In this paper I develop a concept of behavioural ecological individuality. Using findings from a case study which employed qualitative methods, I argue that individuality in behavioural ecology should be defined as phenotypic and ecological uniqueness, a concept that is operationalised in terms of individual differences such as animal personality and individual specialisation. This account make sense of how the term “individuality” is used in relation to intrapopulation variation in behavioural ecology. The concept of behavioural ecological individuality can sometimes be (...) used to identify individuals. It also shapes research agendas and methodological choices in behavioural ecology, leading researchers to account for individuals as sources of variation. Overall, this paper draws attention to a field that has been largely overlooked in philosophical discussions of biological individuality and highlights the importance of individual differences and uniqueness for individuality in behavioural ecology. (shrink)

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and earlier (...) phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than merely the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome. (shrink)

Can heritability estimates provide causal information? This paper argues for an affirmative answer: since a non-nil heritability estimate satisfies certain characteristic properties of causation (i.e., association, manipulability, and counterfactual dependence), it increases the probability that the relation between genotypic variance and phenotypic variance is (at least partly) causal. Contrary to earlier proposals in the literature, the argument does not assume the correctness of any particular conception of the nature of causation, rather focusing on properties that are characteristic of causal relationships. (...) The argument is defended against Lewontin's (1974) locality objection and Kaplan and Turkheimer's (2021) recent critique of Genome-Wide Association Studies (GWAS). (shrink)

Philosophers who study the problem of biological function often begin their deliberations by reflecting on the functions of parts of animals, or the behavior of animals. Applying theories of biological function to unconventional or borderline cases can help us to better evaluate and refine those theories. This is the case when we consider whether parts of transposable elements —bits of “selfish” DNA that move about within a host genome—have functions of their own, that is, whether the parts of TEs have (...) the function of helping the TE move about within the genome. Here I argue that whether or not the parts of TEs have functions depends crucially on whether collections of TEs form “populations,” by which I mean, here, a group of individuals of the same type that impact one another’s chances of persistence or multiplication, by impacting one another’s access to a shared resource. I think there is suggestive, but not conclusive, evidence that some TEs have functions of their own. Considering the problem of TE functionality, then, has value both for philosophy and for biology. (shrink)

This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or dissolved it altogether – so-called (...) We Are Done views. In doing so the paper offers new criticisms of the general lineage species concept (GLSC), evolutionary species concept (EvSC), biological species concept (BSC), other similar concepts, Ereshefsky’s eliminative pluralism about the species category, and both Mishler’s pessimism and Wilkins’ phenomenalism about that category. Opposed to We Are Done views, the paper argues for a Revving Up view, on which we are nearly ready to begin the hard species problem in earnest. To help work towards these conclusions, the paper begins with an outline of a new kind of view of species (Barker 2019a), which proposes they are feedback systems of a mathematically specifiable and empirically testable sort. (shrink)

The levels of selection debate is generally taken to be a debate about how natural selection can occur at the various levels of biological organization. In this paper, we argue that questions about levels of selection should be analyzed separately from questions about levels of organization. In the deflationary proposal we defend, all that is necessary for multilevel selection is that there are cases in which particles are nested in collectives, and that both the collectives and the particles that compose (...) them each separately undergo natural selection. We argue that adopting this deflationary account helps to disentangle the levels of selection and the levels of organization, and thereby contributes to advancing the levels of selection debate. (shrink)

This essay offers some reflections on Samir Okasha’s new monograph Agents and Goals in Evolution, his style of doing philosophy, and the broader philosophy of nature project of trying to make sense of agency and rationality as natural phenomena.

Darwin provided us with a powerful theoretical framework to explain the evolution of living systems. Natural selection alone, however, has sometimes been seen as insufficient to explain the emergence of new levels of selection. The problem is one of “circularity” for evolutionary explanations: how to explain the origins of Darwinian properties without already invoking their presence at the level they emerge. That is, how does evolution by natural selection commence in the first place? Recent results in experimental evolution suggest a (...) way forward: Paul Rainey and his collaborators have shown that Darwinian properties could be exogenously imposed via what they call “ecological scaffolding.” This could solve the “black box” dilemma faced by Darwinian explanations of new levels of organization. Yet, despite “scaffolding” recently becoming a popular term in the study of cognition, culture, and evolution, the concept has suffered from vagueness and ambiguity. This article aims to show that scaffolding can be turned into a proper scientific concept able to do explanatory work within the context of the major evolutionary transitions. Doing so will allow us to once again extend the scope of the Darwinian model of evolution by natural selection. (shrink)

This MPhil dissertation presents a novel account of teleological explanations in biology. I outline the “shorthand approach” to such explanations, on which they are taken to convey implicit evolutionary explanations. “Selected effects” accounts of teleological explanation dominate recent literature, but they struggle to accommodate teleological explanations of complex traits built through cumulative selection. I articulate the general notion of a landscape explanation, which, applied to biology, explains the evolution of complex features in a population by citing salient features of the (...) population’s fitness landscape. I show that such explanations lend themselves to a teleological shorthand. I close with remarks concerning when a teleological explanation of a trait is legitimate, and why teleological language strikes us as appropriate when we give evolutionary explanations. (shrink)

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. (...) Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives. (shrink)

In his 2009 monograph, Darwinian Populations and Natural Selection, Peter Godfrey-Smith accuses biologists of demonstrating ‘Darwinian Paranoia’ when they engage in what he dubs ‘agential thinking’. But as Daniel Dennett points out, he offers neither an illuminating set of examples nor an extended argument for this assertion, deeming it to be a brilliant propaganda stroke against what is actually a useful way of thinking. Compared to the dangers of teleological thinking in biology, the dangers of agential thinking have unfortunately rarely (...) been discussed. Drawing on recent work by Samir Okasha, I attempt to remedy this omission, through analyzing the nature of agential thinking, and providing a philosophical treatment of the unexamined dangers in this peculiar, yet tempting way of thinking. (shrink)

1. IntroductionIn What Biological Functions Are and Why They Matter, Justin Garson offers a novel theory of biological functions, the generalized selected effects (GSE) theory.1 He presents the theory in a clear and comprehensive way, defends it against various objections and applies it to different areas of philosophy, including the philosophy of psychiatry, the debate about mechanisms and the debate about teleosemantic theories of mental content.2Like other proponents of the aetiological approach to functions, Garson maintains that a trait’s biological functions (...) are grounded in its selectional history. However, his GSE theory differs from standard versions of the aetiological approach – so-called selected effects (SE) theories – in a crucial respect: while SE theories assume that all biological functions must ultimately be grounded in phylogenetic processes of natural selection or other (closely analogous) processes of differential reproduction (Millikan 1984: 15–82, Neander 1991, Godfrey-Smith 1994), the GSE theory allows that functions may also be grounded in processes of differential retention (see §2 for details). Garson forcefully argues that this broader account is theoretically well-motivated and has significant advantages over standard SE accounts when it comes to accommodating certain important classes of ontogenetically determined functions. (shrink)

The vast literature on negative treatment of outgroups and favoritism toward ingroups provides many local insights but is largely fragmented, lacking an overarching framework that might provide a unified overview and guide conceptual integration. As a result, it remains unclear where different local perspectives conflict, how they may reinforce one another, and where they leave gaps in our knowledge of the phenomena. Our aim is to start constructing a framework to help remedy this situation. We first identify a few key (...) ideas for creating a theoretical roadmap for this complex territory, namely the principles of etiological functionalism and the dual inheritance theory of human evolution. We show how a “molecular” approach to emotions fits into this picture, and use it to illuminate emotions that shape intergroup relations. Finally, we weave the pieces together into the beginnings of a systematic taxonomy of the emotions involved in social interactions, both hostile and friendly. While it is but a start, we have developed the argument in a way that illustrates how the foundational principles of our proposed framework can be extended to accommodate further cases. (shrink)

The goal of this essay is to assess the Selected-Effects Etiological Theory of biological function, according to which a trait has a function F if and only if it has been selected for F. First, I argue that this approach should be understood as describing the paradigm case of functions, rather than as establishing necessary and sufficient conditions for function possession. I contend that, interpreted in this way, the selected-effects approach can explain two central properties of functions and can satisfactorily (...) address some recent counterexamples. This reading, however, shows that there is only a partial overlap between biological functions and selected effects, so the former cannot be reduced to the latter. Finally, I maintain that this result is still compatible with a naturalistic theory of function that appeals to some evolutionary process. (shrink)

In this dissertation, I aim to develop and defend a novel, pragmatist approach to foundational questions about meaning, especially the meaning of deontic moral vocabulary. Drawing from expressivists and inferentialists, I argue that meaning is best explained by the various kinds of norms that govern the use of a vocabulary. Along with inferential norms, I argue we must extend our account to discursive norms that govern normative statuses required to felicitously utter certain speech-acts—norms of authority—and the transitions in normative statuses (...) affected by speech-acts—pragmatic norms. These structural discursive norms differentiate discursive practices and account for distinctive features such as objectivity and motivational import that some have and others lack. The structure exhibited by a practice is then explained in terms of its utility, making it possible to see how different discursive practices are answerable to the different needs and purposes of the discursive beings who use them. I call the resulting explanatory framework a pragmatic analysis of linguistic meaning (PALM). -/- Turning my attention to moral “ought,” I argue that the structural discursive norms of moral discourse differentiate it from other objective discourses, like empirical discourse, on the one hand, and from other normative discourses, like prudential discourse, on the other. Drawing on work in evolutionary psychology and anthropology, I complete the PALM with an account of moral discourse a meta-normative practice with a metacoordinative function. Its utility for the discursive beings who use it lies in its enabling them to remedy certain tensions and instabilities that arise in their other coordinative, normative practices in a way that minimizes the risk of domination by alpha-type freeriders, the fracturing of social groups, and individual defection from cooperative endeavors. -/- In the final two chapters, I leverage the account to defend a pragmatist-friendly notion of objectivity in terms of a structure of distributed epistemic authority according to which no claim within a practice is ultimately authoritative or immune from challenge and to reconcile this sense of objectivity with a persistent pressure toward a kind of relativism that restricts the standing to make moral claims to members of the relevant communities. (shrink)

An understanding of the factors behind the evolution of multicellularity is one of today’s frontiers in evolutionary biology. This is because multicellular organisms are made of one subset of cells with the capacity to transmit genes to the next generation and another subset responsible for maintaining the functionality of the organism, but incapable of transmitting genes to the next generation. The question arises: why do somatic cells sacrifice their lives for the sake of germline cells? How is germ/soma separation maintained? (...) One conventional answer refers to inclusive fitness theory, according to which somatic cells sacrifice themselves altruistically, because in so doing they enhance the transmission of their genes by virtue of their genetic relatedness to germline cells. In the present article we will argue that this explanation ignores the key role of policing mechanisms in maintaining the germ/soma divide. Based on the pervasiveness of the latter, we argue that the role of altruistic mechanisms in the evolution of multicellularity is limited and that our understanding of this evolution must be enriched through the consideration of coercion mechanisms. (shrink)

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)

There is a certain metaphor that has enjoyed tremendous longevity in the evolution of ageing literature. According to this metaphor, nature has a certain goal or purpose, the perpetuation of the species, or, alternatively, the reproductive success of the individual. In relation to this goal, the individual organism has a function, job, or task, namely, to breed and, in some species, to raise its brood to maturity. On this picture, those who cannot, or can no longer, reproduce are somehow invisible (...) to, or even dispensable to, the evolutionary process. Here, I argue that the metaphor should be discarded, not on the grounds that it is a metaphor, but on the grounds that this particular metaphor distorts our understanding of the evolution of ageing. One reason the metaphor is problematic is that it frames senescence and death as nature’s verdict on the value of older individuals. Instead, we should explore a different metaphor: the lengthy post-reproductive period in humans and some other animals is not an accident of culture, but designed by nature for the purpose of supporting and guiding younger generations. On this alternate picture, different stages of life have their own evolutionary rationales, their distinctive design features, their special mandates. (shrink)

The received view holds that there is a significant divide between full-blown representational states and so called ‘detectors’, which are mechanisms set off by specific stimuli that trigger a particular effect. The main goal of this paper is to defend the idea that many detectors are genuine representations, a view that I call ‘Strong Liberal Representationalism’. More precisely, I argue that ascribing semantic properties to them contributes to an explanation of behavior, guides research in useful ways and can accommodate misrepresentation.

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (shrink)

Throughout the literature on Cultural Evolutionary Theory (CET) attention is drawn to the existence and significance of an analogy between biological phenomena and socio-cultural phenomena (the “biology-culture analogy”). Mesoudi (2017) seems to argue that it is the accuracy of the analogy, and the magnitude of accurate instances of this analogy at work, which provides warrant for an evolutionary approach to the study of socio-cultural phenomena, and, thus, for CET. An implication of this is that if there is evidence to suggest (...) that the analogy is not accurate, or that there aren’t many cases where it is accurate, this would constitute evidence to reject an evolutionary approach to the study of socio-cultural phenomena. As such, opponents of CET raise objections highlighting the weakness of the biology-culture analogy. These objections, in turn, have standard replies in the literature that serve to reinforce the realism of the biology-culture analogy. Curiously, this situation would appear to support a position in the philosophy of social science called “Ontology Matters” (Lauer 2019). It is the view that social ontology can contribute to the empirical success of the social sciences (among which I include CET) by providing an accurate account of what there is in the domain of the social world which can be used to generate better explanations and/or predictions of social phenomena. If ontology matters, in this sense, perhaps this can help to clarify and resolve the dispute regarding the realism of the biology-culture analogy. In turn, perhaps this can help us determine what warrant there is for CET. However, I think this situation is indicative of severe confusion and misunderstanding as to the significance of the biology-culture analogy. This confusion is caused by inattention to two things. First, the useful distinction between it’s methodological, epistemological, and ontological significance. Second, the abstract (ontologically minimalist) nature of Darwinian evolution by natural selection. By drawing attention to these two things, I hope to take the sting out of, and deflate the significance of, disputes regarding the accuracy of the analogy, for both proponents and opponents of CET, as well as to bring into contact a classical dispute in the philosophy of social science with some relevant aspects of theoretical biology. (shrink)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a new (...) aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

Although the definition of ‘signal’ has been controversial for some time within the life sciences, current approaches seem to be converging toward a common analysis. This powerful framework can satisfactorily accommodate many cases of signaling and captures some of its main features. This paper argues, however, that there is a central feature of signals that so far has been largely overlooked: its special causal role. More precisely, I argue that a distinctive feature of signals is that they are minimal causes. (...) I explain this notion, suggest some strategies for identifying its instances and defend its relevance by means of conceptual and empirical considerations. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, molecular networks) that are themselves complex and competent in their own context. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger (...) organism. In this paper I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: “Scale-Free Cognition”. I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization, and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface – the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive “light cone” which defines the scale and limits of its cognition. I hypothesize that higher-level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress – the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggests a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology. (shrink)

Niche construction theory concerns how organisms can change selection pressures by altering the feature–factor relationship between themselves and their environment. These alterations are standardly understood to be brought about through two kinds of organism–environment interaction: perturbative and relocational niche construction. We argue that a reconceptualization is needed on the grounds that if a niche is understood as the feature–factor relationship, then there are three fundamental ways in which organisms can engage in niche construction: constitutive, relational, and external niche construction. We (...) further motivate our reconceptualization by showing some examples of organismic activities that fall outside of the current categorization of niche construction, but nonetheless should be included. We end by discussing two objections to niche construction and show how our reconceptualization helps to undercut these objections. 1Introduction2Niche Construction Theory 2.1The standard account of niche construction2.2Two problems with the standard account of niche construction3Three Kinds of Niche Construction 3.1Constitutive niche construction3.2Relational niche construction3.3External niche construction4Conceptual Improvement on Niche Construction Theory 4.1Constitutive niche construction4.2Relational niche construction4.3External niche construction5The Status of Niche Construction Theory within Evolutionary Theory 5.1Is niche construction a helpful addition to evolutionary theory?5.2Is niche construction an evolutionary process?6Conclusion. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...) our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...) been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

The concept of “life” certainly is of some use to distinguish birds and beavers from water and stones. This pragmatic usefulness has led to its construal as a categorical predicate that can sift out living entities from non-living ones depending on their possessing specific properties—reproduction, metabolism, evolvability etc. In this paper, we argue against this binary construal of life. Using text-mining methods across over 30,000 scientific articles, we defend instead a degrees-of-life view and show how these methods can contribute to (...) experimental philosophy of science and concept explication. We apply topic-modeling algorithms to identify which specific properties are attributed to a target set of entities (bacteria, archaea, viruses, prions, plasmids, phages and the molecule of adenine). Eight major clusters of properties were identified together with their relative relevance for each target entity (two that relate to metabolism and catalysis, one to genetics, one to evolvability, one to structure, and—rather unexpectedly—three that concern interactions with the environment broadly construed). While aligning with intuitions—for instance about viruses being less alive than bacteria—these quantitative results also reveal differential degrees of performance that have so far remained elusive or overlooked. Taken together, these analyses provide a conceptual “lifeness space” that makes it possible to move away from a categorical construal of life by empirically assessing the relative lifeness of more-or-less alive entities. (shrink)

There is hardly anything more central to our universe than conservation. Many scientific fields and disciplines view the law of conservation as one of the most fundamental universal laws. The Darwinian model pivots the process of evolution on variability, reproduction, and natural selection. Conservation plays a marginal role in this model and is not really universal, as the model allows exceptions to conservation, i.e. non-conservation, to play an equally important role in evolution. This anomalous role of conservation in the Darwinian (...) model raises questions: What is the reason for this anomaly? Is conservation really universal, as we tend to believe or is it not, as the Darwinian model suggests? This contribution proposes a new model of evolution that focuses on levels of organization, rather than of species, organisms, or populations. It argues that conservation is central to evolution. Not only does this new model restores the universal status of conservation but it also makes possible to resolve some outstanding problems and controversies that continue to plague the Darwinian model. The article tries to advance the broad Darwinian project that seeks to explain the process of evolution as a product of the spontaneous processes in nature. (shrink)

I distinguish two roles for a fitness concept in the context of explaining cumulative adaptive evolution: fitness as a predictor of gene frequency change, and fitness as a criterion for phenotypic improvement. Critics of inclusive fitness argue, correctly, that it is not an ideal fitness concept for the purpose of predicting gene-frequency change, since it relies on assumptions about the causal structure of social interaction that are unlikely to be exactly true in real populations, and that hold as approximations only (...) given a specific type of weak selection. However, Hamilton took this type of weak selection, on independent grounds, to be responsible for cumulative assembly of complex adaptations. In this special context, I argue that inclusive fitness is distinctively valuable as a criterion for improvement and a standard for optimality. Yet to call inclusive fitness a criterion for improvement and a standard for optimality is not to make any claim about the frequency with which inclusive fitness optimization actually occurs in nature. This is an empirical question that cannot be settled by theory alone. I close with some reflections on the place of inclusive fitness in the long running clash between ‘causalist’ and ‘statisticalist’ conceptions of fitness. (shrink)

Mainstream teleosemantics is the view that mental representation should be understood in terms of biological functions, which, in turn, should be understood in terms of selection processes. One of the traditional criticisms of teleosemantics is the problem of novel contents: how can teleosemantics explain our ability to represent properties that are evolutionarily novel? In response, some have argued that by generalizing the notion of a selection process to include phenomena such as operant conditioning, and the neural selection that underlies it, (...) we can resolve this problem. Here, we do four things: we develop this suggestion in a rigorous way through a simple example, we draw on recent neurobiological research to support its empirical plausibility, we defend the move from a host of objections in the literature, and we sketch how the picture can be extended to help us think about more complex “conceptual” representations and not just perceptual ones. (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)

Le texte suivant s'appuie assez largement sur des informations scientifiques de la biologie végétale. Ce choix de philosopher à partir de la technicité et de l'historicité des objets botaniques correspond à un parti pris. La proximité de l’humain à ses objets d’étude, sa tendance à anthropomorphiser, voire anthropocentrer, les observations ou les problèmes qui se présentent à lui, a fait l’objet de multiples réflexions philosophiques et épistémologiques. Kant, pour qui « tout intérêt est finalement pratique [...] même celui de la (...) raison spéculative n’est que conditionné et n’est complet que dans l’usage pratique » 1 , Bachelard, qui appelle à « substituer à la notion anthropomorphe de cause la notion scientifique de fonction » 2 , ou Canguilhem pour qui « l’anthropocentrisme est plus aisé à rejeter que l’anthropomorphisme [...] Peut-on être biologistes sans se sentir du côté des vivants ? » 3 . Ces réflexions ne sont-elles pas toujours centrées sur les modes de connaissance ou de pensée de l’humain, alors que les « objets d’étude » en question demeurent souvent dans un certain flou, voire une large indétermination ? La démarche suivie ici tente d’aller dans une autre direction. Elle interroge les effets de l’anthropocentrisation d’objets spécifiques à la biologie végétale, envisagée aussi bien dans sa profondeur historique que dans ses développements techniques récents. Nous tentons ici un pari : une analyse précise de nos connaissances botaniques, actuelles et passées, peut nourrir la réflexion philosophique sur notre rapport aux plantes et, à travers elles, sur nous-mêmes. (shrink)

Natural kinds, real kinds, or, following J.S Mill simply, Kinds, are thought to be an important asset for scientific realists in the non-fundamental (or “special”) sciences. Essential natures are less in vogue. I show that the realist would do well to couple her Kinds with essential natures in order to strengthen their epistemic and ontological credentials. I argue that these essential natures need not however be intrinsic to the Kind’s members; they may be historical. I concentrate on assessing the merits (...) of historical essential natures in a paradigm case of Kinds in the non-fundamental sciences: species. I specify two basic jobs for essential natures: 1) offering individuation criteria, and 2) providing a causal explanation of the Kind’s multiple projectable properties. I argue that at least in the case of species historical essences are fit for both tasks. The principled resistance to Kinds with historical essences should also be cleared. (shrink)

Questioning the nature of individuality has a long and a rich history, both in philosophy and in biology. Because they differ in several features from the pervasive vertebrate-human model, plants have been considered as complicating the question. Here, the various plant species on which authors—whether biologists or philosophers—rely to build the picture of plant individuality are examined and tracked for their peculiarities, thus constituting an “herbiary” of plant individuality. The herbiary of plant individuality has as its members species exhibiting a (...) diverse collection of traits and illustrating different questions related to plant individuality. This essay assesses the peculiarity of the features of these plants and the reality of their differences from animals. Because some plant features are supposed to pose a threat to individual genetic homogeneity, higher heterogeneity has been assumed for plants compared to animals. Moreover, individual plants are sometimes identified with communities. How does this supposed heterogeneity appear in particular species? Cultivated plants exhibit distinctive diversity, and their overrepresentation in the study of plant diversity might bias the way plant individuality is understood. Just as there is a vertebrate bias, there may also be a cultivated plant bias. Recent results bring plants much closer to animals in terms of cellular functioning, so plants might not be so different from animals with respect to their diversity, and consequently their individuality. (shrink)

I argue that verbal models should be included in a philosophical account of the scientific practice of modelling. Weisberg (2013) has directly opposed this thesis on the grounds that verbal structures, if they are used in science, only merely describe models. I look at examples from Darwin's On the Origin of Species (1859) of verbally constructed narratives that I claim model the general phenomenon of evolution by natural selection. In each of the cases I look at, a particular scenario is (...) described that involves at least some fictitious elements but represents the salient causal components of natural selection. I pronounce the importance of prioritising observation of scientific practice for the philosophy of modelling and I suggest that there are other likely model types that are excluded from philosophical accounts. (shrink)

We argue that the economy of nature constitutes an invocation of structure in the biological sciences, one largely missed by philosophers of biology despite the turn in recent years toward structural explanations throughout the philosophy of science. We trace a portion of the history of this concept, beginning with the theologically and economically grounded work of Linnaeus, moving through Darwin’s adaptation of the economy of nature and its reconstitution in genetic terms during the first decades of the Modern Synthesis. What (...) this historical case study reveals, we argue, is a window into the shifting landscape of the explanatory and ontic uses of structural concepts. In Linnaeus, the economy of nature has both ontic and explanatory import; in Darwin the ontic and explanatory aspects start to come apart ; and finally, in the Modern Synthesis, the economy of nature is replaced by the conceptual toolkit of population genetics, the structural elements of which are nearly entirely explanatory. Having traced a historical trajectory of structural concepts that moves from an ontic formulation to an increasingly explanatory one, we conclude by outlining some insights for structural realism. (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)

Evolutionary biology is striking for its ability to explain a large and diverse range of empirical phenomena on the basis of a few general theoretical principles. This article offers a philosophical perspective on the way that evolutionary biology has come to achieve such impressive generality, by focusing on “the strategy of endogenization”. This strategy involves devising evolutionary explanations for biological features that were originally part of the background conditions, or scaffolding, against which such explanations take place. Where successful, the strategy (...) moves biology a step closer to the ideal of explaining as much as possible from evolutionary first principles. The strategy of endogenization is illustrated through a series of biological examples, historical and recent, and its philosophical implications are explored. (shrink)

Causalism is the thesis that natural selection can cause evolution. A standard argument for causalism involves showing that a hypothetical intervention on some population-level property that is identified with natural selection will result in evolution. In a pair of articles, one of which recently appeared in the pages of this journal, Jun Otsuka has put forward a quite different argument for causalism. Otsuka attempts to show that natural selection can cause evolution by considering a hypothetical intervention on an individual-level property. (...) Specifically, Otsuka identifies natural selection with the causal relationship between a trait and fitness, claims an intervention on the strength of this relationship can cause evolution, then concludes that natural selection can cause evolution. Below I describe why Otsuka’s argument for causalism is unconvincing. Central to my criticism is that Otsuka’s argument works only if one adopts an indefensible account of natural selection, according to which natural selection can occur in the absence of trait or fitness variation. I go on to explain why any attempt to demonstrate the truth of causalism via a hypothetical intervention on an individual-level property would appear to require one to adopt an account of natural selection that is inadequate for the same reason. This in turn means the plausibility of causalism does indeed depend on the plausibility of the claim that population-level properties, which supervene on the properties of the individuals in the population, can be causally efficacious. (shrink)

Is there anything that members of each binary category of gender have in common? Even many non-essentialists find the lack of unity within a gender worrying as it undermines the basis for a common political agenda for women. One promising proposal for achieving unity is by means of a shared historical lineage of cultural reproduction with past binary models of gender. I demonstrate how such an account is likely to take on board different binary and also non-binary systems of gender. (...) This implies that all individuals construed as members of the category, “women” are in fact not members of the same historical kind after all! I then consider different possible means of modifying the account but conclude negatively: the problem runs deeper than has been appreciated thus far. (shrink)