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.
In his Metamorphosis of Plants, Goethe identified serial homologies in plants. This is also known today as homotypy and serially repeated parts are called homotypes. Goethe seems to have been the first to hit upon the idea that the skull is composed of a number of vertebrae, serially homologous with those of the vertebral column.
"It was one thing to assert in a moment of inspiration that the skull was composed of modified vertebrae; it was quite another to demonstrate the relation of the separate bones of the skull to the supposed vertebrae." ( Russell, Form and Function, p. 97)
Although there are many points of similarity, German Naturphilosophie and French "philosophical anatomy" are separate traditions. Perhaps the distinguishing feature of Naturphilosophie and of dialectics is the search for rational laws which are active in nature, the discontent with merely empirical laws. Despite his transcendentalism, Geoffroy was primarily a morphologist, while the Germans, under the influence of Schelling and Hegel, were transcendental philosophers first and morphologists after. (Russell, p. 100) (see natural form)
In the Twentieth Century, the concept of a coherent body-plan (type) has been reformulated in less idealistic terms. J.H. Woodger uses the term Bauplan to define a common structural plan with identical systems of relations rather than "type" or "schema" . (see "The concept of organism", Quart. Rev. Biol.5, 1-22 (1930) and "On Biological Transformation" in Essays on Growth and Form) This shift in vocabulary parallels the rhetorical oppositions between "building" and "architecture" proposed by twentieth-century architects like Mies van der Rohe. Structuralism revived the notion of homology in the study of culture. Thus Levi-Strauss, in his discussions of totemism, stressed internal homologies over external ressemblance. ("A correspondence of relations does not amount to a becoming." D+G)
Darwin retained Owen's definition of homology -- a morphological correspondence determined primarily by relative position and connection. He used the concepts of homology and Bauplan but turned classification into a phylogenetic account through his theory of evolution. In Darwin's evolutionary framework, material ancestors replaced metaphysical archetypes. The origin of the species is to be found in "the ancient progenitor, the archetype as it may be called..." But in the Darwinian framework, a tension still exists within the definitions of the term. Is homology to be defined as similarity? Or is it only to be defined as ancestry?
In its more extreme neo-Darwinian formulation, the concept of homology is totally absorbed into a geneaological one. But even within modern developmental biology, competing defintions of the term of "homology" expose conceptual tensions among scientists -- since common ancestry and similarity do not always coincide, and the primary work of biologists is to look for structural patterns, and perhaps to assume ancestry, but not actually to look for it. (?) Contemporary arguments for a "science of form" that would follow from D'Arcy Thompson, Bateson, and Driesch... criticize neo-Darwinians for losing all interest in morphological similarities.
(see population / typological)
Obapina , from Gould, Wonderful LifeSome contemporary accounts of homology relate it to developmental pathways rather than inheritance. Brian Goodwin believes that attention to the generative dynamics underlying morphogenesis will allow a return to "the original definition of homology": "an equivalence relation on a set of structures, partitioning the set into classes whose members share certain invariant internal relationships and are transformable one into the other while preserving the invariance." ("Development and evolution," Journal of Theoretical Biology 97; 43-45, quoted in Michael J. Donoghue, "Homology," in Keywords in Evolutionary Biology.) As Donoghue observes, "In this context, 'transformation' is not to be interpreted in historical terms, but instead refers to the possibility of deriving one structure from another in a formal, atemporal sense. If not for the difference in motivation, Goodwin could easilty be allied with those who hold a classical or phenetic view of homology." (p. 178) (what is relation between Goodwin's transformations and D'Arcy Thompson's "cartesian mappings?)
The concept of homology articulates a relationship between human inquiry -- the comprehensible order which systematic thought depends upon -- and the exploration of the complexities and accidents of the natural world. (these are the types of questions that Kant so deftly handled) Definitions of homology vary in response to challenges and conceptual change, but the term occupies a strategic point between conceptually structured observation and scientific theory.
Part of the method of biological thought is to develop hypothetical hierarchies based on homologies and to test them against the available information. Are empirical taxonomies "classificatory preparation for the knowledge of the rational in the forms of nature?" (Driesch, 1914, p. 140) Is the concept of rational morphology a purely epistemic one or is it ontological as well? Or is the question totally secondary to issues of geneaology?
One reason for the particular importance of homology in comparative biology may lie in the relatively few body-plans in existence today. In modern phyla species proliferate within a few stereotypical designs. In Wonderful Life, Stephen J. Gould's recounts the story of the analysis the Burgess Shale, the major source of fossil information on the Cambrian explosion. In this account, modern species descend from only a small fraction of profoundly different organisms that have lived at other times, and the reasons for the survival of some and not others may be far more accidental than theories of adaptation would suggest.
The rise of "organic structure," no longer part of a system of visibilities, is described by Michel Foucault, in The Order of Things, as a move away from representation. (Chapt. 7) see organicism.