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 paper reinforces the current consensus against the applicability of the selected effect theory of function in ecology. It does so by presenting an argument which, in contrast with the usual argument invoked in support of this consensus, is not based on claims about whether ecosystems are customary units of natural selection. Instead, the argument developed here is based on observations about the use of the function concept in functional ecology, and more specifically, research into the relationship between biodiversity and (...) ecosystem functioning. It is argued that a selected effect account of ecological functions is made implausible by the fact that it would conflict with important aspects of the understanding of function and ecosystem functional organization which underpins functional ecology’s research program. Specifically, it would conflict with (1) Functional ecology’s adoption of a context-based understanding of function and its aim to study the functional equivalence between phylogenetically-divergent organisms; (2) Functional ecology’s attribution to ecosystems of a lower degree of part-whole integration than the one found in paradigm individual organisms; and (3) Functional ecology’s adoption of a physiological or metabolic perspective on ecosystems rather than an evolutionary one. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey-Smith (...) puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

I spell out and update the individuality thesis, that species are individuals, and not classes, sets, or kinds. I offer three complementary presentations of this thesis. First, as a way of resolving an inconsistent triad about natural kinds; second, as a phylogenetic systematics theoretical perspective; and, finally, as a novel recursive account of an evolved character. These approaches do different sorts of work, serving different interests. Presenting them together produces a taxonomy of the debates over the thesis, and isolates ways (...) it has been productive. This goes to the larger point of this paper: a defense of the individuality thesis in terms of its utility, and an update of it in light of recent theoretical developments and empirical work in biology. (shrink)

Microbes are generally thought of as unicellular organisms, but we know that many microbes live as parts of biofilms—complex, surface-attached microbial communities numbering millions of cells. Some authors have recently argued in favour of reconceiving biofilms as biological entities in their own right. In particular, some have claimed that multispecies biofilms are evolutionary individuals : 10126–10132 2015). Against this view, I defend the conservative consensus that selection acts primarily upon microbial cells.

I consider the relationship between scientific practice and the philosophical debate surrounding biological individuality. I argue for the sensitivity account, on which biologists do not require a resolution to the individuality debate. This view puts me in disagreement with much of the literature on biological individuality, where it has become common to claim that there is a relationship of dependence between biologists’ conceptions of individuality and the quality of their empirical work.

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ of Life, (...) but conversely has also been the target of influential rejections: as just an instrument of transmission for the selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, sometimes even as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. This paper does not seek to adjudicate between these debates, either in terms of scientific validity or historical coherence; nor does it return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to focus on the emergence and transformation of the concept of organism, but has not emphasized so much the way in which organism is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or an epistemic limit case, all of which partly overlap with the idea of ‘nomadic concepts’. Thereby the concept of organism continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

This is a critical review essay on John Martin Fischer's Deep Control: Essays on Free Will and Value.

This is a highly welcome book that offers a fresh perspective on the philosophy of biology. It is of interest to both philosophers and biologists and to experienced readers as well as novices. The book is structured into four sections ‘Science’, ‘Biology’, ‘Microbes’ and ‘Humans’ and consists of a collection of articles written by John Dupré over the past few years.

Type specimens are used to designate species. What is the nature of the relation between a type specimen and the species it designates? If species names are rigid designators, and type specimens ostensively define species, then that relation is, at the very least, a close one. Levine :325–338, 2001) argues that the relationship of type specimen to a named species is one of necessity—and that this presents problems for the individuality thesis. Namely, it seems odd that a contingently selected specimen (...) should belong to a species of necessity. In considering Levine’s argument, LaPorte suggests that recognizing the distinction between de re and de dicto necessity resolves Levine’s worries. I reconsider the motivating question: does a type specimen belong of necessity to the species that it designates? In light of taxonomic cases and practice the answer is clear: definitively not. This is particularly clear in the case of re-designation of types by taxonomic decree. I explain how this helps reveal how taxonomists prioritize competing theoretical commitments, and offer a defense of the individuality thesis as applied to these particular cases. In short, I demonstrate how to misidentify a type specimen. (shrink)

Immunology and its philosophy are a primary source for thinking about biological individuality. Through its discriminatory function, the immune system is believed to delineate organism and environment within one generation, thus defining the physiological individual. Based on the paradigmatic instantiations of immune systems, immune interactions and, thus, the physiological individual are believed to last only for one generation. However, in recent years, transgenerationally persisting immune responses have been reported in several phyla, but the consequences for physiological individuality have not yet (...) been explored. In this article, I will introduce an invertebrate immune system that is RNA-based and operates through a heritable silencing/licensing paradigm. I will discuss how such a perspective on immune systems can illuminate our conceptions of individuality. I will particularly introduce an account of immunological individuality that is not restricted to one generation. (shrink)

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken (...) in Clarke :413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided. (shrink)

Through a critical engagement with Merleau-Ponty’s discussion of the concepts of nature, life, and behavior, and with contemporary accounts of animal groups, this article argues that animal groups exhibit sociality and that sociality is a fundamental ontological condition. I situate my account in relation to the superorganism and selfish individual accounts of animal groups in recent biology and zoology. I argue that both accounts are inadequate. I propose an alternative account of animal groups and animal sociality through a Merleau-Pontian inspired (...) definition of behavior. I criticize Merleau-Ponty’s individualistic prejudice, but show that his philosophy contains the resources necessary to overcome this bias. I define behavior as a holistic, ongoing, meaningful and Umwelt-oriented intrinsically configured expression of living forms of existence. By looking at cases of animal groups drawn from contemporary studies in zoology and behavioral ecology, I show that animal groups, in the fact that they behave, manifest themselves to be a fundamental form of existence, namely, the social form of existence. (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles, sometimes masked, often normative, throughout the history of biology. Indeed, it has often been presented as a key-concept in life science and its ‘theorization’, but conversely has also been the target of influential rejections: as just an instrument of transmission for the (...) selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. I do not seek to adjudicate between these debates, either regarding scientific validity or historical coherence; nor do I return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to discuss the emergence and transformation of the organism concept, but has not emphasized the way the latter is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or a limit case, which continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

Biological individuals are usually defined by evolutionists through a reference to natural selection. This article looks for a concept of individuality that would hold at the same time for organisms and for communities or ecosystems, the latter being unaffected by natural selection. In the wake of Simon’s notion of “quasi-independence,” I elaborate a concept of “weak individuality” defined by probabilistic connections between sub-entities, read off our knowledge of their interactions. This formal scheme of connections allows one to infer what are (...) the individuals in the domain addressed by the theory of the interactions. The article argues that if ecosystems do not have strong individuality, they still possess a weak individuality, ecological theories providing the values of the variables in the formula for individuality. (shrink)

According to the species-as-individuals thesis(hereafter S-A-I), species are cohesive entities. Barker and Wilson recently pointed out that the type of cohesion exhibited by species is fundamentally different from that of organisms (paradigmatic individuals), suggesting that species are homeostatic property cluster kinds. In this article, I propose a shift in how to approach cohesion in the context of S-A-I: instead of analyzing the different types of cohesion and questioning whether species have them, I focus on the role played by cohesion in (...) the identity of individuals. This shift allows us to recognize why cohesion matters to S-A-I, as well as to reconceive the analogy between species and organisms (paradigmatic individuals), and also allows us to highlight the context sensitivity of both ‘‘cohesion’’ and ‘‘individuals.’’ From this perspective, I identify two problems in Barker and Wilson’s argumentation. Firstly, the authors fail to recognize that species are individuals even if they do not have the same type of cohesion that organisms have. Secondly, their argument relies on a misinterpretation of S-A-I. I conclude that species cohesion is still best framed as a feature of species individuality rather than a feature of species as homeostatic property cluster kinds. The arguments presented here contribute to the re-articulation and reevaluation of S-A-I in the face of contemporary discussions. (shrink)

Eusociality is broadly defined as: colonies consisting of overlapping generations, cooperative brood care, and a reproductive division of labour where sterile (or non-reproductive) workers help the reproductive members. Colonies of many complex eusocial insect species (e.g. ants, bees, termites) exhibit traits, at the collective level, that are more analogous to biological individuals rather than to groups. Indeed, due to this, colonies of the most complex species are typically a unit of selection, which has led many authors to once again apply (...) the concept of the superorganism to eusocial insects. However, unlike W. M. Wheeler, who originally employed the concept from a physiological and evolutionary perspective, today the superorganism is typically understood only from an evolutionary perspective, using group selection. This is because of the widely held view that eusocial colonies are self-organized systems. According to this view, even the most complex eusocial systems can be explained by appealing to a set of local interactions between parts of an initially disordered system (i.e. self-organization), without the need of any hierarchical control. In this paper we challenge the presupposition that hierarchical control and regulation is not possible in complex eusocial colonies. Using a case study of honey bees (Apis mellifera), we develop an alternative to the self-organization approach, that focuses on the hierarchical nature of the organization of complex eusocial systems—that we refer to as the hierarchical-organizational approach. In addition, we will analyse how colonies of eusocial insects show a complex set of interactions between the different organisms that bring forth a new cohesive collective organization, and how in turn the constitutive entities of this collective organization are transformed in this process. This paper argues that an inter-identity (namely the superorganism) emerges at the collective level in complex eusocial colonies, such as honey bees, due to the hierarchically-organized network of interactions within the colony. (shrink)

“The Role of the Individual in Evolution” is a prescient yet neglected 1941 work by the 20th century’s most important paleontologist, George Gaylord Simpson. In a curious intermingling of explanation and critique, Simpson engages questions that would become increasingly fundamental in modern biological theory and philosophy. Did individuality, adaptation, and evolutionary causation reside at more than one level: the cell, the organism, the genetically coherent reproductive group, the social group, or some combination thereof? What was an individual, anyway? In this (...) introduction, we highlight two points in a wider historical context. First, recognizing the political context of Simpson’s writing profoundly deepens our understanding of the development of his science as the Modern Evolutionary Synthesis infused biology. Second, this story illuminates the emergence of debates around what would eventually come to be called multilevel selection theory. The organism-centered concept of biological individuality defended by Simpson is situated in relation to the then-emerging Synthesis, in which he was a renowned player, and also in relation to the views he opposed: the “metaphysical” ideas of paleontologists such as Henry Fairfield Osborn, who claimed that some evolutionary trends derived from potentialities already implanted in the germplasm; and the organicist ideas of Ralph W. Gerard and the Chicago School of ecologists, which he derided as all too congenial to totalitarianism. We find parallels between the ways that Simpson thought then about human individuality under totalitarianism and the way he thought about individuality in evolution; not that any causal relationship linked the two, but that commonalities of hierarchical structure exist between single entities and groups in both instances. We then trace the subsequent development of Simpson’s political and philosophical takes on the role of the individual in evolution through the 1960s and lightly sketch out the later fate of the organicist ideas of the Chicago School. Simpson’s paper, originally published in the Journal of the Washington Academy of Sciences, is available as supplementary material in the online version of this article, as part of the "Classics in Biological Theory" collection. (shrink)

Thomas Pradeu’s The Limits of the Self provides a precise account of biological identity developed from the central concepts of immunology. Yet the central concepts most relevant to this task are themselves deemed inadequate, suffering from ambiguity and imprecision. Pradeu seeks to remedy this by proposing a new guiding theory for immunology, the continuity theory. From this, an account of biological identity is provided in terms of uniqueness and individuality, ultimately leading to a defense of the heterogeneous organism as expressing (...) the highest degree of individuality. (shrink)

The concept of superorganism has a mixed reputation in biology—for some it is a convenient way of discussing supra-organismal levels of organization, and for others, little more than a poetic metaphor. Here, I show that a considerable step forward in the understanding of superorganisms results from a thorough review of the supra-organismal levels of organization now known to exist among the “unicellular” protists. Limiting the discussion to protists has enormous advantages: their bodies are very well studied and relatively simple, and (...) they exhibit an enormous diversity of anatomies and lifestyles. This allows for unprecedented resolution in describing forms of supra-organismal organization. Here, four criteria are used to differentiate loose, incidental associations of hosts with their microbiota from “actual” superorganisms: obligatory character, specific spatial localization of microbiota, presence of attachment structures and signs of co-evolution in phylogenetic analyses. Three groups—that have never before been described in the philosophical literature—merit special attention: Symbiontida, Oxymonadida and Parabasalia. Specifically, it is argued that in certain cases—for Bihospites bacati and Calkinsia aureus, Streblomastix strix, Joenia annectens and Mixotricha paradoxa and Kentrophoros —it is fully appropriate to describe the whole protist-microbiota assocation as a single organism and its elements as “tissues” or, arguably, even “organs”. To account for this level of biological complexity, I propose the term “structured superorganism”. (shrink)