Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (shrink)

A recent development in biology has been the growing acceptance that holobionts, entities comprised of symbiotic microbes and their host organisms, are widespread in nature. There is agreement that holobionts are evolved outcomes, but disagreement on how to characterize the operation of natural selection on them. The aim of this paper is to articulate the contours of the disagreement. I explain how two distinct foundational accounts of the process of natural selection give rise to competing views about evolutionary individuality.

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (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)

Human persons exist longer than a single moment in time; they persist through time. However, so far it has not been possible to make this natural and widespread assumption metaphysically comprehensible. The philosophical debate on personal identity is rather stuck in a dilemma: reductionist theories explain personal identity away, while non-reductionist theories fail to give any informative account at all. This chapter argues that this dilemma emerges from an underlying commitment, shared by both sides of in the debate, to an (...) ontology which that gives the priority to static unchanging things. The claim defended here is that the dilemma of personal identity can be overcome if we acknowledge the biological nature of human persons and switch to a process- ontological framework that takes process and change to be ontologically primary. Human persons are biological higher-order processes, rather than things, and their identity conditions can be scientifically investigated. (shrink)

There is no consensus on how to define substance, but one popular view is that substances are entities that are independent in some sense or other. E. J. Lowe’s version of this approach stresses that substances are not dependent on other particulars for their identity. I develop the meaning of this proposal, defend it against some criticisms, and then show that others do require that the theory be modified.

The paper takes off from the problem of finding a proper content for the relation of identity as it holds or fails to hold among ordinary things or substances. The necessary conditions of identity are familiar, the sufficient conditions less so. The search is for conditions at once better usable than the Leibnizian Identity of Indiscernibles (independently suspect) and strong enough to underwrite all the formal properties of the relation.It is contended that the key to this problem rests at the (...) level of metaphysics and epistemology alike with a sortalist position. Sortalism is the position which insists that, if the question is whether a and b are the same, it has to be asked what are they? Any sufficiently specific answer to that question will bring with it a principle of activity or functioning and a mode of behaviour characteristic of some particular kind of thing by reference to which questions of persistence or non-persistence through change can be adjudicated.These contentions are illustrated by reference to familiar examples such as the human zygote, the Ship of Theseus and Shoemaker's Brown-Brownson. The first example is hostage for a mass of unproblematical cases. The problems presented by the second and third sort of examples arise chiefly (it is claimed) from an incompleteness in our conceptions of the relevant sort—the what the thing in question is. That incompleteness need not prevent us from knowing perfectly well which thing we are referring to. In the concluding section, sortalism is defended against various accusations of anthropocentrism.The paper touches on the interpretation of Heraclitus, Leibniz's theory of clear indistinct ideas, the difficulties of David Lewis's ‘perdurantist’ or stroboscopic view of persistence, four-dimensionalism, and the relation of personal identity both to experiential memory and to the particular bodily physiognomy of a subject. At some points—as in connection with the so-called Only a and b rule—the paper corrects, supplements or extends certain theses or formulations proposed in the author's Sameness and Substance Renewed (2001). (shrink)

Traditionally, independence accounts of substance have held pride of place. Aristotle, Aquinas, Descartes and Spinoza—among many others—accepted independence accounts in one form or another. The general thrust of such views is that substances are those things that are apt to exist in themselves. In this paper, I argue that several contemporary independence theories of substance—including those of Kit Fine, E.J. Lowe and Michael Gorman—include an ad hoc element that renders them unacceptable. I'll also consider the theories of Hoffman and Rosenkrantz.

This paper defends a substance-based metaphysics for organisms against three arguments for thinking that we should replace a substantial understanding of living things with a processual one, which are offered by Dan Nicholson and John Dupré in their edited collection, Everything Flows: Towards a Processual Philosophy of Biology. Dupré and Nicholson consider three main empirical motivations for the adoption of a process ontology in biology. These motivations are alleged to stem from facts concerning metabolism; the life cycles of organisms; and (...) ecological interdependence. The paper discusses each of the three arguments in turn and concludes that none gives us any compelling reason to abandon the metaphysics of things. At best, they are arguments against a kind of caricature substance metaphysics that ought never to have been in the running in any case. Then, at the end of the paper, it is suggested that there may be more positive arguments for insisting on retaining things in our metaphysics, arguments which, perhaps ironically get their main impetus from the phenomenon of life. (shrink)

The paper considers and opposes the view that processes are best thought of as continuants, to be differentiated from events mainly by way of the fact that the latter, but not the former, are entities with temporal parts. The motivation for the investigation, though, is not so much the defeat of what is, in any case, a rather implausible claim, as the vindication of some of the ideas and intuitions that the claim is made in order to defend — and (...) the grounding of those ideas and intuitions in a more plausible metaphysics than is provided by the continuant view. It is argued that in addition to a distinction between events and processes there is room and need for a third category, that of the individual process, which can be illuminatingly compared with the idea of a substance. Individual processes indeed share important metaphysical features with substantial continuants, but they do not lack temporal parts. Instead, it is argued that individual processes share with substantial continuants an important property I call ‘modal robustness in virtue of form’. The paper explains what this property is, and further suggests that the category of individual process, thus understood, might be of considerable value to the philosophy of action. (shrink)

Persistence through time is like extension through space. A road has spatial parts in the subregions of the region of space it occupies; likewise, an object that exists in time has temporal parts in the various subregions of the total region of time it occupies. This view — known variously as four dimensionalism, the doctrine of temporal parts, and the theory that objects “perdure” — is opposed to “three dimensionalism”, the doctrine that things “endure”, or are “wholly present”.1 I will (...) attempt to resolve this dispute in favor of four dimensionalism by means of a novel argument based on considerations of vagueness. But before argument in this area can be productive, I believe we must become much clearer than is customary about exactly what the dispute is, for the usual ways of formulating the dispute are flawed, especially where three dimensionalism is concerned. (shrink)

A natural picture to have of events and processes is of entities which extend through time and which have temporal parts, just as physical objects extend through space and have spatial parts. While accepting this picture of events, in this paper I want to present an alternative conception of processes as entities which, like physical objects, do not extend in time and do not have temporal parts, but rather persist in time. Processes and events belong to metaphysically distinct categories. Moreover (...) the category of events is not the more basic of the two. (shrink)

This paper is about the neglected question of what sort of things we are metaphysically speaking. It is different from the mind-body problem and from familiar questions of personal identity. After explaining what the question means and how it differs from others, the paper tries to show how difficult it is to give a satisfying answer.

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the (...) most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

Kit Fine; XIV*—Ontological Dependence, Proceedings of the Aristotelian Society, Volume 95, Issue 1, 1 June 1995, Pages 269–290, https://doi.org/10.1093/aristote.

The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...) possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation. (shrink)

The concept of genidentity has been proposed as a way to better understand identity through time, especially in physics and biology. The genidentity view is utterly anti-substantialist in so far as it suggests that the identity of X through time does not presuppose whatsoever the existence of a permanent “core” or “substrate” of X. Yet applications of this concept to real science have been scarce and unsatisfying. In this paper, our aim is to show that a well-defined concept of functional (...) genidentity can be crucial to shed light on identity through time in classical physics and especially in biology. Finally, we show that understanding identity on the basis of continuity suggests a move towards an ontology of processes. (shrink)