Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...) at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

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)

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)

The paper 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 paper concludes by summarizing my responses to the objection that, according to current “species concepts,” species are relational, (...) and to the objection that essentialism cannot accommodate features of Darwinism associated with variation and change. (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)

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)

The Linnaean system of classification is a threefold system of theoretical assumptions, sorting rules, and rules of nomenclature. Over time, that system has lost its theoretical assumptions as well as its sorting rules. Cladistic revisions have left it less and less Linnaean. And what remains of the system is flawed on pragmatic grounds. Taking all of this into account, it is time to consider alternative systems of classification.

Biological species have been treated traditionally as spatiotemporally unrestricted classes. If they are to perform the function which they do in the evolutionary process, they must be spatiotemporally localized individuals, historical entities. Reinterpreting biological species as historical entities solves several important anomalies in biology, in philosophy of biology, and within philosophy itself. It also has important implications for any attempt to present an "evolutionary" analysis of science and for sciences such as anthropology which are devoted to the study of single (...) species. (shrink)

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.

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)

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)

Although it is possible to regard a species as a set with a special internal structure, it is preferable to regard a species as an individual precisely to emphasize this internal structure. It is necessary to recognize, moreover, that two organisms that are part of a single entity with respect to one process need not be part of a single entity with respect to another process. Furthermore, choosing to regard two entities (with respect to one process) as conspecific is not (...) to deny that there are two entities within this species. Thus, the systematist need not propose formal names for every entity he discovers, but the names he proposes ought to be as faithful to the relationship among the entities as is possible. (shrink)

Biological diversity (BD) explored by biological systematics is a complex yet organized natural phenomenon and can be partitioned into several aspects, defined naturally with reference to various causal factors structuring biota. These BD aspects are studied by particular research programs based on specific taxonomic theories (TTs). They provide, in total, a framework for comprehending the structure of biological systematics and its multi-aspect relations to other fields of biology. General principles of individualizing BD aspects and construing TTs as quasi-axiomatics are briefly (...) considered. It is stressed that each TT is characterized by a specific combination of interrelated ontological and epistemological premises most adequate to the BD aspect a TT deals with. The following contemporary research programs in systematics are recognized and characterized in brief: phenetic, rational (with several subprograms), numerical, typological (with several subprograms), biosystematic, biomorphic, phylogenetic (with several subprograms), and evo-devo. From a scientific pluralism perspective, all of these research programs, if related to naturally defined particular BD aspects, are of the same biological and scientific significance. They elaborate “locally” natural classifications that can be united by a generalized faceted classification. (shrink)

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical (...) pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials. (shrink)

Taxonomies of living things and the methods used to produce them changed little with the institutionalization of evolutionary thinking in biology. Instead, the relationships expressed in existing taxonomies were merely reinterpreted as the result of evolution, and evolutionary concepts were developed to justify existing methods. I argue that the delay of the Darwinian Revolution in biological taxonomy has resulted partly from a failure to distinguish between two fundamentally different ways of ordering identified by Griffiths : classification and systematization. Classification consists (...) of ordering entities into classes, groups defined by the attributes of their members; in contrast, systematization consists of ordering entities into systems, more inclusive entities whose existence depends on some natural process through which their parts are related. Evolutionary, or phylogenetic, systematics takes evolutionary descent to be the natural process of interest in biological taxonomy. I outline a general framework for a truly phylogenetic systematics and examine some of its consequences. (shrink)

Four ordering systems have been used most frequently in taxonomy: (1) special purpose classifications, (2) downward classifications (identification schemes), (3) upward or grouping classifications (traditional), and (4) Hennigian phylogenetic systems. The special properties of these four systems are critically evaluated. Grouping classifications and phylogenetic systems have very different objectives: the former the documentation of similarity and closeness of relationship, the latter of phylogeny. Both are legitimate ordering systems.

In recent years two groups of taxonomists have attempted to influence the general goals and methods of biological classification. The first group, which emerged in the late 1950’s, has been called variously neo-Adansonian, numerical, computer and phenetic taxonomy. The founders of this school, Robert R. Sokal and P.H.A. Sneath, termed their unified approach to systematics “neo-Adansonian” because of the affinities which they saw between their views and those of the 18th century botanist, Michel Adanson (1727-1806). Today little mention is made (...) of Adanson. His ideas turned out not to be as prescient as Sokal and Sneath had at first thought. Besides, he had served his purpose as a patron saint ([79], p. 23). Sokal and Sneath also termed their approach “numerical” because they believed that taxonomists should make greater use of available mathematical techniques. Not only should taxonomic characters be coded quantitatively but also estimates of affinity should be made on the basis of explicitly stated clustering procedures. (shrink)

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term ‘species’ as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation (...) is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem. (shrink)

Abstract The ‘species problem’ in the philosophy of biology concerns the nature of species. Various solutions have been proposed, including arguments that species are sets, classes, natural kinds, individuals, and homeostatic property clusters. These proposals parallel debates in ecology as to the ontology and metaphysics of populations, communities and ecosystems. A new solution—that species are processes—is proposed and defended, based on Robert Ulanowicz’s metaphysics of process ecology. As with ecological systems, species can be understood as emergent, autocatalytic systems with propensities (...) for centripetality and mutuality in the course of dynamically balancing ascendency (order and persistence) and overhead (randomness and change). The species-as-processes perspective accords with the Ulanowicz’s postulates of process ecology and it can be accommodated by existing theories of species—particularly in a reframing of Richard Boyd’s metaphysics such that species are homeostatic process clusters. Rather than contending that process-based metaphysics is the only, best or true account of species, a pluralist-realist approach is advocated based on the pragmatic principles that are reflected in modern view of species and ecology. If species are understood to be comprised of processes and to be emergent processes themselves, there are important implications for the life sciences, including: animal models in medical and environmental studies, conservation biology, extinction, biodiversity, restoration ecology, and evolutionary biology. Content Type Journal Article Category Invited Paper Pages 1-30 DOI 10.1007/s10516-011-9169-5 Authors Jeffrey A. Lockwood, Department of Philosophy, University of Wyoming, Laramie, WY 82071, USA Journal Axiomathes Online ISSN 1572-8390 Print ISSN 1122-1151. (shrink)