This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...) evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’. In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely (...) Metaphysics for Biology and Metaphysics in Biology. (shrink)

In this paper, I delineate the first pages of a philosophical genealogy which outlines the cornerstones of a philosophy of bio-technical forms. In so doing, the essay contributes to the philosophical understanding of some key scientific concepts. In particular, it analyses the philosophical and historical preconditions, the epistemic assumptions, as well as the ontological commitments of the concept of form as used in digital design and in bionics. In the first section, I investigate Ernst Kapp’s philosophy of technical forms. In (...) the second section, I analyse the emergence of biotechnology, today’s bionics, as an independent technical discipline. At the beginning of the 20th century, the Austro-Hungarian botanist Raoul Heinrich Francé (1874–1943) founded this discipline with the aim of imitating the technical solutions chosen by nature. In the conclusion, I draw broader conclusions about the philosophy of bio-technical forms. Particularly, I argue, first, that the role of materiality and form-intrinsic propriety is of central importance in processes of form design. Second, I define morphology as a theory of possible constructions of forms in space and not, as in evolutionary biology, a science of the changes of forms in time. This characterises what I have called the ontological turn in form-design disciplines: nature operates technically to conceive new forms. (shrink)

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...) species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

This paper seeks to develop a theory of health that aligns with the shift in contemporary medical practice and research toward a temporally extended epidemiological view of health. The paper describes how such a theory is at the core of life course based approaches to health, and finds theoretical grounding in recent work in the philosophy of biology promulgating a process theory of life.

Recent years have witnessed an increase in bear sightings in Latvia, causing a change of tone in the country’s media outlets, regarding the return of “wild” animals. The unease around bear reappearance leads me to investigate the affective side of relations with beings that show strength and resilience in more-than-human encounters in human-inhabited spaces. These relations are characterized by the contrasting human feelings of alienation vis-à-vis their environments today and a false sense of security, resulting in disbelief to encounter beings (...) capable of challenging human exceptionalism. In a broader sense, the unease connects to human self-constitution and the fragility of the self, fueled by the domination of substance ontologies. This article considers bears as beings “in exile,” as potential threats to human self-pronounced exceptionality, and thus, examples of experienced abject regarding human subjectivity. The article aims to analyze the way the constitution of human selfhood is tied to the alienation of wildlife and its genealogical and biopolitical context and to question if a reconceptualization of the human/nonhuman relations via process, instead of substance ontology, is needed. (shrink)

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

The philosophy of biology is witnessing an increasing enthusiasm for what can be called “individuals thinking”. Individuals thinking is a perspective on the metaphysics of biological entities according to which conceiving of them as individuals rather than kinds enables us to expose ongoing metaphysical debates as focusing on the wrong question, and to achieve better accounts of the metaphysics of biological entities. In this paper, I examine two cases of individuals thinking, the claim that species are individuals and the claim (...) that life on Earth is an individual. I argue that these claims fail to do the metaphysical work that one would want them to do. I highlight problems with the specific claims as well as with the general notion of ‘individual’, and argue that naturalistic metaphysicians of biology should think of the metaphysical status of theoretical entities, such as species and life, as fundamentally theory-dependent. This implies a metaphysical pluralism, that allows that in some theories species, life, and other such entities may feature as individuals, whereas in others they may feature as kinds. (shrink)

Natural mimicry is ubiquitous. Plants mimic animals, animals mimic plants, animals mimic each other and animals may even mimic counterfactual states that deceive or distract other animals. Almost all natural mimicry is based on iconicity which hence anchors it in real world resemblances. The vast majority of natural mimicry is done unconsciously but when humans mimic, they know what they are doing. As Merlin Donald suggest, mimicry may in fact have played a crucial role in the emergence of the human (...) condition, allowing new forms of cognition to emerge. Here it is suggested that the role played by mimicry may have involved the evolution of a capacity for metaphorical perception, where an object may not only be seen ‘as is’ but also ‘as if’ it was a functional mimic of something else. This new form of mimicry made possible new forms of communication, co-operation and creative engagement with the environment. Once these developed to the point where they produced symbolic systems and other cultural tools, the nature of human mimicry expanded radically. No longer anchored in resemblance, it became detached and qualitatively distinct from natural forms. The consequences of this detachment are now becoming clear. (shrink)

How many individuals are present where we see a pregnant individual? Within a substance ontological framework, there are exactly two possible answers to this question. The standard answer—two individuals—is typically championed by scholars endorsing the predominant Containment View of pregnancy, according to which the foetus resides in the gestating organism like in a container. The alternative answer—one individual—has recently found support in the Parthood View, according to which the foetus is a part of the gestating organism. Here I propose a (...) third answer: a pregnant individual is neither two individuals nor one individual but something in between one and two. This is because organisms are better understood as processes than as substances. With a special focus on the Parthood View, I explain why a Process View of pregnancy, according to which a pregnant individual is a bifurcating hypercomplex process, surpasses the substance ontological approaches. (shrink)

In recent years, an increasing number of theoretical biologists and philosophers of biology have been opposing reductionist research agendas by appealing to the concept of biological autonomy which draws on the older concept of autopoiesis. In my paper, I investigate some of the ontological implications of this approach. The emphasis on autonomy and autopoiesis, together with the associated idea of organisational closure, might evoke the impression that organisms are to be categorised ontologically as substances: ontologically independent, well-individuated, discrete particulars. However, (...) I argue that this is mistaken. Autopoiesis and biological autonomy, properly understood, require a rigorous commitment to a process ontological view of life. (shrink)

Process ontology is making deep inroads into the hard sciences. For it offers a workable understanding of dynamic phenomena which sits well with inquiries that problematize the traditional conception of self-standing, definite, independent objects as the basic stuff of the universe. Process-based approaches are claimed by their advocates to yield better ontological descriptions of various domains of physical reality in which dynamical, indefinite activities are prior to definite “things” or “states of things”. However, if applied to physics, a main problem (...) comes up: the notion itself of process appears to pivot on a conception of evolution through time that is at variance with relativistic physics. Against this worry, this article advances a conception of process that can be reconciled with general relativity. It claims that, within timeless physical frameworks, a process should not be conceived as activities evolving through time. Rather, processes concern the identity that entities obtain within the broader sets of relations in which they stand. To make this case, the article homes in on one of the physical approaches that most resolutely removes time from the basic features of reality, that is, canonical quantum gravity. As a case in point, it addresses Carlo Rovelli’s Evolving Constant approach as a physical paradigm that resolutely rejects time as an absolute parameter and recasts processualism as an inquiry into how physical systems affect one another. (shrink)

It remains at best controversial to claim, non-figuratively, that plants are cognitive agents. At the same time, it is taken as trivially true that many animals are cognitive agents, arguably through an implicit or explicit appeal to natural science. Yet, any given definition of cognition implicates at least some further processes, such as perception, action, memory, and learning, which must be observed either behaviorally, psychologically, neuronally, or otherwise physiologically. Crucially, however, for such observations to be intelligible, they must be counted (...) as evidence for some model. These models in turn point to homologies of physiology and behavior that facilitate the attribution of cognition to some non-human animals. But, if one is dealing with a model of animal cognition, it is tautological that only animals can provide evidence, and absurd to claim that plants can. The more substantive claim that, given a general model of cognition, only animals but not plants can provide evidence, must be evaluated on its merits. As evidence mounts that plants meet established criteria of cognition, from physiology to behavior, they continue to be denied entry into the cognitive club. We trace this exclusionary tendency back to Aristotle, and attempt to counter it by drawing on the philosophy of modelling and a range of findings from plant science. Our argument illustrates how a difference in degree between plant and animals is typically mistaken for a difference in kind. (shrink)

In the interwar period, biologists employed a diverse set of holistic approaches that were connected to different research methodologies. Against this background, this article explores attempts in the 1920s and 1930s to negotiate quantitative and qualitative methods in the field of neurophysiology. It focuses on the work of two scientists on different sides of the Atlantic: the Dutch animal psychologist and physiologist Frederik J.J. Buytendijk and the American neuropsychologist Karl S. Lashley, specifically analyzing their critical correspondence, 1929–1932, on the problems (...) surrounding the term _intelligence._ It discusses the inexplicable anomalies in neurophysiology as well as the reliability of quantitative and qualitative methods. While in his laboratory work Lashley adhered to a strictly analytic approach, Buytendijk tried to combine quantitative methods with phenomenological and hermeneutical approaches. The starting point of their discussion is Lashley’s monograph on _Brain Mechanisms and Intelligence_ (1929) and the rat experiments discussed therein. Buytendijk questioned the viability of the maze-learning method and the use of statistics to test intelligence in animals; he reproduced Lashley’s experiments and then confronted Lashley with his critical findings. In addition to elucidating this exchange, this paper will, more generally, shed light on the nature of the disagreements and shared assumptions prevalent among interwar neurophysiologists. In turn, it contributes to historiographical debates on localization and functionalism and the discrepancy between analytic (quantitative) and interpretative (qualitative) approaches. (shrink)

Reductionism relies on expectations that it is possible to make sense of the whole by studying its parts, whereas emergentism considers that program to be unattainable, partly due to the existence of emergent properties. The emergentist holistic stance is particularly relevant in biology and cognitive neuroscience, where interactions amongst system components and environment are key. Here we consider Alfred North Whitehead's philosophy as providing important insights to metaphysics of science in general, and to the reductionism vs. emergentism debate in particular. (...) An appraisal of Whitehead's perspective reveals a difficulty shared by both approaches, referred to him as “simple location”: the commitment to the idea that the nature of things is exhausted by their intrinsic or internal properties, and does not take into account relations or dynamic interactions denoting “togetherness.” In a word, that things are simply where they are. Whitehead criticizes this externalist ontological perspective in which each interacting element exists, and can be thought, without essential reference to other elements. The aim of this work is to uncover such a stance, particularly in the context of dynamical systems, and to show its shortcomings. We propose an alternative relational approach based on Whitehead's notion of “internal relations,” which we explicate and illustrate with several examples. Our work aims to criticize the notion of simple location, even in the framework of emergentist accounts, so as to contribute to a “relational turn” that will conceive “inter-identities” as “intra-identities” in which interactants are not enduring substances, but internally related processes. In sum, we argue that the notion of internal relations has a strong theoretical power to overcome some fundamental difficulties in the study of life and mind. (shrink)

Werkhoven’s ‘A Dispositional Theory of Health’ is an important and original contribution to debates about the disease concept, which persuasively demonstrates that dispositions must play some role in a full account of what it is to be healthy or ill. Unfortunately, as a theory, it cannot as it stands be correct.I first demonstrate what appears to be a significant, and possibly fatal, flaw; the proliferation of dispositions which Werkhoven’s theory requires makes impossible, at least in the absence of significant further (...) metaphysical work, the comparative numerical judgements on which its account of health and illness are based. I then demonstrate two further problems, concerning the exclusion of ‘technological’ dispositions from those under consideration, and a large class of compensatory biological functions which Werkhoven’s theory seems to have overlooked. (shrink)

Establishing Dispositionalism as a viable theory of modality requires the successful fulfilment of two tasks: showing that all modal truths can be derived from truths about actual powers, and offering a suitable metaphysics of powers. These two tasks are intertwined: difficulties in one can affect the chances of success in the other. In this paper, I generalise an objection to Dispositionalism by Jessica Leech and argue that the theory in its present form is ill-suited to account for de re truths (...) about merely possible entities. I argue that such difficulty is rooted in a problem in the metaphysics of powers. In particular, I contend that the well-known tension between two key principle of powers ontology, namely Directedness and Independence has received an unsatisfactory solution so far, and that it is this unsatisfactory solution concerning the status of “unmanifested manifestations” that makes it hard for Dispositionalism to account for mere possibilia. I develop a novel account of the status of unmanifested manifestations and an overall metaphysics of powers which allows to better respond to Leech's objection and handle mere possibilia. The central idea of the proposal is that unmanifested manifestations are akin to mere logical existents, and are best characterised as non-essentially non-located entities. (shrink)

We have two theses about scientific knowledge in the age of computation. Our general claim is that scientific Knowledge Management practices emerge as second-order practices whose aim is to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data. Our specific thesis is that knowledge management practices are transforming biological research in at least three ways. We argue that scientific Knowledge Management a. operates with founded concepts of biological knowledge as explicated and computable, b. enables new outputs and (...) ways of knowing within biology, and c. risks enforcing objectivist epistemologies of knowledge as some one objective thing. (shrink)

Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...) is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: means reification, when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and target reification, when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used. (shrink)

Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...) claims that arise from a position on individuation and identity known as sortalism. An examination of biological examples shows that these sortalist requirements cannot be plausibly met due to differences between individuation by functional biological criteria and by physical criteria. Even without assuming sortalism, token physicalism faces the more basic problem of excluding functionally irrelevant detail from the individuation of biological tokens. I close by suggesting that the philosophical roles for token identity are better fulfilled by a notion of token composition, which promotes a hierarchical picture of individuality. (shrink)

Enactivism and ecological psychology converge on the relevance of the environment in understanding perception and action. On both views, perceiving organisms are not merely passive receivers of environmental stimuli, but rather form a dynamic relationship with their environments in such a way that shapes how they interact with the world. In this paper, I suggest that while enactivism and ecological psychology enjoy a shared specification of the environment as the cognitive domain, on both accounts, the structure of the environment, itself, (...) is unspecified beyond that of contingent relations with the species-typical sensorimotor capacities of perceiving organisms. This lack of specification creates a considerable gap in theory regarding the organization of organisms as coupled with their environments. I argue that this gap can be filled by drawing from resources in developmental systems theory, namely, specifying the environmental state-space as a developmental niche that shapes and is shaped by individual organisms over developmental and, on a population scale, evolutionary time. Defining the environment as an organism’s developmental niche makes it clearer how and why certain contingencies have arisen, in turn, strengthening a joint appeal to both enactivism and ecological psychology as theories asserting complementarity between organisms and their environments. (shrink)

In the 1940s, the ‘modern synthesis’ (MS) of Darwinism and genetics cast genetic mutation and recombination as the source of variability from which environmental events naturally select the fittest, such ‘natural selection’ constituting the cause of evolution. Recent biology increasingly challenges this view by casting genes as followers and awarding the leading role in the genesis of adaptations to the agency and plasticity of developing phenotypes—making natural selection a consequence of other causal processes. Both views of natural selection claim to (...) capture the core of Darwin’s arguments in On the Origin of Species. Today, historians largely concur with the MS’s reading of Origin as a book aimed to prove natural selection the cause (vera causa) of adaptive change. This paper finds the evidence for that conclusion wanting. I undertake to examine the context and meaning of all Darwin’s known uses of the phrase vera causa, documenting in particular Darwin’s resistance to the pressure to prove natural selection a vera causa in letters written early in 1860. His resistance underlines the logical dependence of natural selection, an unobservable phenomenon, on the causal processes producing the observable events captured by the laws of inheritance, variation, and the struggle for existence, established in Chapters 1–3 of Origin. (shrink)

This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...) terms of the Zsyntax language allows us to represent causal interactions by taking into account their context-sensitivity, and amounts to partly reviving the spirit of the so-called received view of explanation – which aimed to capture scientific explanatory accounts in terms of their logical structure and their appealing to nomological relations. Such a partial revival is pursued by invoking here non-classical deductions and empirical generalisations, which are called to provide the epistemic norms to explain the behavior of molecular pathways. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ as one entity (...) over time. In this paper, I offer a novel defence of substance ontology by arguing that the coherency and plausibility of the radical reconceptualisation of organisms proffered by process ontology ultimately depends upon its making use of the ‘substantial’ principles it purports to replace. (shrink)

Journal Name: Semiotica Issue: Ahead of print.

It is a matter of contention whether or not a general explanatory framework for the biological sciences would be of scientific value, or whether it is even achievable. In this paper we suggest that both are the case, and we outline proposals for a framework capable of generating new scientific questions. Starting with one clear characteristic of biological systems – that they all have the potential to make mistakes - we aim to describe the nature of this potential and the (...) common processes that lie behind it. Given that under most circumstances biological systems function effectively, an examination of different kinds of mistake-making provides pointers to mechanisms that must exist to make failure uncommon. This in turn informs a framework for systematic enquiry, which in this paper we apply to the haemostatic system, but which we believe could be applied to any system across biology. (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)

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)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

This is an article in Thomas J.J. McCloughlin (Ed.) The Nature of Science in Biology: A Resource for Educators. Graphikon Teo, Dublin. -/- Abstract: Philosophers usually tend to think of animals when they think about life, plants often only appear in their works as on the margins, in the background; they are rarely in the centre. However, plant life involves unique processes, including remarkable modes of interaction between plants and their environments. Needless to say, plants are vital parts of ecosystems. (...) Serious attention to plants provides novel and interesting perspectives on many topics in philosophy of biology, including individuality, organisation and disease. Plant biology should have a substantial part in philosophy education. To support this assertion, this paper briefly describes three topics related to plant-environment interaction and explains some of their philosophical implications. These topics are growth, plant hormones and plant-plant microbiota interactions, all of which present crucial aspects related to some prevalent topics in philosophy of biology such as individuality, systems thinking, and holobiont. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

Both biosemiotics and evolutionary epistemology are concerned with how knowledge evolves. (Applied) Evolutionary Epistemology thereby focuses on identifying the units, levels, and mechanisms or processes that underlie the evolutionary development of knowing and knowledge, while biosemiotics places emphasis on the study of how signs underlie the development of meaning. We compare the two schools of thought and analyze how in delineating their research program, biosemiotics runs into several problems that are overcome by evolutionary epistemologists. For one, by emphasizing signs, biosemiotics (...) needs to delineate a semiotic threshold, which is a problem not encountered by evolutionary epistemologists. Instead, the latter recognizes that all organisms are knowers that evolve knowledge, which they recognize to extend toward phenomena produced by organisms such as behavior, cognition, language, culture, science, and technology. Secondly, biosemiotics attempts at continuing adaptationist notions on how organisms relate to their environment, while especially Applied Evolutionary Epistemology comes to redefine the nature of the organism–environment relationship in such a way that it recognizes the spatiotemporal boundedness of existence, which in turn makes adaptationist accounts obsolete. (shrink)

This edited collection highlights the valuable ontological and creative insights gathered from anticipation studies, which orients itself to the future in order to recreate the present. The gathered essays engage with many writers from speculative metaphysics to poetic philosophy, ancient writing systems to the fringes of pataphysics. The book situates itself as a creative intervention in and with various thinkers, designers, artists, scientists and poets to offer insight into ways of anticipating. It brings together philosophical practices for which creativity is (...) both a fundamental area of consideration and a mode of working, a characterization of recent Continental Philosophy which takes a departure from traditional futures studies thinking. This book will be of interest to scholars and research in futures studies, anticipation, philosophy, creative practice and theories about creative practice, as well as the intersections between philosophy, creativity and business. (shrink)

With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...) KM in semantic systems biology. Through an empirical philosophical account of KM-enabled biological research, we argue that KM helps produce new first-order biological knowledge that did not exist before, and which could not have been produced by traditional means. KM work is enabled by conceiving of ‘knowledge’ as an object for computational science: as explicated in the text of biological articles and computable via appropriate data and metadata. However, these founded knowledge concepts enabling computational KM risk focusing on only computationally tractable data as knowledge, underestimating practice-based knowing and its significance in ensuring the validity of ‘manageable’ knowledge as knowledge. (shrink)

The long standing and still highly influential mindreading framework claims that social cog- nition is best understood as an ability to predict and explain others’ behavior in terms of their mental states. This ability is explained by appealing to mental representations and inferential reasoning via rule-based knowledge. However, recent enactive work on social cognition questions most, if not all, of the main assumptions on which mindreading is founded. Enac- tivism’s emphasis on the structural coupling of the brain-body-world constitutes the foundation (...) of the framework, which rejects the representational and inferential reasoning claims of the mindreading framework. For enactivists, social cognition is best explained in terms of the direct embodied and embedded interactions an agent has with her socio-material world. In continuing this work, the thesis provides new developments of the enactive project for investigating and explaining social cognition. The thesis utilizes two approaches to achieve this goal. First, it dialectally defends enactivism vis-a-vis the mindreading framework. It does this by both securing established enactive claims from criticism, and by developing new objections against the mindreading framework. Secondly, the thesis offers new enactive interpretations of empirical developmental data, and presents new ways of investigating three central areas of debate within the field of social cognition: the metaphysical basis of social cognitive processes, the false-belief test literature, and the concept of empathy in relation to therapeutic practices and autism. The thesis is composed of five different, but thematically intertwined papers. The first paper targets the constitutive basis of social cognition by attempting to dissolve the causal-constitutive fallacy through appealing to a diachronic conception of constitution. This move both secures established enactive claims and develops a more thorough account of what is meant by enactive constitutive claims. The second paper then examines infant social cognitive capacities, arguing cognitivist explanations of these capacities rely on fallacious as- sumptions regarding the nature of perception. The paper then offers an alternative enactive and ecological account of these capacities. The third paper argues both innate and construc- tivist mindreading accounts of the folk psychological know-how required to reliably succeed on false-belief tests fall prey to an infinite regress problem. The paper ends by briefly pre- senting an alternative enactive, narrative explanation of the empirical data. The fourth paper then shifts focus to examine the concept empathy and practice of empathizing. It argues there are advantages to conceiving of empathy as enactive and exploratory, in the sense that when we empathize with others we understand them in a deeper and richer way, through exploring their self-authored narratives. Finally, the fifth paper re-examines our understand- ing of autism by integrating the enactive framework with a neurodiversity approach to cognition. It argues this integration can help us better understand how neurotypical social practices and institutions effect the development, and well-being, of autistic individuals. Through these substantial expansions of established enactivist accounts, and by offering new objections to the mindreading framework, the thesis provides reasons to prefer an enactivist framework in exploring human abilities for social cognition. (shrink)

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...) origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is ‘transduction’ as part of ‘ontogenesis’ of individuals in a process of ‘individuation’, that is, the emergence of ‘individuals’ from preindividual fields or milieux. (shrink)

The widespread particularist account of the onset of molecular biology that identifies it with the discovery of the DNA structure in 1953 has been recently contested. The paper contributes to this debate by focusing on a more recent discovery of small noncoding RNAs. First, it outlines a particularist account of the microRNAs discovery and the origins of the particularist predilection of the modern scientometric studies of science dynamics. Next, it discusses its limitations and proposes an alternative, modified processualist account of (...) the discovery. In the final part, the paper applies this approach to unravel network dynamics of the research on the first two microRNAs that were discovered, namely lin-4 and let-7. (shrink)

“What is a gene?” is an important philosophical question that has been asked over and over. This paper approaches this question by understanding it as the individuation problem of genes, because it implies the problem of identifying genes and identifying a gene presupposes individuating the gene. I argue that there are at least two levels of the individuation of genes. The transgenic technique can individuate “a gene” as an individual while the technique of gene mapping in classical genetics can only (...) individuate “a gene” as a type or a kind. The two levels of individuation involve different techniques, different objects that are individuated, and different references of the term “gene”. Based on the two levels of individuation, I discuss important philosophical implications including the relationship between individuality and individuation and that between individuals and kinds in experimental contexts. I also suggest a new gene conception, calling it “the transgenic conception of the gene.”. (shrink)

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)