Abstract
The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis.
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Notes
In this paper I will bracket issues regarding classification and taxonomy. My concern is with the character analysis and the phylogenetic analysis of cladistic inference.
Moreover, both can be descriptive as well as normative. Indeed, the project of this paper is ultimately normative. The objectivity criteria developed in Sect. (6) are gleaned from good practice and are norms for how a cladist should engage in proper character analysis. (I thank Elliot Sober for pushing me on this.)
Although I am one of its defenders, the latter interpretation of the co-construction of epistemology/methodology and ontology is, strictly speaking, optional for the argument of this paper. For instance, a strong philosophical realist who distinguishes epistemological from ontological matters (e.g., Devitt 1991) can still read this paper for insight into how scientists go about discovering characters that exist in the world independently of science. Under this realist light, practice-based investigations of scientific reasoning are useful particularly because they indicate the myriad ways in which biased scientists produce representations that deviate from a true or ideal description of the world. Some strong realists (“the world is difficult to know” realist) could then find my project interesting because it gives us a handle on the many difficulties we always encounter in the discovery process. Other strong realists, however, would of course be free to downplay my project because it does not address ontological questions directly (whatever exactly that would mean), either in science or in a philosophical rendition of science, but instead “conflates” ontological and epistemological matters by focusing on practices. A final note in this context. Strong realism is not the only sort of theory-based philosophical analysis available. Other sorts of theory-based investigations insist on a much more nuanced relation—social, Kantian or otherwise—between epistemology/methodology and ontology (e.g., Kuhn 1970; Goodman 1978; Putnam 1981; Friedman 1999). Thus, the (i) theory-based versus practice-based philosophical analysis distinction is emphatically not co-extensive, let alone identical with, the (ii) epistemology/methodology versus ontology dichotomy on which the strong realist intently insists. That is, a theory-based investigation need not be premised on distinction (ii).
Strictly speaking, there is an important link between character analysis and phylogenetic analysis: character coding. That is, even once we have abstracted characters and character-states, we need to write them out in proper form for a data matrix. There is significant debate regarding the best way to formalize characters: e.g., whether we should use “present” / ”absent” or focus primarily on positive statements of character-state properties [e.g., Pleijel 1995; Fitzhugh 2006, 2008 (see options A-F on p. 275 of 2006); Sereno 2007; see also Freudenstein 2005 who usefully distinguishes characters from character-states in terms of their exhibiting either “paralogous” or “orthologous” relationships (sensu Fitch 1970), respectively, with other characters or character-states; the titles of Pimentel and Riggins 1987 and Hawkins 2000 suggests that they will write about primary homology assessment, but in fact they each end up addressing character coding]. Character coding as a problem is clearly important, but well beyond the scope of this paper as it concerns the link between character and phylogenetic analysis, rather than character analysis sensu stricto. Put differently, I am concerned with the abstraction and reification process that occurs prior to writing out the characters and character-states in the data matrix. Of course, I realize that the two problems (i.e., “primary homology”/character assessment problem, and coding problem) are not independent (e.g., Stevens 2000), but conceptual progress can still be made by focusing exclusively on the former. And certainly the former cannot be reduced to the latter (contra Fitzhugh and Sereno)! Another issue I will not address here is the polarization of characters (e.g., Patterson 1982; Nixon and Carpenter 1993; Brusca and Brusca 2003). Since methods of polarization (e.g., outgroup comparison) do not affect the nature or quality of the characters, but attend to which of two or more character-states is postulated to be ancestral/synapomorphic (a topic crucial to phylogenetic, but not character, analysis), this important topic is not germane to this article.
The establishment of the polarity of a character state—i.e., the determination of a particular state as either ancestral or derived—is done through ontogeny or outgroup comparison, or both. Under ontogenetic analysis, the character state that appears first during development is considered the primitive character state (e.g., a two-chambered as opposed to a four-chambered vertebrate heart). Under outgroup comparison, the character state that is most frequent in groups other than the ones being investigated is considered the primitive state (see Radinsky 1987, p. 6).
A word about “true System or Tree” or “true cladogram”. As argued in Sect. 2, I adopt a sort of epistemically-conditioned realism here, rather than an instrumentalism. However, the argument in this section goes through regardless of one’s commitments in the realism debates. There is presumably a fact of the matter about the pattern and process of the evolution of life; there is presumably a true System or Tree. This is so regardless of how difficult it is to infer it or whether there is an “irreducible” human-abstraction component to it. I trust that the reader will grant this. (See Vergara-Silva, this issue, for discussion and healthy skepticism about such a view.) Now, given that there is a fact of the matter about patter and process, do we need to use explicit methodologies and criteria for character analysis in order to get close to this cladogram? This paper argues that we should and can have recourse to objectivity criteria for character analysis (or else we will miss the mark). In contrast, many others (solution 1, see below) argue that even granting the in principle existence of a true cladogram, explicit criteria are not necessary in our search for it. A final point. I am here concerned specifically with those regions of the universal history of life where cladistic assumptions hold (e.g., vertical inheritance and branching modification with descent, as is the case for chordate evolution). It is at best unclear what the true System or Tree would be for domains of the history of life (e.g., early microbial evolution) where cladistic assumptions do not hold in particular because there is horizontal gene transfer (e.g., Woese 2000; Doolittle and Bapteste 2007; O’Malley and Dupré 2007). I bracket this important issue here.
Mishler (2005, p. 665) provides a useful “pro and con” table for molecular and morphological data. Molecular data have at least two disadvantages: they have neither “complexity and comparability” nor “many possible character states.”
I have not employed the interesting character rejection criteria from Poe and Wiens (2000) (see also Sereno 2007), such as high character variation or substantial missing data, because their criteria do not get at primary homology claims or character analysis as such. Rather, they are investigating something more like character coding (see note 4 above). Stevens (1991, 2000) discusses some of the reification problems entailed by such criteria.
And, I suspect, reification, but showing that would be part of another project.
I realize that some will disagree because they will only want to make “secondary homology” and “character” co-extensive, under the cladistic paradigm. I will simply say that the motivation for employing objectivity criteria is that they give us good characters—i.e., ones that are highly likely to be synapomorphic. Recall [Sect. 3] that I take issue with those who abstract any character whatsoever, without applying the objectivity criteria. Put differently, using objectivity criteria brings primary homology claims closer to secondary homology affirmations.
They could be considered homologous at a higher level of resolution: qua vertebrae of vertebrates, in general. Rieppel and Kearney 2006 make this exact point (p. 101). It is generally true that homology claims need to be relativized to a particular level of comparison: e.g., bird and bat wings are not homologous qua wings, but they are homologous qua tetrapod limbs. For the purposes of this paper, and for stipulating the same “character”, I will focus primarily on low, concrete levels of resolution (e.g., wings rather than tetrapod limbs) and will not further discuss this important issue.
This is also the case for molecular characters. These also receive biological meaning from investigations into the causal reasons (in historically-conditioned genetic systems) for sequence similarity.
Note that this criterion is pragmatic as well as epistemic, sensu stricto. That is, it concerns both (1) the practices of discovering and developing primary homology claims, as well as the use and usefulness of such claims (pragmatic), and (2) the truth of primary homology assertions [i.e., the truth relation between character claims and the (potentially co-constructed) world] (epistemic). (On epistemic versus pragmatic virtues, see, e.g., van Fraassen 1980.) That this criterion is pragmatic should be evident (Sober, personal communication). But I argue that it is also epistemic. Consider the following gross idealization of the practice of character analysis: each phylogenetically-relevant discipline produces its own list of characters. For instance, comparative morphology, molecular genetics, and developmental biology have different “partitioning frames” (Winther 2006c) and each therefore articulates a different list. Given these lists, inter-disciplinary communication has at least two aims. First, it attempts to find the characters that are shared across disciplinary contexts. It thereby produces a collated list of strongly empirically adequate characters—i.e., of robust characters. Since the empirical adequacy of a shared character is bolstered through inter-disciplinary communication, this criterion has epistemic weight. Second, communication aims to identify the empirical relations among characters that are not shared across contexts (e.g., causal or common-cause relations). Discovering relations among non-shared characters also increases the empirical adequacy of the total inter-disciplinary list of characters. Again, inter-disciplinary communication is epistemically relevant.
Although I cannot argue for this further here, the indeterminacy and the under determination of rule application is a generalized worry relevant to all of science. Despite indeterminacy and under determination—explored by Quine, Goodman, and “Kripkenstein”, as well as other philosophers—scientists productively employ rules, heuristics, and methodology that allow science to progress. This suggests that the strong skepticism about rule application and rule existence entertained by Richards is unwarranted.
It is important to note that Quine was a thoroughgoing empiricist and naturalist. That is, he was skeptical about the analytical role, even coherence, of notions like “cause”, “disposition” or “the real”. And yet, he felt that science was progressing—its inductions were to a large extent successful. I will not delve further into important and finer points of Quine scholarship.
Richard Boyd (1999) also has an account of how natural kinds can be grounded causally (mechanistically). Although his “homeostatic property cluster kind” account differs radically with Quine and Putnam with respect to both the semantic tightness of the intension, and the uniformity of the extension, of natural kind terms, he shares their view that (a broader) similarity of the extension of objects or processes of natural kinds should be explained by a causal (mechanistic) account.
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Acknowledgments
This paper emerged from multiple conversations with Olivier Rieppel. I am also grateful to Niels Bonde, Kirk Fitzhugh, David Hull, Fabrizzio McManus Guerrero, Brent Mishler, Elliot Sober, Peter Stevens, Francisco Vergara-Silva, and David M Williams for discussion and comments on an earlier draft. Springer Science and Business Media (Fig. 1), John Wiley & Sons, Inc. (Figs. 2 and 3), and University of Chicago Press (Fig. 4) kindly granted permission to reproduce original material.
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An erratum to this article can be found at http://dx.doi.org/10.1007/s10441-009-9074-0
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Winther, R.G. Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity. Acta Biotheor 57, 129–162 (2009). https://doi.org/10.1007/s10441-008-9064-7
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DOI: https://doi.org/10.1007/s10441-008-9064-7