In this paper, I address the charge that the category species should be abandoned in biological work. The widespread appeal to species in scientific discourse provides a presumption in favor of the category’s usefulness, but a defeasible presumption. Widely acknowledged troubles attend species: these troubles might render the concept unusable by showing that ‘species’ is equivocal or meaningless or in some similar way fatally flawed. Further, there might be better alternatives to species. I argue that the presumption in favor of (...) species is not defeated on these scores. Troubles attending species, which arise on account of contextual variation attending the use of ‘species’, do not indicate that the concept is unusable. And alternatives to the use of ‘species’, which have been proposed in connection with rank-free systematics and in connection with conservation efforts, fail to provide a proper replacement for species. (shrink)

This collection of original essays--by philosophers of biology, biologists, and cognitive scientists--provides a wide range of perspectives on species. Including contributions from David Hull, John Dupre, David Nanney, Kevin de Queiroz, and Kim Sterelny, amongst others, this book has become especially well-known for the three essays it contains on the homeostatic property cluster view of natural kinds, papers by Richard Boyd, Paul Griffiths, and Robert A. Wilson.

Exploring whether clades can reproduce leads to new perspectives on general accounts of biological development and individuation. Here we apply James Griesemer's general account of reproduction to clades. Griesemer's account of reproduction includes a requirement for development, raising the question of whether clades may bemeaningfully said to develop. We offer two illustrative examples of what clade development might look like, though evaluating these examples proves difficult due to the paucity of general accounts of development. This difficulty, however, is instructive about (...) what a general account of development should look like and how it may usefully be applied to research problems (further suggesting a means for evaluating general accounts of development). Reproduction also requires individuation of parent and offspring. We argue that there is no special problem of individuating older and younger clades. The vagaries involved with determining when clades begin, mature, and end are precisely the same as those that arise when the same questions are asked of cells, organisms, or species. Though the question of clade reproduction and selection may still be open, the process of discovery presents new insights into old problems. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

Evolutionary conceptions of species place special weight on each species having dynamic independence as a unit of evolution. However, the idea that species have their own historical fates, tendencies, or roles has resisted systematic analysis. Growing evidence from population genomics shows that many paradigm species regularly engage in hybridization. How can species be defined in terms of independent evolutionary identities if their genomes are dynamically coupled through lateral exchange? I introduce the concept of a “composite lineage” to distinguish species and (...) subspecies on the basis of the proportion of a group’s heritable traits that are uncoupled from reproductive exchange. (shrink)

This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.

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)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population lineages (...) that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

In this paper, we discuss the following four alternative ways of understanding the outcomes of resurrection biology. Implications of each of the ways are discussed with respect to concepts of species and extinction. Replication: animals created by resurrection biology do not belong to the original species but are copies of it. The view is compatible with finality of extinction as well as with certain biological and ecological species concepts. Re-creation: animals created are members of the original species but, despite their (...) existence, the species remains extinct. The view is incompatible with all species concepts presented. Non-extinction: animals produced belong to the original species which actually never went extinct. The view may be consistent with phenetic and phylogenetic species concepts as well as with finality of extinction. According to literal resurrection, resurrection biology is successful in reversing extinction through the creation of new members of species that once went extinct. This view presupposes non-finality of extinction and it is compatible with phenetic species concepts. It is notable that no species or extinction concept is consistent with all possible views of resurrection biology nor is any view of resurrection biology consistent with all species or extinction concepts. Thus, one’s views regarding species and extinction determine which views one can adopt regarding resurrection biology and vice versa. (shrink)

The circumscription of taxa and classification of organisms are fundamental tasks in the systematization of biological diversity. Their success depends on a unified idea concerning the species concept, evolution, and taxonomy; paradoxically, however, it requires a complete distinction between taxa and evolutionary units. To justify this view, I discuss these three topics of systematics. Species concepts are examined, and I propose a redefinition for the Taxonomic Species Concept based on nomenclatural properties, in which species are classes conventionally represented by a (...) binomial. Speciation is subsequently discussed, to demonstrate that concepts on the evolutionary process are damaged when species are considered as evolutionary units. Speciation should be considered a transition among patterns of a population and, consequently, always a sympatric process. This view contrasts with the majority of speciation models, which analyze cladogeneses and classify speciation geographically, usually considering allopatry the essential condition for the differentiation process. Finally, taxonomy is considered, to show that the equivalence between evolutionary and taxonomic units may also damage the practice of biological systematization. Principles and rules of nomenclature and classification should offer freedom to accommodate divergent opinions about systematics and to incorporate the evolution of knowledge; therefore, they should remain independent of biological theories. (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)

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species (...) and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. (shrink)

The formal definition of species as explanatory hypotheses presented by Fitzhugh is emended. A species is an explanatory account of the occurrences of the same character among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In addition to species, biological systematics also employs hypotheses that are ontogenetic, tokogenetic, intraspecific, and phylogenetic, each of which provides explanatory hypotheses for distinctly different classes of causal questions. It is suggested that species hypotheses can not be applied (...) to organisms with obligate asexual, parthenogenetic, and self-fertilizing modes of reproduction. Hypotheses explaining shared characters among such organisms are, instead, strictly phylogenetic. Several implications of this emended definition are examined, especially the relations between species, intraspecific, and phylogenetic hypotheses, as well as the limitations of species names to be applied to temporally different characters within populations. (shrink)

De-extinction technology aims to bring extinct species back into existence, often with the goal of releasing created organisms into natural environments. In this paper, I argue that there are aesthetic reasons to avoid engaging in de-extinction and release projects, even if they pass moral permissibility criteria. The strength of these reasons depends on conclusions regarding species authenticity – a problem that arises at the intersection of de-extinction technology and the ‘species problem’ in the philosophy of biology. Since species authenticity affects (...) the perceived naturalness of ‘natural’ environments, and thus the aesthetic judgments thereof, I contend that there will be negative aesthetic consequences of de-extinction efforts that ought to be further explored before such projects move forward. (shrink)

The Darwinian theory of evolution is itself evolving and this book presents the details of the core of modern Darwinism and its latest developmental directions. The authors present current scientific work addressing theoretical problems and challenges in four sections, beginning with the concepts of evolution theory, its processes of variation, heredity, selection, adaptation and function, and its patterns of character, species, descent and life. The second part of this book scrutinizes Darwinism in the philosophy of science and its usefulness in (...) understanding ecosystems, whilst the third section deals with its application in disciplines beyond the biological sciences, including evolutionary psychology and evolutionary economics, Darwinian morality and phylolinguistics. The final section addresses anti-Darwinism, the creationist view and issues around teaching evolution in secondary schools. The reader learns how current experimental biology is opening important perspectives on the sources of variation, and thus of the very power of natural selection. This work examines numerous examples of the extension of the principle of natural selection and provides the opportunity to critically reflect on a rich theory, on the methodological rigour that presides in its extensions and exportations, and on the necessity to measure its advantages and also its limits. Scholars interested in modern Darwinism and scientific research, its concepts, research programs and controversies will find this book an excellent read, and those considering how Darwinism might evolve, how it can apply to the human sciences and other disciplines beyond its origins will find it particularly valuable. Originally produced in French (Les Mondes Darwiniens), the scope and usefulness of the book have led to the production of this English text, to reach a wider audience. This book is a milestone in the impressive penetration by Francophone scholars into the world of Darwinian science, its historiography and philosophy over the last two decades. Alex Rosenberg, R. Taylor Cole Professor of Philosophy, Duke University Until now this useful and comprehensive handbook has only been available to francophones. Thanks to this invaluable new translation, this collection of insightful and original essays can reach the global audience it deserves. Tim Lewens, University of Cambridge. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

Species are central to biology, but there is currently no agreement on what the adequate species concept should be, and many have adopted a pluralist stance: different species concepts will be required for different purposes. This thesis is a multidimensional analysis of species pluralism. First I explicate how pluralism differs monism and relativism. I then consider the history of species pluralism. I argue that we must re-frame the species problem, and that re-evaluating Aristotle's role in the histories of systematics can (...) shed light on pluralism. Next I consider different forms of pluralism: evolutionary and extra-evolutionary species pluralism, which differ in their stance on evolutionary theory. I show that pluralism is more than a debate about the species category, but a debate about which concepts are legitimate and a claim about how they interact with one another. Following that, I consider what sort of ontology is required for different forms of species pluralism. I argue that pluralists who deny the unity of biology will require a further plurality of frameworks, while those that ground their pluralism in evolution need only one framework. Finally, I consider what pluralism means for biological practice. I argue that species concepts are tools, and reflect on how pluralism can illuminate the way systematists approach the discovery of new species of yeast. Pluralism can make sense of the way species concepts are used, and can be developed to aid researchers in thinking about how to use the right tools for the right jobs. (shrink)

Kripke argues for origin essentialism, the view that the same individual cannot have multiple origins. Sober hypothesises that Kripke's origin essentialism applies to biological species. This paper shows that Sober's hypothesis fails. Because Kripke's original argument is invalid, it cannot vindicate Sober's proposal. Salmon offers an influential reformulation of Kripke's argument but his argument fails to extend to species: the notion of an individual's origin is too narrow to apply to species, and Salmon's argument rests on a thought experiment that (...) conflicts with how species evolve. Thus, Sober and others are wrong to think that Kripke's origin essentialism can save species essentialism. (shrink)

Biological type specimens are a particular kind of voucher specimen stored in natural history collections. Their special status and practical use are discussed in relation to the description and naming of taxonomic zoological diversity. Our current system, known as Linnaean nomenclature, is governed by the International Code of Zoological Nomenclature. The name of a species is fixed by its name-bearing type specimen, linking the scientific name of a species to the type specimen first designated for that species. The name-bearing type (...) specimen is not necessarily a typical example of the species, while establishment of the boundaries of a species requires empirical taxonomic studies. The International Code of Zoological Nomenclature allows for the naming of new species in the absence of preserved specimens. However, photos and DNA sequences should not function as primary type material, while new species should not be described and named without deposition of at least one type specimen in a collection. Philosophically, species are individuals, spatiotemporally restricted entities. Therefore, Linnaean species names are proper names, which do not define the taxon but serve as a label, providing an ostensive definition of a species. Paratypes have no name-bearing function but, nevertheless, are highly valued specimens in natural history collections. Paratypes should be restricted to those specimens originating from the same sample as the holotype. Diagnosis of a species taxon involves establishment of a connection between a Linnaean name and determination of the boundaries of the species. A first step in this process is the choice of an appropriate species concept. It is not the examination of holotypes and paratypes that necessarily provides the best estimate of the taxonomic boundaries of a species, but this is facilitated by a set of voucher specimens known as the hypodigm. Dissatisfaction with the present nomenclatural code led some researchers to propose emendations. Other taxonomists suggested abandoning Linnaean nomenclature and proposed the alternative PhyloCode, albeit that it relegates the naming of species taxa to the traditional nomenclatural codes. (shrink)

After decades of debates about species concepts, there is broad agreement that species are evolving lineages. However, species classification is still in a state of disorder: different methods of delimitation lead to competing outcomes for the same organisms, and the groups recognised as species are of widely different kinds. This paper considers whether this problem can be resolved by developing a unitary scale for evolutionary independence. Such a scale would show clearly when groups are comparable and allow taxonomists to choose (...) a conventional threshold of independence for species status. Existing measurement approaches to species delimitation are typically shot down by what I call the heterogeneity objection, according to which independently evolving groups are too heterogeneous to be captured by a single scale. I draw a parallel with the measurement of temperature to argue that this objection does not provide sufficient reasons to abandon the measurement approach, and that such an approach may even help to make the vague notion of evolutionary independence more precise. (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)

At least three different issues are commonly referred to by the term “the species problem”: one concerns the necessary properties of species, a second the processes responsible for the existence of species, and a third methods for inferring species limits. Solutions have recently been proposed to the first two problems, which are conceptual in nature (the third is methodological). The first equates species with metapopulation lineages and proposes that existence as a separately evolving metapopulation lineage be considered the only necessary (...) property of species. The second views the species category as a cluster concept and proposes that no single process or set of processes be considered necessary for the existence of species. Although these two solutions have been portrayed as being in conflict, they are, in fact, highly compatible. Moreover, the proposals in question clarify the problem concerning methods for inferring the limits of species, which has for a long time been confused with the problem concerning the necessary properties of species. Together these proposals provide the opportunity for biology to move beyond debates about the definition of the species category and focus on estimating the boundaries and numbers of species as well as studying the diverse processes involved in their origin and persistence. BioEssays 27:1263–1269, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

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)

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)

Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for revisions (...) and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. (shrink)

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)