First, a brief history is provided of Popper's views on the status of evolutionary biology as a science. The views of some prominent biologists are then canvassed on the matter of falsifiability and its relation to evolutionary biology. Following that, I argue that Popper's programme of falsifiability does indeed exclude evolutionary biology from within the circumference of genuine science, that Popper's programme is fundamentally incoherent, and that the correction of this incoherence results in a greatly expanded and much more realistic (...) concept of what is empirical, resulting in the inclusion of evolutionary biology. Finally, this expanded concept of empirical is applied to two particular problems in evolutionary biology — viz., the species problem and the debate over the theory of punctuated equilibria — and it is argued that both of them are still mainly metaphysical. (shrink)

Species serve as both the basic units of macroevolutionary studies and as the basic units of taxonomic classification. In this paper I argue that the taxa identified as species by the Phylogenetic Species Concept (Mishler and Brandon 1987) are the units of biological organization most causally relevant to the evolutionary process but that such units exist at multiple levels within the hierarchy of any phylogenetic lineage. The PSC gives us no way of identifying one of these levels as the privileged (...) level on which taxonomic classifications can be based. (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.

Over the decades, there has been substantial empirical evidence showing that the unity of species cannot be maintained by gene flow. The biological species concept is inconclusive on this point. The suggestion is made that the unity of species is maintained rather by selection constantly spreading new alleles throughout the species, or bygene circulation. There is a lack in conceptual distinction between gene flow and gene circulation which lies at the heart of the problem. The concept of gene circulation also (...) sheds some new light on the problem of typology and on such a broad concept as evolution. A new species definition is proposed. (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.

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)

This paper offers an overview of "the species problem", arguing for a view of species as homeostatic property cluster kinds, positioning the resulting form of realism about species as an alternative to the claim that species are individuals and pluralistic views of species. It draws on taxonomic practice in the neurosciences, especially of neural crest cells and retinal ganglion cells, to motivate both the rejection of the species-as-individuals thesis and species pluralism.

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)

Cladism, today the dominant school of systematics in biology, includes a classification component – the view that classification ought to reflect phylogeny only, such that all and only taxa are monophyletic (i.e. consist of an ancestor and all its descendants) - and a metaphysical component – the view that all and only real groups or kinds of organisms are monophyletic. For the most part these are seen as amounting to much the same thing, but I argue they can and should (...) be distinguished, in particular that cladists about classification need not accept the typically cladist view about real groups or kinds. Cladists about classification can and should adopt an explanatory criterion for the reality of groups or kinds, on which being monophyletic is neither necessary nor sufficient for being real or natural. Thus the line of reasoning that has rightly led to cladism becoming dominant within systematics, and the attractive line of reasoning in the philosophical literature that advocates a more liberal approach to natural kinds, are seen to be, contrary to appearances, compatible. (shrink)

This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or dissolved it altogether – so-called (...) We Are Done views. In doing so the paper offers new criticisms of the general lineage species concept (GLSC), evolutionary species concept (EvSC), biological species concept (BSC), other similar concepts, Ereshefsky’s eliminative pluralism about the species category, and both Mishler’s pessimism and Wilkins’ phenomenalism about that category. Opposed to We Are Done views, the paper argues for a Revving Up view, on which we are nearly ready to begin the hard species problem in earnest. To help work towards these conclusions, the paper begins with an outline of a new kind of view of species (Barker 2019a), which proposes they are feedback systems of a mathematically specifiable and empirically testable sort. (shrink)

We argue that the logical outcome of the cladistics revolution in biological systematics, and the move towards rankless phylogenetic classification of nested monophyletic groups as formalized in the PhyloCode, is to eliminate the species rank along with all the others and simply name clades. We propose that the lowest level of formally named clade be the SNaRC, the Smallest Named and Registered Clade. The SNaRC is an epistemic level in the classification, not an ontic one. Naming stops at that level (...) because there is no currently acceptable evidence for clades within it, not because no smaller clades exist. Later, included clades may be named. They would then become the SNaRCs, while the original SNaRC would keep its original name. We argue that all theoretical tasks of biology, in evolution and ecology, as well as practical tasks such as conservation assessment, are better approached using this rankless phylogenetic approach. (shrink)

Some astronomers believe that we have discovered that Pluto is not a planet. I contest this assessment. Recent discoveries of trans-Neptunian Pluto-sized objects do not require that we exclude Pluto from the planets. But the obvious alternative, that classificatory revision is a matter of arbitrary choice, is also unpalatable. I argue that this classificatory controversy — which I compare to the controversy about the classification of the platypus — illustrates how our classificatory practices are laden with normative commitments of a (...) distinctive kind. I argue that the “norm-ladenness” of classification has philosophically significant ramifications for how we think about scientific disputes and debates in the metaphysics of classification such as the monism/pluralism debate. (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 vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an (...) alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system. (shrink)

Scientific pluralism is an issue at the forefront of philosophy of science. This landmark work addresses the question, Can pluralism be advanced as a general, philosophical interpretation of science?

At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous (...) to classifications of supraspecific taxa, our forging inappropriate and ambiguous information relating to theoretical and operational discussions of species ultimately results in a trade-off between convenience, accuracy, precision, and the successful recovery of natural biological diversity. Hence, none of these expectations or intentions of species or classifications is attainable through composite, and possibly discordant, concepts of biological diversity or its descent. Reviewing and evaluating the concepts of species for their theoretical and operational qualities illustrates that a monistic, primary concept of species, applicable to the various entities believed to be species, is essential. This evaluation reveals only one theoretical concept as appropriate for species, the Evolutionary Species Concept. This conceptualization functions as a primary concept and is essential in structuring our ideas and perceptions of real species in the natural world. The remaining concepts are secondary, forming a hierarchy of definitional guidelines subordinate to the primary concept, and are essential to the study of species in practice. Secondary concepts should be used as operational tools, where appropriate, across the variance in natural diversity to discover entities in accord with the primary concept. Without this theoretical and empirical structuring of concepts of species our mission to achieve reconciliation and understanding of pattern and process of the natural world will fail. (shrink)

En What Emotions Really Are y en otros artículos, Griffiths afirma que las clases naturales de los organismos vivos en Biología son cladistas. La afirmación está inmersa en una nueva teoría acerca de las clases naturales. En este trabajo examinaré los argumentos esgrimidos por Griffiths para sostener el estatus privilegiado de las clasificaciones cladistas frente a otras clasificaciones. No se discutirá la teoría de las clases naturales ofrecida, de cuyos méritos no dudo, sino su capacidad para ofrecer una solución en (...) la cuestión particular de qué sistema de clasificación de organismos debería utilizarse en Biología. In What emotions really are and in other papers Griffiths states that in Biology, natural classes ofliving organisms are clades. This assertion is made within the bounds of a new theory of natural classes. In this paper I wiIl consider the arguments employed by Griffiths to support the privileged status of the cladistic classification over other classifications. It is not Griffith's theory of natural classes what will be discussed, but his ability to offer a solution to the particular issue ofwhich classification system of organisms should be used in Biology. (shrink)

The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical liter- atures on the species problem, (...) focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is con- ceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion pre- sented here is Templeton’s cohesion idea. (shrink)

Good chefs know the importance of maintaining sharp knives in the kitchen. What’s their secret? A well-worn Taoist allegory offers some advice. The king asks about his butcher’s impressive knifework. “Ordinary butchers,” he replied “hack their way through the animal. Thus their knife always needs sharpening. My father taught me the Taoist way. I merely lay the knife by the natural openings and let it find its own way through. Thus it never needs sharpening” (Kahn 1995, vii; see also Watson (...) 2003, 46). Plato famously employed this image as an analogy for the reality of his Forms (Phaedrus, 265e). Just like an animal, the world comes pre-divided for us. Ideally, our best theories will be those which “carve nature at its joints”. While Plato employed the “carving” metaphor to convey his views about the reality of his celebrated Forms, its most common contemporary use involves the success of science -- particularly, its success in identifying distinct kinds of things. Scientists often report discovering new kinds of things -- a new species of mammal or novel kind of fundamental particle, for example -- or uncovering more information about already familiar kinds. Moreover, we often notice considerable overlap in different approaches to classification. As Ernst Mayr put it: No naturalist would question the reality of the species he may find in his garden, whether it is a catbird, chickadee, robin, or starling. And the same is true for trees or flowering plants. Species at a given locality are almost invariably separated from each other by a distinct gap. Nothing convinced me so fully of the reality of species as the observation . . . that the Stone Age natives in the mountains of New Guinea recognize as species exactly the same entities of nature as a western scientist. (Mayr 1987, 146) Such agreement is certainly suggestive. It suggests that taxonomies are discoveries rather than mere inventions. Couple this with their utility in scientific inference and explanation and we have compelling reason for accepting the objective, independent reality of many different natural kinds of things.. (shrink)

This paper is a critical discussion of John Dupré's recent defence of promiscuous realism in Part 1 of his The Disorder of Things: Metaphysical Foundations of the Disunity of Science. It also discusses some more general issues in the philosophy of biology and science. Dupré's chief strategy of argumentation appeals to debates within the philosophy of biology, all of which concern the nature of species. While the strategy is well motivated, I argue that Dupré's challenge to essentialist and unificationist views (...) about natural kinds is not successful. One conclusion is that an integrative conception of species is a real alternative to Dupré's pluralism. (shrink)

In this paper I explore Aristotle’s views on natural kinds and the compatibility of pluralism and realism, a topic that has generated considerable interest among contemporary philosophers. I argue that, when it came to zoology, Aristotle denied that there is only one way of organizing the diversity of the living world into natural kinds that will yield a single, unified system of classification. Instead, living things can be grouped and regrouped into various cross-cutting kinds on the basis of objective similarities (...) and differences in ways that subserve the explanatory context. Since the explanatory aims of zoology are diverse and variegated, the kinds it recognizes must be equally diverse and variegated. At the same time, there are certain constraints on which kinds can be selected. And those constraints derive more from the causal structure of the world than from the proclivities of the classifier (hence the realism). This distinguishes Aristotle’s version of pluralistic realism from those contemporary versions (like Dupré’s “promiscuous realism”) that treat all or most classifications of a given domain as equally legitimate and not just a sub-set of kinds recognized by the science that studies it. By contrast, Aristotle privileges scientifically important kinds on the basis of their role in causal investigations. On this picture natural kinds are those kinds with the sort of causal structure that allows them to enter into scientific explanations. In the final section I argue that Aristotle’s zoology should remain of interest to philosophers and biologists alike insofar as it combines a pluralistic form of realism with a rank-free approach to classification. (shrink)

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, (...) species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees. (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)

In addition to the distinction between species as a category and speciesas a taxon, the word species is ambiguous in a very different butequally important way, namely the temporal distinction between horizontal andvertical species. Although often found in the relevant literature, thisdistinction has thus far remained vague and undefined. In this paper the use ofthe distinction is explored, an attempt is made to clarify and define it, andthen the relation between the two dimensions and the implications of thatrelation are examined. (...) Using Darwin's analogy of language evolution forspeciesevolution, and by appealing to a major change in the conception of languagebetween 19th- and 20th-century linguistics, it is argued that the horizontaldimension has priority (pragmatic, epistemological, logical, and ontological)over the vertical dimension. This has immense ramifications for the modernspecies problem. Fundamentally, it favors horizontal species concepts oververtical ones. In so doing it places species realism on a much more securefoundation and largely undercuts species pluralism. In addition it raises aserious problem for the increasingly popular family of phylogenetic speciesconcepts, which generally suffer from a dimensionality confusion. However,thereis a recent trend within this family that attempts to restore the priority ofthe horizontal dimension. It is concluded that this trend should be affirmedandthat the species-as-individuals view should be abandoned. (shrink)

Gayon's recent claim that Buffon developed a concept of species as physical individuals is critically examined and rejected. Also critically examined and rejected is Gayon's more central thesis that as a consequence of his analysis of Buffon's species concept, and also of Darwin's species concept, it is clear that modern evolutionary theory does not require species to be physical individuals. While I agree with Gayon's conclusion that modern evolutionary theory does not require species to be physical individuals, I disagree with (...) his reasons and instead provide logical rather than historical reasons for the same conclusion. (shrink)

This paper presents the leading idea of my doctoral dissertation and thus has been shaped by the reactions of all the members of my thesis committee: Charles Chastain, Walter Edelberg, W. Kent Wilson, Dorothy Grover, and Charles Marks. I am especially grateful for the help of Professors Chastain, Edelberg, and Wilson; each worked closely with me at one stage or another in the development of the ideas contained in the present work. Shorter versions of this paper were presented at the (...) 47th Annual Northwest Conference on Philosophy (1995), the 1996 Mid-South Philosophy Conference, the 1997 meeting of the Central Division of the American Philosophical Association, and at the University of Washington, Seattle; thanks to all audiences for their insightful comments and questions and also to my conference commentators, Eric Gampel, Jonathan Cohen, and Bruce Glymour, respectively, each of whom offered a thoughtful critique. Lastly, I extend my gratitude to anonymous referees, including two from Mind and Language, whose remarks led to significant improvements in the paper. Address for correspondence: 13416, 4th Ave. S., Seattle, WA 98168, USA E-mail: [email protected].. (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)

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable (...) of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next. (shrink)

The continuing discussion of the species problem suffers from the lack of a coherent ontological theory as a basis for determining whether species have an ontological status. It has attempted to apply a full-fledged metaphysical theory to the species problem: the ontology of Mario Bunge. In doing so a few ontological fundamentals including system, individual, real and conceptual object, and law are briefly introduced. It is with the help of these fundamentals that an analysis of the species-as-individuals thesis is carried (...) out, concluding that species are not individuals (things), but natural kinds, and that they have no ontological status. In contradistinction to the traditional view of natural kinds involving possible worlds metaphysics and semantics a notion of natural kind is given in terms of the state space approach and of nomological equivalence. (shrink)

Marc Ereshefsky argues that pluralism about species suggests that the species concept is not theoretically useful. It is to be abandoned in favor of several concrete species concepts that denote real categories. While accepting species pluralism, the present paper rejects eliminativism about the species category. It is argued that the species concept is important and that it is possible to make sense of a general species concept despite the existence of different concrete species concepts.

The continuing discussion of the species problem suffers from the lack of a coherent ontological theory as a basis for determining whether species have an ontological status. It has attempted to apply a full-fledged metaphysical theory to the species problem: the ontology of Mario Bunge. In doing so a few ontological fundamentals including system, individual, real and conceptual object, and law are briefly introduced. It is with the help of these fundamentals that an analysis of the species-as-individuals thesis is carried (...) out, concluding that species are not individuals (things), but natural kinds, and that they have no ontological status. In contradistinction to the traditional view of natural kinds involving possible worlds metaphysics and semantics a notion of natural kind is given in terms of the state space approach and of nomological equivalence. (shrink)

We divide analytic metaphysics into naturalistic and non-naturalistic metaphysics. The latter we define as any philosophical theory that makes some ontological (as opposed to conceptual) claim, where that ontological claim has no observable consequences. We discuss further features of non-naturalistic metaphysics, including its methodology of appealing to intuition, and we explain the way in which we take it to be discontinuous with science. We outline and criticize Ladyman and Ross's 2007 epistemic argument against non-naturalistic metaphysics. We then present our own (...) argument against it. We set out various ways in which intellectual endeavours can be of value, and we argue that, in so far as it claims to be an ontological enterprise, non-naturalistic metaphysics cannot be justified according to the same standards as science or naturalistic metaphysics. The lack of observable consequences explains why non-naturalistic metaphysics has, in general, failed to make progress, beyond increasing the standards of clarity and precision in expressing its theories. We end with a series of objections and replies. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (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 theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined by gene genealogies. On this view, (...) an exclusive group is a group of organisms that forms a clade for a higher proportion of the genome than any conflicting clade. Taxa occupy a unique position in what can be called the ‘primary concordance tree’. But each gene has its own historical ‘Tree of Life’. I conclude by arguing that both organismal pedigrees with their corresponding Tree as well as gene genealogies and their trees are objectively real and play important, but different, roles in biological practice. (shrink)

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)

The species category is defined as thesmallest historical individual within which there is a parental pattern of ancestry and descent. The use of historical individual in this definition is consistent with the prevailing notion that speciesper se are not involved in processes — they are effects, not effectors. Reproductive isolation distinguishes biparental historical species from their parts, and it provides a basis for understanding the nature of the evidence used to discover historical individuals.

This article defends a selective eliminativist position with respect to the concept of “biological lineage” as used in certain areas of contemporary evolutionary biology. We argue that its primary epistemic roles in these contexts—explaining social evolution and cumulative selection—clash with empirical evidence, and that enforcing the concept of “lineage” even obstructs fruitful research avenues in several biological research fields, including phylogenetic research. Drawing on this, we suggest that, in many instances, it would be best to get rid of the concept (...) of “lineage” and think in terms that are more closely aligned with the empirical complexity of the biological world. Specifically, this entails that, instead of looking for the lineage that may have given rise to the entities possessing certain biological characteristics, biologists should generally look for any potential process allowing such possession, with the formation of a lineage just one possibility among many. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (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)

The phenomenon of species extinction raises more and more concern among ecologists facing the actual crisis of biodiversity. Scientific investigations of the causes and effects of extinction must be completed by a philosophical analysis of the concept of extinction that aims to clarify the meanings of the term ‘extinction’ and to analyse modalities, criteria and degrees of extinction. We will focus our attention on the apparent paradox of the possible ‘resurrection’ of species in the near future with the help of (...) genetic biotechnology and cloning techniques. The ontological background of the extinction concept is analysed in relation to the idea of species as classes. We will also show that there is no simple analogy between death and species extinction, and develop a conceptualist and dualistic system of supra-individual entities , supported by an instrumentalist approach to genetic manipulations which transform species into interactive kinds, which can go extinct and be recreated. (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)