Jamniczky, H.A., Biological Pluralism and Homology, Philosophy of Science, Vol. 72, No. 5, Proceedings of the 2004 Biennial Meeting of The Philosophy of Science Association, Part I: Contributed Papers, Edited by Miriam Solomon (December 2005), pp. 687-698

The use of multiple, explicitly articulated homology concepts, applicable at different levels of the biological hierarchy, allows a more thorough investigation of the nature of biological similarity. Responsible epistemological pluralism as advocated herein is generative of fruitful and innovative biological research, and is appropriate given the metaphysical pluralism that underpins all of biology.
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The term ‘homologue’ was first formally defined as 'the same organ in different animals under every variety of form and function' (Owen 1843). (..) There has since been considerable debate over the exact meaning of the terms ‘same’, ‘organ’, ‘form’, and ‘function’ in the formulation of homology concepts by biologists in different fields, but these concepts remain among the most important theoretical tools in the biological sciences.
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Many continue to take a monistic approach to homology, searching for a single homology concept that is applicable to all disciplines within biology (Patterson 1982; van Valen 1982; Roth 1988; Bock 1989; Wagner 1989; Haszprunar 1992; Young 1993; Nelson 1994; Abouheif 1997; Brigandt 2002).
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The list of authors who advocate a pluralistic approach to homology is substantially and strikingly shorter (Striedter and Northcutt 1991; Sluys 1996; Minelli 1998), but also interesting in that some previous advocates of monistic approaches to homology have recently begun to suspect that pluralism may be more appropriate (Wagner 2000; Brigandt 2003).
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The goal of the present project is to argue for epistemological pluralism in understanding and describing homology (..) such an approach is more compatible with the fundamentally pluralistic nature of biology (Kitcher 1987; Dupre´ 1993; Mitchell 2003).
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there have been an enormous number of homology concepts proposed, and these can be broadly grouped into phylogenetic, developmental, and hierarchical accounts
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while these accounts are functional in the domains in which they were developed, attempts to extend their scope beyond their original bailiwicks are highly problematic. I argue that this failure is symptomatic of the pluralistic nature of biology
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The pluralistic approach to homology advocated herein is founded upon both epistemological and metaphysical considerations, and as such is a cogent example of the critical, integrative pluralism advocated by Sandra Mitchell (2003).
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The success of many homology concepts within their domains, and their concomitant failure in other domains, indicates that epistemological pluralism is warranted.
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There is no fundamental characteristic of organisms or biological phenomenon that can be extracted and given precedence over any other (Kitcher 1987; Dupre´ 1993). Biology is, therefore, a pluralistic science
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Darwin (1859): while natural selection may be the main mechanism by which organisms evolve, it is not the only factor at work. Rather, a plurality of factors comes into play, and often these do not act in concert with one another (Gould and Lewontin 1979).
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Case Study: Lens Induction in Anurans (frogs and toads). Analysis of a biological example illustrates the intricacies and complications of homology in biology. (..) a number of anuran species are able to generate a lens in the absence of an optic vesicle (..) different series of inductive and suppressive interactions, and the influence of tissues as diverse as the neural plate and heart mesoderm, are responsible for lens formation in various anurans, and that the optic vesicle plays only a supportive role in lens development (Jacobson and Sater 1988). (..) A complete picture of biological phenomena thus requires multiple homology concepts.
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If a homology concept does not include an explicit definition, operational criteria, and independently testable hypotheses of causality, then the utility of the concept as a whole is compromised.
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The standard objections to pluralism are that it is relativistic and subjective, and as such can lead only to confusion, ambiguity and problems of communication. (..) The approach to homology presented here is emphatically not an ‘anything goes’ proposal, and requires explicit and responsible articulation of the definition, criteria, and causes associated with any homology concept.
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A pluralistic approach, rather than being relativistic, subjective, and generative of chaos, will bring a new richness of perspective and will open new areas and directions for biological inquiry.