Species Concepts

One potentially extremely fruitful use of the tools of corpus analysis in the philosophy of science is to help us understand disputed terrains within the sciences that we study. For philosophers of biology, for instance, few controversies are as heated as those over the concepts we use in taxonomy to classify the living world, with the definition of ‘species’ perhaps most fundamental among them. As many understandings of biodiversity, in turn, involve counting the number of species present in a given (...) area, these taxonomic concepts thus become crucially implicated in our efforts in conservation biology and our response to climate change. In this chapter, we present a corpus of taxonomic journal papers, and illustrate how it might be used to make progress in the history and philosophy of taxonomy. What parts of the biological world do taxonomists most often study? Are these areas of focus related to other methodological commitments, or perhaps to their underlying conceptual disagreement? Are species that are more important to conservation, or economic concerns, or more important to local cultures, more or less likely to be the target of biological study? Corpus-based methods, we argue, are uniquely powerful for approaching questions such as these, and we hope that the case we present can serve as a fruitful example for others considering their implementation. (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)

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.

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

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)

A critical exposition of plans to colonize other planets , especially Mars, and their costs. The final chapter links with issues about the value and future of human life. See the extended summary uploaded to this site.

Are the methods of synthetic biology capable of recreating authentic living members of an extinct species? An analogy with the restoration of destroyed natural landscapes suggests not. The restored version of a natural landscape will typically lack much of the aesthetic value of the original landscape because of the different historical processes that created it—processes that involved human intentions and actions, rather than natural forces acting over millennia. By the same token, it would appear that synthetically recreated versions of extinct (...) natural organisms will also be less aesthetically valuable than the originals; that they will be, in some strong sense, ‘inauthentic’, because of their peculiar history and mode of origin. I call this the ‘genesis argument’ against de-extinction. In this article I critically evaluate the genesis argument. I highlight an important disanalogy between living organisms and natural landscapes: viz., it is of the essence of the former, but not of the latter, to regularly reproduce and die. The process of iterated natural reproduction that sustains the continued existence of a species through time obviously does not undermine the authenticity of the species. I argue that the authenticity of a species will likewise be left intact by the kind of artificial copying of genes and traits that a de-extinction project entails. I conclude on this basis that the genesis argument is unsound. (shrink)

As the digitization of information accelerates, the push to encode our surrounding numerically instead of linguistically increases. The role that language has traditionally played in the nomenclature of an integrative taxonomy is being replaced by the numeric identification of one or few quantitative characteristics. Nineteenth-century scientific systems of color identification divided, grouped, and named colors according to multiple characteristics. Now color identification relies on numeric values applied to spectrographic readings. This means of identification of color lacks the taxonomic rigor of (...) nineteenth century systems. Identifying color by numeric value instead of by grouping and naming them, strips color taxonomy of all but one quantitative aspect of a color. I use the case of color taxonomy to argue against a similar trend of numeric identification in the biological sciences. Unlike historically more integrative approaches to taxonomy in biology, genomic sequencing identifies one or few quantitative characteristics to encode an organism. If genomic sequencing becomes the primary means of identification in the biological sciences, just as in numeric systems of color identification, scientific taxonomy would suffer. Basing my analysis on theories of perception of division and on theories of language, I use the cases of color and species to argue for the advantages of an integrative taxonomic system of naming and categorizing over a method of identification, which encodes limited characteristics numerically. I hold that language is the most sophisticated tool for systematic taxonomy and that taxonomic nomenclature should be retained. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...) and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: (...) this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper. (shrink)

For more than fifty years, taxonomists have proposed numerous alternative definitions of species while they searched for a unique, comprehensive, and persuasive definition. This monograph shows that these efforts have been unnecessary, and indeed have provably been a pursuit of a will o’ the wisp because they have failed to recognize the theoretical impossibility of what they seek to accomplish. A clear and rigorous understanding of the logic underlying species definition leads both to a recognition of the inescapable ambiguity that (...) affects the definition of species, and to a framework-relative approach to species definition that is logically compelling, i.e., cannot not be accepted without inconsistency. An appendix reflects upon the conclusions reached, applying them in an intellectually whimsical taxonomic thought experiment that conjectures the possibility of an emerging new human species. (shrink)

John Wilkins and Malte Ebach respond to the dismissal of classification as something we need not concern ourselves with because it is, as Ernest Rutherford suggested, mere ‘‘stamp collecting.’’ They contend that classification is neither derivative of explanation or of hypothesis-making but is necessarily prior and prerequisite to it. Classification comes first and causal explanations are dependent upon it. As such it is an important (but neglected) area of philosophical study. Wilkins and Ebach reject Norwood Russell Hanson’s thesis that classification (...) relies on observation that is theory-laden and deny the need for aetiological assumptions and historical reconstruction to justify its arrangement. What they offer instead is a significant (albeit controversial) contribution to the philosophical literature on classification, a pre-theoretic natural classification based on the observation of patterns in data of ready-made phenomena. Their notion of ready-made phenomena rests on a conception of tacit knowledge or know-how. This is evident in their distinction between strong Theory-dependence and na ̈ıve theory-dependence. Their small t-theory-dependence permits patterns of observation that facilitate know-how but does not rely on a domain-specific explanatory theory of their aetiology. Wilkins and Ebach suggest classification differs from theory building in that it is passive (whereas theory building is active). Classification is possible just because it does not require the sieve of theory to capture classes that are ‘‘handed to you by your cognitive dispositions and the data that you observe’’ (p. 18). Finding regularities sans-theory is just something we do and can do without any prior theory about the underlying causes or origins of the resultant regularities. Luke Howard’s classification of clouds serves as an exemplar of a passive, theory-free classification system and the periodic table and the DSM help to illustrate this type of non-aetiological patterning. A recurrent theme is the nature of naturalness. For Wilkins and Ebach, the conception of naturalness is not one that is based on the generation or discovery of natural kind categories popular in both the traditional metaphysics of Mill and Wittgenstein as well as updated notions within philosophy of biology such as Boyd’s Homeostatic Property Cluster kinds. Instead, Wilkins and Ebach define the naturalness of classification as the falling into hierarchical patterns, aligning the search for natural arrangement with the aim of systematics, and as something that is grounded in a cognitive task or activity. However, they leave the question of realism v. antirealism open. ‘‘In natural classification...we must have real relations no matter how we might interpret ‘real’’’ (p. 70). There is tension with regard to their ontological commitments as they vacillate between constructive, operationalist, and realist approaches. Wilkins and Ebach initially define real as that which is causal and important (pp. 70–71), and later as that which ‘‘depends in no way upon a mind or observer’’ (p. 122). This makes their claim that there was ‘‘no real theory involved [in the pre-Darwinian classifications of Jussieu and Adanson]’’ (p. 64) difficult to interpret. Cont’d……. (shrink)

We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T.A. Knight and C. Darwin, and sketch a decomposition result (...) involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels’ question, “Can biology lead to new theorems?”. (shrink)

Species concepts aim to define the species category. Many of these rely on defining species in terms of natural lineages and groupings. A dominant gene-centred metaconception has shaped notions of what constitutes both a natural lineage and a natural grouping. I suggest that relying on this metaconception provides an incomplete understanding of what constitute natural lineages and groupings. If we take seriously the role of epigenetic, behavioural, cultural, and ecological inheritance systems, rather than exclusively genetic inheritance, a broader notion of (...) what constitutes a natural grouping or lineage may be required. I conclude by outlining an alternative metaconception that is a de-centred metaschema for species. (shrink)

The text discusses Linnaeus’ binominal classification and the idea of mathesis unversalis of Leibniz in the ground of Michel Foucault’s conception of ‘epistema’ as well the connexion of XVIII century’s representation of universal order with viewpoints of Descartes (Rules for the Direction of the Mind) and Kant (The Critique of Pure Reason, The Critique of (the Power of) Judgment).

A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene flow that (...) are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

I begin with a description of the benefits and limits of DNA barcoding as presented by its advocates not its critics. Next, I argue that due to the mutually dependent relationship between defining and delimiting species, all systems of classification are grounded in theory, even if only implicitly. I then proceed to evaluate DNA barcoding in that context. In particular, I focus on the barcoders’ use of a sharp boundary by which to delimit species, arguing that this boundary brings along (...) additional theoretical commitments inconsistent with the way taxonomists conceive of species, viz., as entities that have vague boundaries and that cannot be defined by any single attribute other than ancestry. Given these inconsistencies, I conclude that even if groupings based on DNA barcodes match those of an existing taxonomy, the two systems of classification are not necessarily tracking the same entities, i.e., species. (shrink)

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. (...) We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views. (shrink)

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...) arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (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 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)

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.

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.

This paper argues against the common, often implicit view that theories are some specific kind of thing. Instead, I argue for theory concept pluralism: There are multiple distinct theory concepts which we legitimately use in different domains and for different purposes, and we should not expect this to change. The argument goes by analogy with species concept pluralism, a familiar position in philosophy of biology. I conclude by considering some consequences for philosophy of science if theory concept pluralism is correct.