Systematic Biology

Abstract for Descent and Logic in Biosystematics: An Essay AUTHOR: THOMAS MCCABE PUBLISHER: PERSEVERANT PUBLISHING Descent and Logic in Biosystematics: An Essay is a short book about biological systematics and taxonomy. Some of the subjects con- sidered in it are philosophical: taxonomic theory, species concepts, speciation models, and evolutionary theories. Yet the book also covers matters not philosophical, such as taxonomic operations, experi- mental taxonomy, and a new suggested taxonomic method with worked examples. The author finds relationships among these topics. (...) The book is addressed to biosystematists, practicing biological tax- onomists, and philosophers of biology. It will also interest others who draw on biological taxonomy and biosystematics in their work. Descent and Logic in Biosystematics: An Essay goes into some old topics such as traditional biological identifying, classifying, and nomenclature; some recent, such as cladistic analysis, phylogenetics, and phylogenomics; and a few new, such as the logic of mutually exclusive taxon definitions, and techniques for using directly obser- ved reproductive events and pedigree analysis to untangle certain taxonomic dilemmas. There is a chapter about minimizing am- biguities when defining biological taxa, a chapter on the relevance of human biology to biosystematics, chapters addressing some biosys- tematic problems associated with the phenomenon of hybridization, a chapter on the relationship of biological taxonomy to conservation biology, and a chapter about the scientificity of evolutionary theories. Descent and Logic in Biosystematics: An Essay is published with a glossary, twelve black and white line figures, a dynamic table of contents, linked cross references, linked bibliographic citations, and a detailed index in the print and PDF versions. Descent and Logic in Biosystematics: An Essay, is available from the publisher in print and PDF formats, and from distributors and retailers as an ebook. It should be considered for academic libraries, research libraries, natural history museum libraries, the libraries of conservation organizations, and some private libraries. (shrink)

The utilisation of quantum theories within social science and biology is often reasonably met with dubiety. It would be even more controversial should such theories be applied to concepts under the domain of eugenics. Nonetheless, this can open up a fresh and unique understanding of theories that are usually understood by their classical structure. We will provide quantum interpretations of dysgenics and dysgenic traits from different scopes and procedures. The way dysgenic traits are in a flux with the environment that (...) they interact will be analysed as well as how they interact with each other under quantum conditions. We will also take into account of factors such as intelligence, genetic heritability, and other biological and cognitive factors and try to study their frameworks in non-classical ways. Using what we have theorised, we will also attempt to create numerical and empirical analyses of some of the theories that we have proposed. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

This dissertation argues that cognition is a kind of natural agency. Natural agency is the capacity that certain systems have to act in accordance with their own norms. Natural agents are systems that bias their repertoires in response to affordances in the pursuit of their goals. -/- Cognition is a special mode of this general phenomenon. Cognitive systems are agents that have the additional capacity to actively take their worlds to be certain ways, regardless of whether the world is really (...) that way. In this way, cognitive systems are desituated. Desituatedness is the root of specifically cognitive capacities for representation and abstraction. -/- There are two main reasons why this view needs defending. First, natural agency is typically viewed as incompatible with natural science because it is committed to a teleological mode of explanation. Second, cognition is typically held to be categorically distinct from natural agency. This dissertation argues against both of these views. It argues against the incompatibility of agency and natural science by demonstrating that systems biology, general systems theory, and sciences that deal with complex systems have typically underappreciated conceptual and theoretical resources for grounding agency in the causal structure of the world. These conceptual resources do not, however, reduce agency to systems theory because the normativity inherent in agency demands descriptive resources beyond those of even the most sophisticated systems theory. It argues against the categorical difference between natural agency and cognition by pointing out that separating cognition from a richer web of situated, ecologically embedded relations between the agent and the world generates the frame problem, which is an insuperable obstacle to making cognition that is sufficiently responsive to the complexity of the world. Rooting cognition in natural agency is a more robust empirical bet for theorizing cognition and artificial intelligence. (shrink)

Biodiversity science is in a pivotal period when diverse groups of actors—including researchers, businesses, national governments, and Indigenous Peoples—are negotiating wide-ranging norms for governing and managing biodiversity data in digital repositories. These repositories, often called biodiversity data portals, are a type of organization for which governance can address or perpetuate the colonial history of biodiversity science and current inequities. Researchers and Indigenous Peoples are developing and implementing new strategies to examine and change assumptions about which agents should count as salient (...) participants in scientific projects, especially in projects that build and manage large digital data portals. Two notable efforts are the FAIR (Findable, Accessible, Interoperable, Reusable) and CARE (Collective benefit, Authority, Responsibility, Ethics) Principles for scientific data management and governance. To characterize how these principles influence the governance of biodiversity data portals, we develop an account of fit-for-use data that makes explicit its social as well as technical conditions in relation to agents and purposes. The FAIR Principles, already widely adopted by biodiversity researchers, prioritize machine agents and efficient computation, while the CARE Principles prioritize Indigenous Peoples and their data sovereignty. Both illustrate the potency of an emerging general strategy by which groups of actors craft and implement governance principles for data fitness-of-use to change assumptions about who are salient participants in data science. (shrink)

The Western world has led the development of material science for over 200 years. But they have reached an impasse in confronting the problem of consciousness. Scientific knowledge requires a scientist, but regarding knowledge concerning the scientist, they must remain silent. India has always emphasized knowledge of the conscious self or atma. Vedanta-sutra begins with the aphorism “athatho brahma jijnasa” – now, therefore, inquire about brahma (pure consciousness). Even in the West, the Greek philosopher Socrates stated, “Above all else know (...) the self.” But since the time of Newton, the objective world became the focus of science to the exclusion of the conscious observer or scientist. (shrink)

Modern science generally assumes that the same laws of logic apply to mechanical, chemical and biological entities alike because they are all ultimately material objects. This may seem to be so obvious that there would be no need to validate it -- experimentally or logically. In this article we would like to critically examine this assumption and show that from an experiential/observational level, as well as from a rational/logical level, it is not valid. This becomes apparent, for instance, when we (...) consider the simple observation in which we distinguish animate from inanimate objects: those objects that seem to spontaneously move themselves and those that move only when impelled by some applied force outside or beyond the object. This distinction may be valid at the macroscopic level more than at the level of theoretical atomic particles. Thus the detailed nature of spontaneous movement must also be understood. (shrink)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation (...) and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies. (shrink)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...) genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (shrink)

Neo-Darwinism can be usefully studied with the help of a Computerised Genetic Algorithm. Only a mathematical approach can reveal the shortcomings of the current dogma and point the way to a revised definition of the theory of evolution.

Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) in a more primitive one – namely, the homeodynamic capacity for the “specified variation of form”. In introducing a novel type of causal power – a „structural power‟ – we claim that it is the persistence of their dynamic potential to produce a specified series of structurally adaptive morphologies which grounds organisms‟ privileged status as metaphysically “one over many” over time. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. We discuss how mechanist and vitalist models of organism exist in a more complementary (...) relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...) organisms as essentially possessing some mechanisms that play this role. (shrink)

As part of a series of workshops on different aspects of biomedical ontology sponsored by the National Center for Biomedical Ontology (NCBO), a workshop titled "Ontologies of Cellular Networks" took place in Newark, New Jersey, on 27 to 28 March 2008. This workshop included more than 30 participants from various backgrounds in biomedicine and bioinformatics. The goal of the workshop was to provide an introduction to the basic tools and methods of ontology, as well as to enhance coordination between groups (...) already working on ontologies of cellular networks. The meeting focused on three questions: What is an ontology? What is a pathway? What is a cellular network? (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists sought (...) to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions (...) such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions. (shrink)

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the issues (...) are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

The first form of the inside-outside dichotomy appears as a self-encapsulated system with an active border. These systems are based on two complementary but asymmetric processes: constructive and interactive. The former physically constitute the system as a recursive network of component production, defining an inside. The maintenance of the constructive processes implies that the internal organization also constrains certain flows of matter and energy across the border of the system, generating interactive processes. These interactive processes ensure the maintenance of the (...) constructive processes thus specifying a meaningful outside. Upon this basic form of identity formation, the evolutionary and historical domain is open for the emergence of a whole hierarchy and ecology of insides and outsides. These which mutually subsume and collaborate in the maintenance of the essential inside-outside dichotomy that defines the conditions of possibility of the subjects and the worlds they generate. (shrink)

This chapter proceeds in five steps. First, we will describe and justify the structure of the traditional system of species classification. Second, we will discuss three formal principles governing the development of taxonomies in general. It will emerge that, in addition to these formal principles, a division of living beings must meet certain empirical constraints. In the third section, we will show that the traditional division of living beings into species best meets these constraints. Fourth, we will argue that a (...) taxonomic system based on this notion of species provides a more natural alternative to the many arbitrary classifications that are possible. Hence, the traditional classificatory system is also the most natural one. Finally, we will discuss and reject an alternative account that suggests defining species solely with a view to their evolutionary history. We will argue that taxonomic trees do not depict hereditary connections but, rather, something else. (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

Roderic Page’s new book, Tangled Trees: Phylogeny, Cospeciation and Coevolution (2003), is a worthwhile read for anyone interested in either methodological issues in systematics, or how organisms shape one another’s selective environments. “Cospeciation,” for the uninitiated, is the concurrent speciation of two or more lineages that are ecologically associated (e.g. host-parasite associations, as well as mutualistic or symbiotic associations). “Coevolution,” in contrast, is the reciprocal adaptation of hosts and parasite taxa. The main focus of Page’s book is thus when, how (...) and why the branching process of host taxa mirrors that of parasite taxa. “Parasite” here is broadly conceived to be anything from a louse to a virus to a retrotransposon, and “host” may be anything from a genome to a whale. (shrink)

This project begins with the selective sensory experience suggested by lngarden followed by an insensitivity he insinuates to digestive processes. This is juxtaposed with an oenological explanation of phenomenal sedimentation offered by Jean-Luc Marion. It compares the dynamics of time in the former with the those of wine in the latter. Emphasis is given to lngarden's insinuation of time as fluid, liquid, or aquatic. It revisits Ingarden's physiological explanations of partially-open systems by way of the bilateral excretion and absorption of (...) semi-permeable cellular membranes. The importance he eventually grants to inner secretion is considered alongside perspiration and salivation collateral to skin and membranes. It suggests that Ingarden's interest in thermoregulation, partial permeation, and secretion invites alternative conceptions of temporal consciousness in physiological experiences, beyond sequential and linear clock-time and/or Kantian intuition. Temporality experienced as temperance becomes discernible at a permeable point in which the sedimentation of Husserl, the maturation of Marion, and the fluidity and secretion of Ingarden mix and mingle into the taste of time. (shrink)

Bence Nanay has argued that we must abandon the etiological theory of teleological function because this theory explains functions and functional categories in a circular manner. Paul Griffiths argued earlier that we should retain the etiological theory and instead prevent the circularity by making etiologies independent of functional categories. Karen Neander and Alex Rosenberg reply to Nanay similarly, and argue that we should analyze functions in terms of natural selection acting not on functional categories, but merely on lineages. Nanay replies (...) that these lineages cannot be individuated except by reference to functional categories. Worryingly, Neander and Rosenberg themselves have previously argued persuasively that homology often depends on function. This article addresses their arguments and shows how to escape them: Regardless whether the arguments are right about long-term homological categories, they do not apply to generation-to-generation homology. The latter, moreover, is sufficient for individuating the lineages needed to explain teleological functions. (shrink)

Among philosophical analyses of Darwin’s Origin, a standard view says the theory presented there had no concrete observational consequences against which it might be checked. I challenge this idea with a new analysis of Darwin’s principal geographical distribution observations and how they connect to his common ancestry hypothesis.

There have been several recent attempts to think about psychological kinds as homologies. Nevertheless, there are serious epistemic challenges for individuating homologous psychological kinds, or cognitive homologies. Some of these challenges are revealed when we look at competing claims of cognitive homology. This paper considers two competing homology claims that compare human anger with putative aggression systems of nonhuman animals. The competition between these hypotheses has been difficult to resolve in part because of what I call the boundary problem: boundaries (...) between instances of psychological kinds (e.g., anger and fear) cannot be directly observed. Thus, there are distinctive difficulties for individuating psychological kinds across lineages. I draw four conclusions from this case study: First, recent evidence from the neuroscience of fear suggests that one of the proposed homologies involves a straightforward conflation of anger and fear. Second, this conflation arises because of the boundary problem. Third, there is an implicit constraint on the operational criteria that is easy to overlook in the psychological case. In this case, ignoring the constraint is part of the problem. Fourth, this is a clear case in which knowledge of homology cannot be accumulated piecemeal. Identifying homologs of human anger requires identifying homologs of fear. (shrink)

The function of a trait token is usually defined in terms of some properties of other (past, present, future) tokens of the same trait type. I argue that this strategy is problematic, as trait types are (at least partly) individuated by their functional properties, which would lead to circularity. In order to avoid this problem, I suggest a way to define the function of a trait token in terms of the properties of the very same trait token. To able to (...) allow for the possibility of malfunctioning, some of these properties need to be modal ones: a function of a trait is to do F just in case its doing F would contribute to the inclusive fitness of the organism whose trait it is. Function attributions have modal force. Finally, I explore whether and how this theory of biological function could be modified to cover artifact function. (shrink)

Homology is a natural kind concept, but one that has been notoriously elusive to pin down. There has been sustained debate over the nature of correspondence and the units of comparison. But this continued debate over its meaning has focused on defining homology rather than on its use in practice. The aim of this chapter is to concentrate on the practices of homologizing. I define “homologizing” to be a concept-in-use. Practices of homologizing are kinds of rule following, the satisfaction of (...) which demarcates a category—that of being a homologue. Identifying, explaining, discovering, and understanding are exchanges that connect practice to concept through the performance of a rule by practitioners. These practices are constitutive of natural kinding activities. If homologizing is a kind of kinding, consideration of these practices of discovery, tracking, and identification not only clarifies the meaning, use, and progression of the concept of homology, but provides further understanding of the processes and progression of natural kinds and kinding practices in general. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

Argues that biological organs, including mental capacities, should be identified by homology (not function).

Some plausibly necessary a posteriori theoretical claims include ‘water is H 2 O’, ‘gold is the element with atomic number 79’, and ‘cats are animals’. In this paper I challenge the necessity of the third claim. I argue that there are possible worlds in which cats exist, but are not animals. Under any of the species concepts currently accepted in biology, organisms do not belong essentially to their species. This is equally true of their ancestors. In phylogenetic systematics, monophyletic clades (...) such as the animal kingdom are composed of an ancestral stem species and all of its descendants. If the stem species had not existed, neither would the clade. Thus it could have been the case that all the organisms which actually belong to the animal kingdom might have existed yet not have been animals. (shrink)

Scientists cannot devise theories, construct models, propose explanations, make predictions, or even carry out observations, without first classifying their subject matter. The goal of scientific taxonomy is to come up with classification schemes that conform to nature's own. Another way of putting this is that science aims to devise categories that correspond to 'natural kinds.' The interest in ascertaining the real kinds of things in nature is as old as philosophy itself, but it takes on a different guise when one (...) adopts a naturalist stance in philosophy, that is when one looks closely at scientific practice and takes it as a guide for identifying natural kinds and investigating their general features. This Element surveys existing philosophical accounts of natural kinds, defends a naturalist alternative, and applies it to case studies in a diverse set of sciences. This title is also available as Open Access on Cambridge Core. (shrink)

Despite their centrality to medicine, drugs are not easily defined. We introduce two desiderata for a basic definition of medical drugs. It should: (a) capture everything considered to be a drug in medical contexts and (b) rule out anything that is not considered to be a drug. After canvassing a range of options, we find that no single definition of drugs can satisfy both desiderata. We conclude with three responses to our exploration of the drug concept: maintain a monistic concept, (...) or choose one of two pluralistic outcomes. Notably, the distinction between drugs and other substances is placed under pressure by the most plausible of the options available. (shrink)

Comparative cognitive science often involves asking questions like ‘Do nonhumans have C?’ where C is a capacity we take humans to have. These questions frequently generate unproductive disagreements, in which one party affirms and the other denies that nonhumans have the relevant capacity on the basis of the same evidence. I argue that these questions can be productively understood as questions about natural kinds: do nonhuman capacities fall into the same natural kinds as our own? Understanding such questions in this (...) way has several advantages: it preserves the intuition that these are substantive empirical questions worth asking; it helps us to understand why they so frequently give rise to disagreements of the kind described; and it provides clues about how to diagnose and resolve them. (shrink)

Some philosophers understand natural kinds to be the categories which are constraints on enquiry. In order to elaborate the metaphysics appropriate to such an account, I consider the complicated history of scurvy, citrus, and vitamin C. It may be tempting to understand these categories in a shallow way (as mere property clusters) or in a deep way (as fundamental properties). Neither approach is adequate, and the case instead calls for middle-range ontology: starting from categories which we identify in the world (...) and elaborating their structure, but not pretending to jump ahead to a complete story about fundamental being. (shrink)

This paper details the content and structure of the folk concept of life, and discusses its relevance for scientific research on life. In four empirical studies, we investigate which features of life are considered salient, universal, central, and necessary. Functionings, such as nutrition and reproduction, but not material composition, turn out to be salient features commonly associated with living beings (Study 1). By contrast, being made of cells is considered a universal feature of living species (Study 2), a central aspect (...) of life (Study 3), and our best candidate for being necessary for life (Study 4). These results are best explained by the hypothesis that people take life to be a natural kind subject to scientific scrutiny. (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)

In this paper, we focus on the propensity toward identifying natural kinds with successful scientific categories in contemporary discussions of natural kinds within the philosophy of science. Success in this case is understood as the fulfillment of epistemic interests or goals in a given field of scientific research. The prevailing view is that, in order to have a theory of natural kinds that successfully captures current scientific practice, the relevant epistemic interests are the current interests of scientists working in a (...) particular field. In contrast, we concur with the Franklin-Hall (2015) that a wider range of possible interests needs to be taken into account, in order to avoid making natural kinds too dependent on the current stage of research. But unlike Franklin-Hall who suggests looking for an intersection between the interests and goals of current epistemic agents and our neighboring epistemic agents (the categorical bottleneck view), we advocate the view that all these different interests and goals need to be taken into account, and thus our view takes into account a much wider range of categories. (shrink)

This paper defends an ontology of weak entity realism for homeostatic property cluster (HPC) theories of natural kinds, adapted from Bird’s (Synthese 195(4):1397–1426, 2018) taxonomy of such theories. Weak entity realism about HPC kinds accepts the existence of natural kinds. Weak entity realism denies two theses: that (1) HPC kinds have mind-independent essences, and that (2) HPC kinds reduce to entities, such as complex universals, posited only by metaphysical theories. Strong entity realism accepts (1) and (2), whereas moderate entity realism (...) accepts only (1). Given its commitment to (2), strong entity realism is more theoretically complex than weak entity realism, with little explanatory payoff. Given their commitment to (1), moderate and strong entity realisms cannot explain how the identity conditions of HPC kinds are to be straightforwardly knowable. I argue that weak entity realism avoids such epistemic difficulties. I further rebut two plausible criticisms of weak entity realism, namely that weak entity realism cannot account for quantification over kinds, and that weak entity realism cannot provide identity conditions for HPC kinds which are both scientifically useful and objective. Given the theoretical costs of strong and moderate entity realism, and weak entity realism’s adequate response to its most plausible challenges, weak entity realism about HPCs is to be preferred, especially for biological and chemical kinds. (shrink)