The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

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)

Historians tend to speak of the problem of the origin of species or the species question, as if it were a monolithic problem. In reality, the phrase refers to a, historically, surprisingly fluid and pluriform scientific issue. It has, in the course of the past five centuries, been used in no less than ten different ways or contexts. A clear taxonomy of these separate problems is useful or relevant in two ways. It certainly helps to disentangle confusions that have inevitably (...) emerged in the literature in its absence. It may, secondly, also help us to gain a more thorough understanding, or sharper view, of the history of evolutionary thought. A consequent problem-centric look at that history through the lens of various origin of species problems certainly yields intriguing results, including and particularly for our understanding of the genesis of the Wallace–Darwin theory of evolution through natural selection. (shrink)

Historians tend to speak of the problem of the origin of species or the species question, as if it were a monolithic problem. In reality, the phrase refers to a, historically, surprisingly fluid and pluriform scientific issue. It has, in the course of the past five centuries, been used in no less than ten different ways or contexts. A clear taxonomy of these separate problems is useful or relevant in two ways. It certainly helps to disentangle confusions that have inevitably (...) emerged in the literature in its absence. It may, secondly, also help us to gain a more thorough understanding, or sharper view, of the history of evolutionary thought. A consequent problem-centric look at that history through the lens of various origin of species problems certainly yields intriguing results, including and particularly for our understanding of the genesis of the Wallace–Darwin theory of evolution through natural selection. (shrink)

Current Perspectives in Philosophy of Biology.

The philosophy of biology is witnessing an increasing enthusiasm for what can be called “individuals thinking”. Individuals thinking is a perspective on the metaphysics of biological entities according to which conceiving of them as individuals rather than kinds enables us to expose ongoing metaphysical debates as focusing on the wrong question, and to achieve better accounts of the metaphysics of biological entities. In this paper, I examine two cases of individuals thinking, the claim that species are individuals and the claim (...) that life on Earth is an individual. I argue that these claims fail to do the metaphysical work that one would want them to do. I highlight problems with the specific claims as well as with the general notion of ‘individual’, and argue that naturalistic metaphysicians of biology should think of the metaphysical status of theoretical entities, such as species and life, as fundamentally theory-dependent. This implies a metaphysical pluralism, that allows that in some theories species, life, and other such entities may feature as individuals, whereas in others they may feature as kinds. (shrink)

In a recent article, David Ludwig proposed to reorient the debate on natural kinds away from inquiring into the naturalness of kinds and toward elucidating the materiality of kinds. This article responds to Ludwig’s critique of a recently proposed account of kinds and classification, the Grounded Functionality Account, against which Ludwig offsets his own account, and criticizes Ludwig’s proposal to shift focus from naturalness to materiality in the philosophy of kinds and classification.

Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from ‘varieties’ within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? (...) Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin’s. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species , we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant. (shrink)

Philosophical analyses of scientific concepts are legion. However, this literature is replete with methodological errors that have largely gone unnoticed. Five distinct projects are conflated which has led to faulty inferences, ambiguities, and mischaracterizations. There has also been some recent enthusiasm for approaches that attempt to rectify problematic scientific concepts but the motivations for these approaches are questionable. I am hopeful that by bringing these various issues to light that it will lead practitioners to be more explicit about their aims (...) and subsequently result in better analyses. (shrink)

Marc Ereshefsky’s project of eliminative pluralism holds that, as there is no unifying feature among all species concepts, we ought to doubt the existence of the species category. Here, I argue that one promising strategy for saving the species category is to reframe it as a natural kind after the practice turn. I suggest situating the species category within a recent account of natural kinds proposed by Marc Ereshefsky and Thomas Reydon called “scientific kinds”. Scientific kinds highlight ontological boundaries. More (...) importantly, they recognize boundaries drawn from the lab and the field, not only from the armchair. The point of this exercise is to situate the species category within an account of natural kinds that is sensitive to scientific practice. In order to argue for a realist interpretation of the species category, and not merely a pragmatic one, I rely on an approach to scientific metaphysics from Ken Waters that shifts the attention from “theory focused” to “practice-centered” analysis. (shrink)

The concept of species is one of the core concepts in biology and one of the cornerstones of evolutionary biology, yet it is rife with conceptual problems. Philosophers of biology have been discussing the concept of species for decades, and in doing so they sometimes appeal to the views of biologists. However, their statements as to what biologists think are seldom supported by empirical data. In order to investigate what biologists actually think about the key issues related to the problem (...) of species, we have conducted a survey on the sample of 193 biologists from the population of biologists from over 150 biology departments at universities in the US and the EU. This article presents and discusses the results of the survey. Some results confirm and others falsify the reiterated statements of philosophers of biology as to what biologists think, but all results we obtained should be informative and relevant for future discussions of the problem of species. (shrink)

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...) and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept. (shrink)

-/- Because species names play an important role in scientific communication, it is more important that species be understood to be taxa than that they be equated with functional ecological or evolutionary entities. Although most biologists would agree that taxa are composed of organisms that share a unique common history, 2 major challenges remain in developing a species-as-taxa concept. First, grouping: in the face of genealogical discordance at all levels in the taxonomic hierarchy, how can we understand the nature of (...) taxa? Second, ranking: what criteria should be used to designate certain taxa in a nested series as being species? The grouping problem can be solved by viewing taxa as exclusive groups of organisms— sets of organisms that form a clade for a plurality of the genome (more than any conflicting set). However, no single objective criterion of species rank can be proposed. Instead, the species rank should be assigned by practitioners based on the semisubjective application of a set of species-ranking criteria. Although these criteria can be designed to yield species taxa that approximately match the ecological, evolutionary, and morphological entities that taxonomists have traditionally associated with the species rank, such a correspondence cannot be enforced without undermining the assumption that species are taxa. The challenge and art of monography is to use genealogical and other kinds of data to assign all organisms to one and only one species-ranked taxon. Various implications of the species-as-ranked-taxa view are discussed, including the synchronic nature of taxa, fossil species, the treatment of hybrids, and species nomenclature. I conclude that, although challenges remain, adopting the view that species are ranked taxa will facilitate a much-needed revolution in taxonomy that will allow it to better serve the biodiversity informatic needs of the 21st century. (shrink)

Pluralisms of various sorts are popular in philosophy of science, including those that imply some scientific concept x should be eliminated from science in favour of a plurality of concepts x1, x2, … xn. This article focuses on influential and representative arguments for such eliminative pluralism about the concept species. The main conclusions are that these arguments fail, that all other extant arguments also fail, and that this reveals a quite general dilemma, one that poses a defeasible presumption against many (...) eliminative pluralisms about various scientific concepts. The article ends by outlining a novel integrative alternative in defence of species. 1) Introduction 2) The species Concept, the Category ‘Species’, and the ‘Species’ Category Problem 3) What Are Eliminative Pluralism about species, and the Arguments for It? 4) Evaluation of Arguments 4.1 Splitting? 4.2 Lumping? 4.3 The eliminative pluralist’s dilemma 5) More General Lessons6Species Cohesion: An Integrative Alternative7Conclusion. (shrink)

The species problem is often described as the abundance of conflicting definitions of _species_, such as the biological species concept and phylogenetic species concepts. But biologists understand the notion of species in a non-definitional as well as a definitional way. In this article I argue that when they understand _species_ without a definition in their mind, their understanding is often mediated by the notion of _good species_, or prototypical species, as the idea of ``prototype'' is explicated in cognitive psychology. This (...) distinction helps us make sense of several puzzling phenomena regarding biologists' dealing with species, such as the fact that in everyday research biologists often behave as if the species problem is solved, while they should be fully aware that it is not. I also briefly discuss implications of this finding, including that some extant attempts to answer what the nature of species is have an inadequate assumption about how the notion of species is represented in biologists' minds. (shrink)