Biological individuality is a notoriously thorny topic for biologists and philosophers of biology. In this paper we argue that biological individuality presents multiple, interconnected questions for biologists and philosophers that together form a problem agenda. Using a case study of an interdisciplinary research group in ecology, behavioral and evolutionary biology, we claim that a debate on biological individuality that seeks to account for diverse practices in the biological sciences should be broadened to include and give prominence to questions about uniqueness (...) and temporality. We show that broadening the problem agenda of biological individuality draws attention to underrecognized philosophical issues and discussions and thereby organizes and enriches the existing debate. (shrink)

Chemical kinds are generally treated as having timelessly fixed identities. Biological kinds are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This article defends the thesis that biochemical molecules are clustered chemical kinds, some of which—namely, evolutionarily conserved units—are also biological kinds. On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be either resolved or dissolved. 1 Introduction2 Conflicting Intuitions about Kinds (...) of Proteins3 Against Permissive Pluralism4 Against Nominalism, Toward a Duality of Kinds5 Biological Kinds, Chemical Kinds, and Their Relations6 Implications for Biological Individuals7 Implications for Monism and Scientific Practice. (shrink)

John Dupr explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and society. He reveals how the advance of genetic science is changing our view of the constituents of life, and shows how an understanding of microbiology will overturn standard assumptions about the living world.

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a proper understanding (...) of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated with (...) substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

This Element is an introduction to the metaphysics of biology, a very general account of the nature of the living world. The first part of the Element addresses more traditionally philosophical questions - whether biological systems are reducible to the properties of their physical parts, causation and laws of nature, substantialist and processualist accounts of life, and the nature of biological kinds. The second half will offer an understanding of important biological entities, drawing on the earlier discussions. This division should (...) not be taken too seriously, however: the topics in both parts are deeply interconnected. Although this does not claim to be a scientific work, it does aim to be firmly grounded in our best scientific knowledge; it is an exercise in naturalistic metaphysics. Its most distinctive feature is that argues throughout for a view of living systems as processes rather than things or, in the technical philosophical sense, substances. (shrink)

Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73:864–875, 2006 ). Elements provide paradigmatic examples, since the atomic number should suffice to individuate the kind. In theory, Microstructuralism should also characterise higher-level chemical kinds such as molecules, compounds, and macromolecules based on their constituent atomic properties. In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests that (...) all the forms of microstructuralism cannot accommodate them. (shrink)

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 1020. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide (...) accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity. (shrink)

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

One of the foundational problems of biochemistry concerns the conceptualisation of the relationship between the composition, structure and function of macromolecules like proteins. Part of the recent philosophical literature displays a reductionist bias, that is, the endorsement of a form of microstructuralism mirroring an out-dated biochemical conceptualisation. We shall argue that such microstructuralist approaches are ultimately committed to a potentialist form of micro-predeterminism whereby the macrostructure and function of proteins is accounted for solely in terms of the intrinsic properties and (...) potentialities of the components of the primary structure as if they were self-contained or essentially immutable entities. We shall instead suggest that a conceptualisation of the relationship between proteins’ composition, structure and function consistent with contemporary biochemical practice should account also for the causal role of the cellular, organismal and environmental relations in protein development. The analysis of the folding process we propose suggests that microstructure-laden reductionist approaches are ontologically indefensible. Rather than a potentialist form of micro-predeterminism, our analysis ultimately supports a relational-construction-based view of protein development and potentialities formation, which requires an indispensable analysis of the dynamical interplay between the micro-level of the parts and the macro-level of the relational structures of their systems. (shrink)

Chemistry deals with substances and their transformations. School chemistry provides a picture of this in terms of small balls called atoms and ball-and-stick structures called molecules which, despite its crudity, has been taken to justifiably reflect a reductionist conception of macroscopic concepts like the chemical substances and chemical reactions. But with the recent interest in chemistry within the philosophy of science, an extensive and determined criticism has developed of the idea that the macroscopic world has been, or is likely to (...) be, reduced to microscopic theory. From this perspective, it is of interest to see macroscopic ontology treated autonomously. I try to take a first few steps towards spelling this out. It involves recognising entities falling into two broad categories: continuants-things which can have different properties at different times — and processes — things whose temporal parts may have different features, but which themselves stand in contrast to continuants in this respect. The character of each and their interrelations depends on their mereological structure of parts, the exploration of which is one of the prime purposes of the paper. (shrink)

The general question to be considered in this paper points to the nature of the world described by chemistry: what is macro-chemical ontology like? In particular, we want to identify the ontological categories that underlie chemical discourse and chemical practice. This is not an easy task, because modern Western metaphysics was strongly modeled by theoretical physics. For this reason, we attempt to answer our question by contrasting macro-chemical ontology with the mainstream ontology of physics and of traditional metaphysics. In particular, (...) we introduce the distinction between stuff-ontology, proper of chemistry, and individual-ontology, proper of physics. These two ontologies differ from each other in the basic categories of their own structures. On this basis, we characterize individual-ontology in such a way that the features of stuff-ontology will arise by contrast with it. (shrink)

Reductionism remains the dominant philosophical framework of modern science. Within reductionism, the universe is conceived as a probabilistic and deterministic system guided solely by the laws of physics and mathematics. Under the guidance of reductionist thought, the development of the modern atomic theory and quantum mechanics has drastically changed science, medicine, and philosophy. In particular, the standard model of particle physics remains the crowning achievement of over three hundred years of reductionist thought in both physics and chemistry. Yet developments within (...) chemistry suggest a new paradigm is required to overcome the limitations of reductionism and provide chemists a more fruitful model. This article will argue that a version of relational ontology provides an avenue for elucidating and predicting chemical and atomic phenomena. In relational ontology, the ontological status of an enduring entity in any moment is viewed as a composite of its own inherited properties and the influences of other entities, especially those closely related to it within a system. This view encompasses the causal aspects of the world without denying its dynamic and creative nature while providing a richer understanding of chemistry and other scientific fields. (shrink)

Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be made more complicated (...) in order to accommodate such challenges; and finally, at what this increasingly complicated picture implies for our standard assessment of chemical kindhood—primarily, for the widespread assumption that chemical kinds in general are more neat and tidy than those messy biological ones. _1_ The Received View _2_ A Taxonomy of Chemical Kinds _3_ Atomic Number _4_ H2O, H3O+, OH−, and More _5_ Complicating the Microstructuralist Picture _6_ Concrete and Other Mixtures _7_ Macromolecules, Especially Proteins _8_ Abandoning Sameness of Elemental Composition _9_ Not So Different after All. (shrink)

This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing characteristic (...) of protein taxonomy. (shrink)

Understanding the 'making-up' relations, to put things neutrally, posited in mechanistic explanations the sciences is finally an explicit topic of debate amongst philosophers of science. In particular, there is now lively debate over the nature of the so-called 'realization' relations between properties posited in such explanations. Despite criticism (Gillett, Analysis 62: 316-323, 2002a), the most common approach continues to be that of applying machinery developed in the philosophy of mind to scientific concepts in what is known as the 'Flat' or (...) 'Subset' model of 'realization' (Kim, Mind in a physical world, 1998; Shapiro, J Philos XCVII: 635-654, 2000; Clapp, J Philos XCVIII: 111-136,2001 ; Wilson, Philos Stud 145: 149-169,2009). My primary goal in this paper is to show in still more detail that the Subset model of realization is inadequate for the descriptive task of describing the 'making-up' relations posited between properties or their instances in mechanistic explanations in the higher sciences. And my secondary goal is to highlight why this critique of the Subset view as a first-order descriptive account also shows there are deep difficulties in using the Subset account to address second-order issues in the philosophy of science as well. (shrink)

Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...) reductionism and hence motivate a dual theory of chemical and biological kinds, a type of pluralism about natural kinds. But it will be argued that the challenge, which is based on multiple realization, can be addressed. The upshot is that there are reasonable prospects for ontological reductionism about biochemical kinds, which corroborates natural kind monism. (shrink)

Chemistry deserves more philosophical attention not so much to do justice to a long-neglected science or to enhance its cultural prestige, but to undermine a number of taken-for-granted assumptions about scientific rationality and more importantly to diversify our metaphysical views of nature and reality. In brief, this paper does not make the case for a philosophy of chemistry. It rather urges philosophers of science to listen to chemists and discuss what they learn from them. Because over the course of many (...) centuries chemists have developed a special access to nature and a special way of investigating and dealing with material substances, they have confronted a number of epistemological and ontological issues that are worth discussing. Following critical remarks about the disciplinary partition of philosophy, a historical section presents the contributions to philosophy of a few French twentieth-century chemists-turned philosophers to emphasize how they have challenged the dominant philosophical categories. The final section develops one of the lessons that philosophers can learn from chemists: to pay attention to things, to their materiality and activity in order to develop new ontological perspectives. (shrink)

An individual, as this term will be understood here, is an entity to which the concepts of unity and identity fully and determinately apply. That is to say, an entity x is an individual just in case x determinately counts as one entity and x has a determinate identity. Many philosophers tacitly assume that all entities are individuals in the foregoing sense, and indeed that it is a necessary truth that they are. But this can certainly be disputed. It is, (...) very arguably, both logically and metaphysically possible for there to be nonindividuals. The aim of this chapter is to clarify and explore both the notion of an individual and that of a nonindividual, to propose a typology of entities based on the individual/nonindividual distinction, and to illustrate the potential of these notions for application within and across the sciences. (shrink)

Given the rich diversity of research fields usually ascribed to chemistry in a broad sense, the present paper tries to dig our characteristic parts of chemistry that can be conceptually distinguished from interdisciplinary, applied, and specialized subfields of chemistry, and that may be called chemistry in a very narrow sense, or 'the chemical core of chemistry'. Unlike historical, ontological, and 'anti-reductive' approaches, I use a conceptual approach together with some methodological implications that allow to develop step by step a kind (...) of cognitive architecture for chemistry, which basically contains: (1) systematic chemical knowledge on the experimental level; (2) clarification of chemical species; (3) chemical classification systems; (4) theoretical foundation through the chemical theory of structural formulas. In a succeeding paper the results will be checked for resisting physicalistic reduction. (shrink)

Molecular change is central to chemistry and has traditionally been interpreted within a metaphysical framework that places emphasis on things and substance. This paper seeks an alternative view based on process metaphysics. The core doctrines of process thought, which give ontological priority to becoming over being, cohere well with modern chemical thinking and support a view of molecules as dynamic systems whose identities endure through time as patterns of stability. Molecular change is then seen as excursions to new stability patterns. (...) Finally, when molecular change is viewed as foundational to emergent complexity, process metaphysics allows evolution to be seen as creative molecular advance. (shrink)