attempted to formulate the basic principle of comparison in his "Principle of Connections" and "Principle of Composition," referring respectively to position and structure. He also claimed that the forms produced by perturbations to a natural system (although these would not have been his words) are determined by the "typical" or characteristic instrinsic powers of the being. (see also E. Russell, Form and Function, 1916)
Deleuze and Guattari interpret Geoffroy's search beyond organs and functions to abstract elements he terms "anatomical" as a pure plane of immanence, a single abstract Animal for all the assemblages that effectuate it. (1000 plateaux, p.255) For Geoffroy, all instances of a type are modifications of "one single being, of that abstract being or common type, which it is always possible to denote by the same name." "From this standpoint, there are no different animals. One fact alone dominates; it is as if a single Being were appearing." For Deleuze, "Geoffroy Saint-Hilaire...remains one of the greatest philosophers of organic folding." (The Fold, p.144 n. 25) "Given the modifications of a same Animal, he esteems that one can still move from one to the other by way of folding (a unity of the plan of composition.)
The modern distinction between "homologue" and "analogue" was established by Richard Owen in 1843. Owen defined an analogue as "a part or organ in one animal that has the same function as another part or organ in a different animal," while a homologue is "the same organ in different animals under every variety of form and function." (Lectures on Invertebrate Animals, pp 374,379, 1843.) Thus the leg of a crab or insect is "analagous" to the limb of a quadruped, because they all serve for locomotion, but they are not "homologous." Homologous organs have similar structure or bear similar relations to other organs, whereas analagous organs have similar functions. (see metaphor for another set of meanings for analogy.)
Owen distinguished between Special, General, and Serial Homology.
Special homology followed the description above, the correspondence of part or organ indicating construction on a common plan, or archetype, "on which it has pleased the divine Architect to build up certain of his diversified living works." (p. 73)
General homology is a higher or defining relation between the parts and the concept of the type.
Serial homology, following Goethe, are homologies of parts within a single individual.