I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

The article defends the doctrine that Linnaean taxa, including species, have essences that are, at least partly, underlying intrinsic, mostly genetic, properties. The consensus among philosophers of biology is that such essentialism is deeply wrong, indeed incompatible with Darwinism. I argue that biological generalizations about the morphology, physiology, and behavior of species require structural explanations that must advert to these essential properties. The objection that, according to current “species concepts,” species are relational is rejected. These concepts are primarily concerned with (...) what it is for a kind to be a species and throw little light on the essentialist issue of what it is for an organism to be a member of a particular kind. Finally, the article argues that this essentialism can accommodate features of Darwinism associated with variation and change. (shrink)

Classifying is a fundamental operation in the acquisition of knowledge. Taxonomic theory can help students of cognition, evolutionary psychology, ethology, anatomy, and sociobiology to avoid serious mistakes, both practical and theoretical. More positively, it helps in generating hypotheses useful to a wide range of disciplines. Composite wholes, such as species and societies, are “individuals” in the logical sense, and should not be treated as if they were classes. A group of analogous features is a natural kind, but a group of (...) homologous features is not. Imposing hypotheses justified only on the basis of nominalist, realist, phenomenalist, or conceptualist metaphysics upon the neurophysiology of organisms or upon the causes of behavior exemplifies the “psychologist's fallacy” of William James. Levels should be distinguished from their members and from classes of levels, and the ontological status of entities ranked at levels should be made clear. It is important not to confuse such categories as substance and process with one another. Several genetical terms, such as “gene” and chromosome,” are even more equivocal than has been realized. Discussions about units of selection, behavior, and thinking suffer from the ambiguity of a “unit of” an entity. An important source of misunderstanding about natural selection is the habit of treating it as an “agent”: in an important sense, natural selection does not “act” at all. (shrink)

What is scientific progress? This paper advances an interpretation of this question, and an account that serves to answer it. Roughly, the question is here understood to concern what type of cognitive change with respect to a topic X constitutes a scientific improvement with respect to X. The answer explored in the paper is that the requisite type of cognitive change occurs when scientific results are made publicly available so as to make it possible for anyone to increase their understanding (...) of X. This account is briefly compared to two rival accounts of scientific progress, based respectively on increasing truthlikeness and accumulating knowledge, and is argued to be preferable to both. (shrink)

This paper takes up the cause of species pluralism. An argument for species pluralism is provided and standard monist objections to pluralism are answered. A new form of species pluralism is developed and shown to be an improvement over previous forms. This paper also offers a general foundation on which to base a pluralistic approach to biological classification.

We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with (...) the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. Much potential exists for experimental simulations and field studies of cultural microevolution, where there are opportunities to borrow further methods and hypotheses from biology. Potential also exists for the cultural equivalent of molecular genetics in “social cognitive neuroscience,” although many fundamental issues have yet to be resolved. It is argued that studying culture within a unifying evolutionary framework has the potential to integrate a number of separate disciplines within the social sciences. (shrink)

Species pluralism gives us reason to doubt the existence of the species category. The problem is not that species concepts are chosen according to our interests or that pluralism and the desire for hierarchical classifications are incompatible. The problem is that the various taxa we call 'species' lack a common unifying feature.

Pluralist and eliminativist positions have proliferated within both science and philosophy of science in recent decades. This paper asks the question why this shift of thinking has occurred, and where it is leading us. We provide an explanation which, if correct, entails that we should expect pluralism and eliminativism to transform other debates currently unaffected, and for good reasons. We then consider the question under what circumstances eliminativism will be appropriate, arguing that it depends not only on the term in (...) question, but also on the context of discussion and details of the debate at hand. The resultant selective eliminativism is an appealing compromise for various ‘pluralists’ and ‘eliminativists’ who are currently locking horns. (shrink)

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. (...) A phylogenetic species concept is advocated that uses a grouping criterion of monophyly in a cladistic sense, and a ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not. (shrink)

Race was once thought to be a real biological kind. Today the dominant view is that objective biological races don't exist. I challenge the trend to reject the biological reality of race by arguing that cladism (a school of classification that individuates taxa by appeal to common ancestry) provides a new way to define race biologically. I also reconcile the proposed biological conception with constructivist theories about race. Most constructivists assume that biological realism and social constructivism are incompatible views about (...) race; I argue that the two conceptions can be compatible. (shrink)

I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.

Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed (...) and applied styles, paradigms, and models simultaneously? I address these questions in general and for a specific case study: a brief history of systematics. (shrink)

Some plausibly necessary a posteriori theoretical claims include ‘water is H 2 O’, ‘gold is the element with atomic number 79’, and ‘cats are animals’. In this paper I challenge the necessity of the third claim. I argue that there are possible worlds in which cats exist, but are not animals. Under any of the species concepts currently accepted in biology, organisms do not belong essentially to their species. This is equally true of their ancestors. In phylogenetic systematics, monophyletic clades (...) such as the animal kingdom are composed of an ancestral stem species and all of its descendants. If the stem species had not existed, neither would the clade. Thus it could have been the case that all the organisms which actually belong to the animal kingdom might have existed yet not have been animals. (shrink)

I adopt a cladistic view of species, and explore the possibility that there exists an equally valuable cladistic view of organismic traits. This suggestion seems to run counter to the stress on functional views of biological traits in recent work in philosophy and psychology. I show how the tension between these two views can be defused with a multilevel view of biological explanation. Despite the attractions of this compromise, I conclude that we must reject it, and adopt an essentially cladistic (...) conception of biological traits. (shrink)

There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by relying on (...) abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains, providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together. (shrink)

A number of authors argue that while species are evolutionary units, individuals and real entities, higher taxa are not. I argue that drawing the divide between species and higher taxa along such lines has not been successful. Common conceptions of evolutionary units either include or exclude both types of taxa. Most species, like all higher taxa, are not individuals, but historical entities. Furthermore, higher taxa are neither more nor less real than species. None of this implies that there is no (...) distinction between species and higher taxa; the point is that such a distinction is more subtle than many authors have claimed. (shrink)

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be (...) recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept. (shrink)

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary (...) developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals. (shrink)

I argue for accepting a pluralist approach to species, while rejecting the realism about species espoused by P. Kitcher and a number of other philosophers of biology. I develop an alternative view of species concepts as divisions of organisms into groups for study which are relative to the systematic explanatory interests of biologists at a particular time. I also show how this conception resolves a number of difficult puzzles which plague the application of particular species concepts.

There is no question that the constituents of cells and organisms are joined together by the part-whole relation. Genes are part of cells, and cells are part of organisms. Species taxa, however, have traditionally been conceived of, not as wholes with parts, but as classes with members. But why does the relation change abruptly from part-whole to class-membership above the level of organisms? Ghiselin, Hull and others have argued that it doesn't. Cells and organisms are cohesive mereological sums, and since (...) species taxa are like cells and organisms in the relevant respects, they, too, are cohesive mereological sums. I provide further reasons in support of the thesis that species are mereological sums. I argue, moreover, that the advocate of this thesis is committed to a form of pluralism with respect to the species concept. (shrink)

1. A Historical Look at Unity 2. Field Guide to Modern Concepts of Reduction and Unity 3. Kitcher's Revisionist Account of Unification 4. Critics of Unity 5. Integration Instead of Unity 6. Reduction via Mechanisms 7. Case Studies in Reduction and Unification across the Disciplines.

Several authors have argued that higher taxa are monophyletic homeostatic property cluster natural kinds. On the traditional definition of monophyly, this will not work: the emergence of taxon-defining homeostatic property clusters would not always correspond to unique speciation events. An alternative conception of monophyly is developed and advocated, which can accommodate the homeostatic property cluster proposal. Recent work in philosophy of science shows that it meets appropriate standards of objectivity and precision.

A few philosophers of biology have recently explicitly rejected Essential Membership, the doctrine that if an individual organism belongs to a taxon, particularly a species, it does so essentially. But philosophers of biology have not addressed the broader issue, much discussed by metaphysicians on the basis of modal intuitions, of what is essential to the organism. In this paper, I address that issue from a biological basis, arguing for the Kripkean view that an organism has a partly intrinsic, partly historical, (...) essence. The arguments appeal to the demands of biological explanation and are analogous to arguments that I have given elsewhere that a taxon has a partly intrinsic, partly historical, essence. These conclusions about the essences of individuals and taxa yield an argument for Essential Membership. Finally, I cast doubt on LaPorte’s objection to that doctrine arising from the view that a species cannot survive having a daughter. (shrink)

I spell out and update the individuality thesis, that species are individuals, and not classes, sets, or kinds. I offer three complementary presentations of this thesis. First, as a way of resolving an inconsistent triad about natural kinds; second, as a phylogenetic systematics theoretical perspective; and, finally, as a novel recursive account of an evolved character. These approaches do different sorts of work, serving different interests. Presenting them together produces a taxonomy of the debates over the thesis, and isolates ways (...) it has been productive. This goes to the larger point of this paper: a defense of the individuality thesis in terms of its utility, and an update of it in light of recent theoretical developments and empirical work in biology. (shrink)

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes (...) that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. (shrink)

This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of bacterial species due to their (...) distinctive purposes. Finally, I shall show how my argument provides a new source of defence for bacterial pluralism. (shrink)

This article defends lineage pluralism; the view that biological lineages are not a single, unified type of entity. I analyze aspects of evolutionary theory, phylogenetics, and developmental biology to show that these areas appeal to distinct notions of lineage. I formulate three arguments for lineage pluralism. These arguments undercut the main motivations for lineage monism; the view that biological lineages are a single, unified type of entity. Although this view is rarely made explicit, it is often assumed in philosophy and (...) biology. Hence, this article sheds light on this monistic assumption and shows why lineage pluralism should be adopted instead. (shrink)

Karl Popper has been one of the few philosophers of sciences who has influenced scientists. I evaluate Popper's influence on our understanding of evolutionary theory from his earliest publications to the present. Popper concluded that three sorts of statements in evolutionary biology are not genuine laws of nature. I take him to be right on this score. Popper's later distinction between evolutionary theory as a metaphysical research program and as a scientific theory led more than one scientist to misunderstand his (...) position on evolutionary theory as a scientific theory. In his later work Popper also introduced what he took to be improvements of evolutionary theory. Thus far these improvements have had almost no influence on evolutionary biology. I conclude by examining the influence of Popper on the reception of cladistic analysis. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and (...) concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)

This paper discusses a philosophical issue in taxonomy. At least one philosopher has suggested thc taxonomic principle that scientific kinds are disjoint. An opposing position is dcfcndcd here by marshalling examples of nondisjoint categories which belong to different, cocxisting classification schcmcs. This dcnial of thc disjoinmcss principle can bc recast as thc claim that scientific classification is "int<-:rcst—rclativc". But why would anyone have held that scientific categories arc disjoint in the first place'? It is argued that this assumption is nccdcd (...) in one attempt t0 dcrivc csscntialism. This shows why the csscntialist and intc-:rcst—r<-zlativc approaches to classification arc in conflict. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

Homology is a natural kind term and a precise account of what homology is has to come out of theories about the role of homologues in evolution and development. Definitions of homology are discussed with respect to the question as to whether they are able to give a non-circular account of the correspondence or sameness referred to by homology. It is argued that standard accounts tie homology to operational criteria or specific research projects, but are not yet able to offer (...) a concept of homology that does not presuppose a version of homology or a comparable notion of sameness. This is the case for phylogenetic definitions that trace structures back to the common ancestor as well as for developmental approaches such as Wagner's biological homology concept. In contrast, molecular homology is able to offer a definition of homology in genes and proteins that explicates homology by reference to more basic notions. Molecular correspondence originates by means of specific features of causal processes. It is speculated that further understanding of morphogenesis might enable biologists to give a theoretically deeper definition of homology along similar lines: an account which makes reference to the concrete mechanisms that operate in organisms. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

Recent work in the philosophy of scientific concepts has seen the simultaneous revival of operationalism and development of patchwork approaches to scientific concepts. We argue that these two approaches are natural allies. Both recognize an important role for measurement techniques in giving meaning to scientific terms. The association of multiple techniques with a single term, however, raises the threat of proliferating concepts (Hempel, 1966). While contemporary operationalists have developed some resources to address this challenge, these resources are inadequate to account (...) for the full range of complex behaviors of scientific concepts. We adopt show how the patchwork approach’s repertoire of inter-patch relations can expand the resources available to the operationalist. We focus on one especially important type of inter-patch relation: sharing a general reasoning strategy. General reasoning strategies serve two important functions: (1) they bind together distinct patches of scientific concepts, and (2) they provide normative guidance for extending concepts to new domains. (shrink)

Although emotion is closely associated with motivation, and interacts with perception, cognition, and action, many conceptualizations still treat emotion as separate from these domains. Here, a comparative/evolutionary anatomy framework is presented to motivate the idea that long-range, distributed circuits involving the midbrain, thalamus, and forebrain are central to emotional processing. It is proposed that emotion can be understood in terms of large-scale network interactions spanning the neuroaxis that form “functionally integrated systems.” At the broadest level, the argument is made that (...) we need to move beyond a Newtonian view of causation to one involving complex systems where bidirectional influences and nonlinearities abound. Therefore, understanding interactions between subsystems and signal integration becomes central to unraveling the organization of the emotional brain. (shrink)

The architects of the modern synthesis banned essentialism from evolutionary theory. This rejection of essentialism was motivated by Darwin’s theory of natural selection, and the continuity of evolutionary transformation. Contemporary evolutionary biology witnesses a renaissance of essentialism in three contexts: “origin essentialism” with respect to species and supraspecific taxa, the bar coding of species on the basis of discontinuities of DNA variation between populations, and the search for laws of evolutionary developmental biology. Such “new essentialism” in contemporary biology must be (...) of a new kind that accommodates relational (extrinsic) properties as historical essences and cluster concepts of natural kinds. (shrink)

In this paper I take issue with the doctrine that organisms belong of their very essence to the natural kinds (or biological taxa, if these are not kinds) to which they belong. This view holds that any human essentially belongs to the species Homo sapiens, any feline essentially belongs to the cat family, and so on. I survey the various competing views in biological systematics. These offer different explanations for what it is that makes a member of one species, family, (...) etc. a member of that taxon. Unfortunately, none of them offers an explanation that is compatible with the essentialism in question. (shrink)

In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction (sometimes made in the literature) between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic (...) hypotheses, by using the classical Owenian criteria (for morphological characters) or via multiple sequence alignment (for sequence data). However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level. (shrink)

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (shrink)

Determining whether a homoplastic trait is the result of convergence or parallelism is central to many of the most important contemporary discussions in biology and philosophy: the relation between evolution and development, the importance of constraints on variation, and the role of contingency in evolution. In this article, I show that two recent attempts to draw a black-or-white distinction between convergence and parallelism fail, albeit for different reasons. Nevertheless, I argue that we should not be afraid of gray areas: a (...) clarified version of S. J. Gould's earlier account, based on a separation of underlying developmental mechanisms from the realized trait, still represents a useful approach. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

Much philosophical progress has been made in elucidating the idea of evolutionary contingency in a recent re-burgeoning of the debate. However, additional progress has been impaired on three fronts. The first relates to its characterisation: the under-specification of various contingency claims has made it difficult to conceptually pinpoint the scope to which ‘contingency’ allegedly extends, as well as which biological forms are in contention. That is—there appears to be no systematic means with which to fully specify contingency claims which has (...) led to a tendency for authors to talk past each other. Secondly, on the matter of evidence, recent research has focused on the evidential import of convergent evolution which is taken to disconfirm the evolutionary contingency thesis. However, there has been a neglect of convergent evolution’s converse: ‘evolutionary idiosyncrasies’ or the singular evolution of certain forms, which I argue is evidentially supportive of evolutionary contingency. Thirdly, evolutionary contingency has often been claimed to vary in degrees and that the debate, itself, is a matter of ‘relative significance’. However, there has been no formal method of evaluating the strength of contingency and its relative significance in a particular domain. In this paper, I address all three issues by proposing a systematic means of fully specifying contingency theses with the concept of the modal range. Secondly, I propose an account of evolutionary idiosyncrasies, investigate the explanations for their occurrences, and, subsequently, spell out their significance with respect to the evolutionary contingency thesis. Finally, having been equipped with the evidential counterpart to convergent evolution, I shall sketch a likelihood framework for evaluating, precisely on the basis of a sequence of opposing data, the strength and relative significance of evolutionary contingency in a particular domain. With this in hand, the relative observations of idiosyncrasies and convergences can be informative of the strength and relative significance of contingency in any particular domain. (shrink)

Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...) supporting the conceptualization of taxa as kinds. The focus on a phenomenon of homology based on causal processes (e.g., connectivity, activity-function, genetics, inheritance, and modularity) and implying relationship with modification yields a notion of natural kinds conforming to the phylogenetic-evolutionary framework. Nevertheless, homeostatic property cluster kinds in taxonomic and evolutionary practice must be rooted in the primacy of epistemological classification (homology as observational properties) over metaphysical generalization (series of transformation and common ancestry as unobservational processes). The perspective of individuating characters exclusively by historical-transformational independence instead of their developmental, structural, and functional independence fails to yield a sufficient practical interplay between theory and observation. Purely ontological and ostensional perspectives in evolution and phylogeny (e.g., an ideographic character concept and PhyloCode’s ‘individualism’ of clades) may be pragmatically contested in the case of urgent issues in biodiversity research, conservation, and systematics. (shrink)

Walter Bock was committed to developing a framework for evolutionary biology. Bock repeatedly discussed how evolutionary explanations should be considered within the realm of Hempel’s deductive-nomological model of scientific explanations. Explanation in evolution would then consist of functional and evolutionary explanations, and within the latter, an explanation can be of nomological-deductive and historical narrative explanations. Thus, a complete evolutionary explanation should include, first, a deductive functional analysis, and then proceed through nomological and historical evolutionary explanations. However, I will argue that (...) his views on the deductive proprieties of functional analysis and the deductive-nomological parts of evolution fail because of the nature of evolution, which contains a historical element that the logic of deduction and Hempel’s converting law model do not compass. Conversely, Bock’s historical approach gives a critical consideration of the historical narrative element of evolutionary explanation, which is fundamental to the methodology of the historical nature of evolutionary theory. Herein, I will expand and discuss a modern view of evolutionary explanations of traits that includes the currentacknowledgement of the differences between experimental and the historical sciences, including the token and type event dichotomy, that mutually illuminate each other in order to give us a well confirmed and coherent hypothesis for evolutionary explanations. Within this framework, I will argue that the duality of evolutionary explanations is related to two components of character evolution: origin, with its evolutionary pathways along with the history, and maintenance, the function (mainly a current function) for the character being selected. (shrink)