Which categories of entities qualify as ontological categories? Which combinations of categories qualify as adequate systems of ontological categories? These are the two questions the author focuses on in this article. Contrary to the usual praxis in contemporary ontological literature, he addresses both questions conjointly. First, the author presents some problems of characterizing ontological categories in purely extensional terms, i.e. as widely inclusive natural classes. Second, he introduces the transversality requirement: (...) class='Hi'>ontological categories should be individually and naturally domain-transversal, i.e. ontological categories must be neutral concerning different scientific disciplines like physics, biology and mathematics. As a result, ontological categories must have instances in any domain of reality. Finally, the author checks the adequacy of some systems of ontological categories according to this criterion and meets some possible objections. (shrink)

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his (...) main conclusions are rejected; rather it is main arguments for them that are the focus. (shrink)

A classification of models of reduction into three categories — theory reductionism, explanatory reductionism, and constitutive reductionism — is presented. It is shown that this classification helps clarify the relations between various explications of reduction that have been offered in the past, especially if a distinction is maintained between the various epistemological and ontological issues that arise. A relatively new model of explanatory reduction, one that emphasizes that reduction is the explanation of a whole in terms of its (...) parts is also presented in detail. Finally, the classification is used to clarify the debate over reductionism in molecular biology. It is argued there that while no model from the category of theory reduction might be applicable in that case, models of explanatory reduction might yet capture the structure of the relevant explanations. (shrink)

Feminist philosophers of biology bring the tools of feminist theory, and in particular the tools of feminist philosophy of science, to investigations of the life sciences. While the critical examination of the categories of sex and gender (which will be explained below) takes a central place, the methods, ontological assumptions, and foundational concepts of biology more generally have also enjoyed considerable feminist scrutiny. Through such investigations, feminist philosophers of biology reveal the extent to which the (...) theory and practice of particular scientific disciplines and research programs (and, indeed, their philosophical study) are intertwined with both value judgments and social hierarchies. (shrink)

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual “messiness” (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct (...) some of the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics. (shrink)

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of (...) the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations. (shrink)

In recent years, postgenomic research, and the fields of epigenetics and microbiome science in particular, have described novel ways in which social processes of racialization can become embodied and result in physiological and health-related racial difference. This new conception of biosocial race has important implications for philosophical debates on the ontology of race. We argue that postgenomic research on race exhibits two key biases in the way that racial schemas are deployed. Firstly, although the ‘new biosocial race’ has been characterized (...) as social race entering into biological processes, it is only particular aspects of social race that are taken to cross the biosocial boundary, resulting in a distorted view of the social component of biosocial race. Secondly, racial categories are assumed to be stable across time and space. This assumption is epistemically limiting, as well as indicating a reliance on a fixed racial ontology. However, the causal pathways for the embodiment of social race, and the different possible modes of embodiment, that postgenomic science is uncovering themselves present a challenge for fixed or static racial ontologies. Given these tensions, we argue that the emerging picture of a shifting landscape of entanglement between the social and the biological requires us to increase the complexity of our ontologies of race, or even embrace a deflationary metaphysics of race. (shrink)

Well prior to the invention of the term ‘biology’ in the early 1800s by Lamarck and Treviranus (and lesser-known figures in the decades prior), and also prior to the appearance of terms such as ‘organism’ under the pen of Leibniz and Stahl in the early 1700s, the question of ‘Life’, that is, the status of living organisms within the broader physico-mechanical universe, agitated different corners of the European intellectual scene. From modern Epicureanism to medical Newtonianism, from Stahlian animism to (...) the discourse on the ‘animal economy’ in vitalist medicine, models of living being were constructed in opposition to ‘merely anatomical’, structural, mechanical models. It is therefore striking that the classic narratives of the Scientific Revolution conspicuously avoid any consideration of what status to grant living beings in a newly physicalized universe (I discuss this in Wolfe 2011, 2019 chapt. 1). Neither Harvey, nor Boyle, nor Locke (to name some likely candidates, the latter having studied with Willis and collaborated with Sydenham) ever ask what makes organisms unique, or conversely, what does not. In this chapter I seek to establish how something we might call ‘the knowledge of Life’, to use an expression of Georges Canguilhem’s, emerged as part of early modernity without being part of the mainstream history of life science. This leads to the question, can one can correlate early modern “knowledge of life” with the emergence of a science called ‘biology’? (see Zammito 2018, Wolfe 2019, Bognon-Küss and Wolfe eds. 2019). It was once fashionable to speak of, e.g. ‘precursors of Darwin’, and then Canguilhem and Foucault famously did away with the category of precursor. But how then do we account for the phase that precedes the constitution of a science? With the case of biology, how do we account for the increasing fascination with the ontology of Life during the decades prior to the ‘naming of biology’, as McLaughlin has called it, at the end of the eighteenth century? This increased focus on Life and the ontology of Life sits awkwardly, both with mainstream narratives of the Scientific Revolution and of the history of biology. In seeking to address this increased focus (in which vitalism plays a role but was by no means the only conceptual actor: Wolfe 2020), I critically examine Foucault’s notorious claim (Foucault 1966) that there was no such thing as ‘Life’ in the eighteenth century and thus no such thing as biology. (shrink)

An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in (...) the first two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the anthropic (...) principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

This article is devoted to examining the ontological foundations of computer-generated music scores. Specifically, we focus on the categorial question, i.e., the inquiry that aims to determine the kind of ontological category that musical works belong to. This task involves considerations concerning the existence and persistence conditions for musical works, and it has consequences for the determination of what it is to compose a musical work. Our contention is that not all the possible answers to the categorial question (...) in the ontology of music are equally compatible with the hypothesis that creative music systems compose musical works. The thesis defended here is that musical Platonism is the proposal that best accommodates this hypothesis. We claim that musical Platonism is the answer to the categorial question that offers the most straightforward explanation for the possibility of considering creative music systems as genuinely composing musical works. Moreover, we uphold that the notion of creative-evaluative discovery as the characterization of what it is to compose a musical work entailed by Platonism is the simplest explanation of the process developed by a computer in producing musical works. For this purpose, we will take as empirical data the features of the Iamus computer, a system that produces musical works autonomously using evolutionary algorithms and following an evo-devo strategy. The works generated by this computer have been recorded by the London Symphony Orchestra and other renowned international soloists, and its impact has been notable in the literature (Ball, 2012; Coghlan, 2012; Berger, 2013). (shrink)

The seventeenth century was a period of extraordinary invention, discovery and revolutions in scientific, social and political orders. It was a time of expansive automation, biological discovery, rapid advances in medical knowledge, of animal trials and a questioning of the boundaries between species, human and non-human, between social classes, and of the assumed naturalness of political inequality. This book gives a tour through those objects, ordinary and extraordinary, which captivated the philosophical imagination of the single most important French philosopher of (...) this period, Rene Descartes. Deborah J. Brown and Calvin G. Normore document Descartes' attempt to make sense of the complex, composite objects of human and divine invention, consistent with the fundamental tenets of his metaphysical system. Their central argument is that, far from reducing all the categories of ordinary experience to the two basic categories of substance, mind and body, Descartes' philosophy recognises irreducible composites that resist reduction, and require their own distinctive modes of explanation. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit (...) consisting of parts. But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the brain is (...) evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)

In Kaplan and Winther’s recent article (Biol Theory. doi:10.1007/s13752-012-0048-0, 2012) they argue for three bold theses: first, that “it is illegitimate to read any ontology about ‘race’ off of biological theory or data”; second, that “using biological theory to ground race is a pernicious reification”; and, third, that “race is fundamentally a social rather than a biological category.” While Kaplan and Winther’s theses are thoughtful, I show that the arguments that their theses rest on are unconvincing. In order to be (...) constructive, I go on to show exactly how one can use biological theory and data to legitimately infer an ontological view of race, to infer a biological view of race that is not a reification, and to argue that race is both socially constructed and biologically real. (shrink)

Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the brain is (...) evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)

A novel conceptual framework is introduced for the Complexity Levels Theory in a Categorical Ontology of Space and Time. This conceptual and formal construction is intended for ontological studies of Emergent Biosystems, Super-complex Dynamics, Evolution and Human Consciousness. A claim is defended concerning the universal representation of an item’s essence in categorical terms. As an essential example, relational structures of living organisms are well represented by applying the important categorical concept of natural transformations to biomolecular reactions and relational structures (...) that emerge from the latter in living systems. Thus, several relational theories of living systems can be represented by natural transformations of organismic, relational structures. The ascent of man and other living organisms through adaptation, is viewed in novel categorical terms, such as variable biogroupoid representations of evolving species. Such precise but flexible evolutionary concepts will allow the further development of the unifying theme of local-to-global approaches to highly complex systems in order to represent novel patterns of relations that emerge in super- and ultra-complex systems in terms of compositions of local procedures. Solutions to such local-to-global problems in highly complex systems with ‘broken symmetry’ might be possible to be reached with the help of higher homotopy theorems in algebraic topology such as the generalized van Kampen theorems (HHvKT). Categories of many-valued, Łukasiewicz-Moisil (LM) logic algebras provide useful concepts for representing the intrinsic dynamic ‘asymmetry’ of genetic networks in organismic development and evolution, as well as to derive novel results for (non-commutative) Quantum Logics. Furthermore, as recently pointed out by Baianu and Poli (Theory and applications of ontology, vol 1. Springer, Berlin, in press), LM-logic algebras may also provide the appropriate framework for future developments of the ontological theory of levels with its complex/entangled/intertwined ramifications in psychology, sociology and ecology. As shown in the preceding two papers in this issue, a paradigm shift towards non-commutative, or non-Abelian, theories of highly complex dynamics—which is presently unfolding in physics, mathematics, life and cognitive sciences—may be implemented through realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. (shrink)

This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained (...) by original sin (we were all there). As another example of a theological motivation, some take the organism as an obvious starting point for a teleological argument for God’s existence, and this staring point is sometimes developed into a full-blown theory of pre-existence. The second category could be thought of as non-theological metaphysical, and paramount here is the desire to deal with the metaphysical problem of individuation. So, for example, Leibniz embraces a version of hylomorphism in order to overcome difficulties with Descartes’ theory of material substance, including the difficulty of how to account for enduring material individuals, and Leibniz’s hylomorphism is closely linked with his embrace of pre-existence. The third category might be termed “biological”, and one example of such a concern is how to explain the organic unity of living beings where the whole seems to ontologically precede the parts. This is frequently translated into a temporal priority of whole to parts, and thus pre-existence is posited. Of course, many natural philosophers of the early modern period embrace pre-existence for more than one reason, but in general, these are the three classes of motivations one might have for embracing the theory. In the second part of the paper I examine in detail one argument that appears in the work of Malebranche. On the face of it, this argument seems to be a biological one, specifically the biological or organic holism argument mentioned above. But upon closer examination, I shall argue, Malebranche’s reasons for endorsing pre-existence bring together several of the arguments discussed in the first part of the paper. I conclude with some considerations about what we can learn about Malebranche as a natural philosopher from his motivations for holding the pre-existence doctrine of generation. (shrink)

There have been attempts to get some logic out of belief dynamics, i.e. attempts to define the constants of propositional logic in terms of functions from sets of beliefs to sets of beliefs. It is interesting to see whether something similar can be done for ontological categories, i.e. ontological constants. The theory presented here will be a (modest) expansion of belief dynamics: it will not only incorporate beliefs, but also parts of beliefs, so called belief fragments. On (...) the basis of this we will give a belief-dynamical account of the ontological categories of states of affairs, individuals, properties of arbitrary adicities and properties of arbitrary orders. (shrink)

This chapter contains sections titled: Preliminaries 1 The Highly Problematic Status of the Category of Substance 2 A New Approach: Prime State of Affairs (“Pristate”) as the Only Ontological Category at the Fundamental Level 3 Concluding Remarks.

The category of ‘organism’ has an ambiguous status: is it scientific or is it philosophical? Or, if one looks at it from within the relatively recent field or sub-field of philosophy of biology, is it a central, or at least legitimate category therein, or should it be dispensed with? In any case, it has long served as a kind of scientific “bolstering” for a philosophical train of argument which seeks to refute the “mechanistic” or “reductionist” trend, which has been (...) perceived as dominant since the 17th century, whether in the case of Stahlian animism, Leibnizian monadology, the neo-vitalism of Hans Driesch, or, lastly, of the “phenomenology of organic life” in the 20th century, with authors such as Kurt Goldstein, Maurice Merleau-Ponty, and Georges Canguilhem. In this paper I try to reconstruct some of the main interpretive ‘stages’ or ‘layers’ of the concept of organism in order to critically evaluate it. How might ‘organism’ be a useful concept if one rules out the excesses of ‘organismic’ biology and metaphysics? Varieties of instrumentalism and what I call the ‘projective’ concept of organism are appealing, but perhaps ultimately unsatisfying. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 39.3 (2001) 437-438 [Access article in PDF] Michael V. Wedin. Aristotle's Theory of Substance: The Categories and Metaphysics Zeta. Oxford Aristotle Studies. New York: Oxford University Press, 2000. Pp. xiii + 482. Cloth, $55.00. Michael Wedin has written the equivalent for Aristotle of what biblical scholars would call a "harmony of the gospels." It is a wonderfully rich and argumentatively dense reconstruction (...) of Aristotle's two most important treatises on substance, the Categories and Metaphysics Zeta, works that many of our most able Aristotle scholars have declared irreconcilable.The first chapter, on "the plan" of the Categories, includes a sensible account of the role in that work of the "onymies," as Wedin calls homonymy, synonymy, and paronymy. The second chapter, which focuses on "nonsubstantial individuals" in the Categories, gives the most philosophically sophisticated reconstruction known to me of how Aristotle might have conceived this white in Socrates to be a nonrecurrent particular. Having myself contributed to the glut of recent scholarship on nonsubstantial individuals in the Categories, I have personal, as well as professional, reasons to praise the rigor and insight of this chapter.In Chapter 3 Wedin tries to pin down the ontological commitment of Aristotle's Categories. Since, if there were no primary substances there would not be anything else, the fundamental ontological commitment of the Categories is a commitment to primary substances. Individual nonsubstances exist just in case there are primary substances in which they inhere. As for species and genera of substances and species and genera of the nonsubstantial individuals that inhere in them, Wedin finds Aristotle curiously indifferent to their existence.Chapter 4, a transitional chapter, takes up a range of possible views on the relation between the Categories and Metaphysics Zeta. Incompatibilism is argued against, yet the arguments for compatibilism in recent commentaries are found to be insufficient. In the next chapter Wedin moves on to his own statement of, and justification for, compatibilism.The key to Wedin's compatibilist interpretation is the distinction he draws between being a substance and being the "substance-of" something. Zeta can then be seen to be supplementing, rather than revising, let alone contradicting, the Categories, if Zeta can be understood to be about the substance-of the primary substances of the Categories (157-8).Aristotle proposes in Z3 three candidates for what the substance of, say, Socrates, is, namely, his matter, his form, and the compound of the two. Aristotle settles on form and discusses form as essence in Z4 and Z5, which discussion Wedin takes up in his own [End Page 437] Chapter 6. Then in Chapter 7 Wedin takes on the enigmatic claim of Z6, "In the case of things that are primary and spoken of per se, it is clear that the thing and the essence of the thing are the same" (1032a4-6).Wedin makes Chapter 8, which is primarily a treatment of Z10 and Z11, a discussion of Aristotle on "compositional plasticity," that is, on whether, say, the form of human being might be realized in something other than flesh and bones. "[O]ne could grant," Wedin writes, that to be a human being is just to be a member of a determinate biological species and so to have a very specific material nature, and yet insist that the form of such creatures be realizable in quite different sorts of matter. Creatures so constituted would not be human beings but they would be entities with similar functional capacities and states... From the point of view of philosophy of mind, for example, what matters are the psychological capacities, functions, and states characteristic of persons. Just what these are is determined by a form—the form that happens to be realized in human matter. (340-41) In Chapter 9 Wedin turns to Z13, which, as he acknowledges, has often been thought to be the most confounding chapter in Zeta. Wedin draws on Z16 to help resolve the aporia with which Z13 ends (roughly this... (shrink)

Frank E. Zachos offers a comprehensive review of one of today's most important and contentious issues in biology: the species problem. After setting the stage with key background information on the topic, the book provides a brief history of species concepts from antiquity to the Modern Synthesis, followed by a discussion of the ontological status of species with a focus on the individuality thesis and potential means of reconciling it with other philosophical approaches. More than 30 different species (...) concepts found in the literature are presented in an annotated list, and the most important ones, including the Biological, Genetic, Evolutionary and different versions of the Phylogenetic Species Concept, are discussed in more detail. Specific questions addressed include the problem of asexual and prokaryotic species, intraspecific categories like subspecies and Evolutionarily Significant Units, and a potential solution to the species problem based on a hierarchical approach that distinguishes between ontological and operational species concepts. A full chapter is dedicated to the challenge of delimiting species by means of a discrete taxonomy in a continuous world of inherently fuzzy boundaries. Further, the book outlines the practical ramifications for ecology and evolutionary biology of how we define the species category, highlighting the danger of an apples and oranges problem if what we subsume under the same name ("species") is in actuality a variety of different entities. A succinct summary chapter, glossary and annotated list of references round out the coverage, making the book essential reading for all biologists looking for an accessible introduction to the historical, philosophical and practical dimensions of the species problem. (shrink)

This volume is about ontological categories. The categories of an ontology are designed to classify all existents. They are crucial and characterize an ontology.

In medicine, racial differences are frequently presented as part of the best explanation of differences in the risk of diseases. The problem of using racial classification in biomedical research has become important because of its ethical consequences in society. However, the biological relevance of the concept of race cannot be established by any ethical argument and the epistemological role of racial categorisation requires clarification. In this paper, different issues related to the concept of race are considered. This paper analyses the (...) semantic problem concerning the definition of race, considers the ontological problem of race, drawing attention to the biological evidence for genetic differences among human groups, and presents a promising epistemological approach to the problem of race. The purpose of the paper is to examine whether, or when, racial categories belong in biological explanations. It shows that the concept of race cannot be justified in biology because it does not lead to successful predictions, and that genetic discontinuities are sufficient to explain differences in diseases but not needed in the explanation. The biomedical field should search for genetic patterns related to diseases, and should not assume racial discontinuities among human groups and use racial clusters as proxies for undetected genetic patterns. (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization—the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established—do not require what would have to be a stipulative sharpening of an organism concept.

Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed into (...) their parts and their activities can be decomposed into component operations. A potent bridge between flat networks and hierarchical mechanisms is provided by biological ontologies, both those curated by hand such as Gene Ontology and those extracted directly from databases such as Network Extracted Ontology. I examine several examples in which by applying ontologies to networks, systems biologists generate new hypotheses about mechanisms and characterize these novel strategies for developing mechanistic explanations. (shrink)

The concept of an ontological category is central to metaphysics. Metaphysicians argue about which category of existence an object should be assigned to, whether one category can be reduced to another one, or whether there might be different equally adequate systems of categorization. Answers to these questions presuppose a clear understanding of what precisely an ontological category is, and Jan Westerhoff now provides the first in-depth analysis. After examining a variety of attempted definitions, he proceeds to argue for (...) a new understanding of ontological categories, according to which they are systematizations of our knowledge of the world rather than essential characteristics of the world itself. Metaphysicians will find his work highly stimulating. (shrink)

This paper addresses the ontological status of the ontological categories as defended within E.J. Lowe’s four-category ontology (kinds, objects, properties/relations, and modes). I consider the arguments in Griffith (2015. “Do Ontological Categories Exist?” Metaphysica 16 (1):25–35) against Lowe’s claim that ontological categories do not exist, and argue that Griffith’s objections to Lowe do not work once we fully take advantage of ontological resources available within Lowe’s four-category ontology. I then argue that the (...) claim that ontological categories do not exist has no undesirable consequences for Lowe’s brand of realism. (shrink)

The concept of an ontological category is central to metaphysics. Metaphysicians argue about which category an object should be assigned to, whether one category can be reduced to another one, or whether there might be different equally adequate systems of categorization. Answers to these questions presuppose a clear understanding of what precisely an ontological category is, an issue which is rarely addressed; Jan Westerhoff presents the first in-depth analysis both of the use made of ontological categories (...) in the metaphysical literature, and of various attempts at defining them. He also develops a new theory of ontological categories which implies that there will be no unique system, and that the ontological category an object belongs to is not an essential property of that object. Systems of ontological categories are structures imposed on the world, rather than reflections of a deep metaphysical reality already present. All metaphysicians should find Westerhoff's book highly stimulating. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to (...) those who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

The task of this chapter is to investigate and assess Grossmann’s view of the ontological status of categories. It has two dimensions. Because Grossmann does not offer a full discussion of the ontology of categories, we first need to present an interpretation of his view. Our point of departure is Grossmann’s claim that a category is a fundamental property of being (which implies that he holds view 3 above). Our second task is to assess the adequacy of (...) his view. We do this by raising some problems with Grossmann’s account, offering as an alternative view a version of 4 above, and defending it against what we construe as Grossmann’s possible counter-arguments. We argue that the best way to view categories themselves is as ontologically neutral insofar as this opens the way for particular categories to be linguistic entities, mental acts, or properties of extra-mental things. This requires, in turn, a qualified defense of two views rejected by Grossmann—common natures and modes of being. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended to a Łukasiewicz–Moisil (...) Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

I describe an account of ontological categories which does justice to the facts that not all categories are ontological categories and that ontological categories can stand in containment relations. The account sorts objects into different categories in the same way in which grammar sorts expressions . It then identifies the ontological categories with those which play a certain role in the systematization of collections of categories. The paper concludes by (...) noting that on my account what ontological categories there are is partially interest-relative, and that furthermore no object can belong essentially to its ontological category. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, (...) and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

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

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies (...) via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

Although a considerable degree of precision has been introduced both into the formulation and the discussion of ontological theories by the use of formal methods there is still a remarkable indefiniteness about foundational issues. In particular it is not clear what an ontological category is and why we regard something as an ontological category. This is amazing given that the notion of ontological category is in fact the most basic of the whole of ontology: it is (...) what this discipline is about. (shrink)