Heraclitus uses paradoxical language to present the relationship between opposites in his worldview. This mode of expression has generated much controversy. Some take the paradoxes as evidence of a contradictory identity of opposites (Barnes), while others propose a dynamic union through transformation without identity that avoids the contradiction (Graham). By examining B88 and B62, I seek to identify the stronger and weaker points of such readings. The contradictory identity reading thwarts the transformation between opposites. The dynamic reading offers a plausible (...) alternative. However, it skips a characterization of how Heraclitus conceives of the transformation between opposites in physical terms. To fill this gap, I consider Heraclitus’ use of what I call the anti-cognate internal object in B62. I argue that ‘living the death and dying the life’ is a case of change as mixture, a popular conception among the early Presocratics. Upon closer examination, the anti-cognate internal object suggests that real contradictions belong to Heraclitus conception of change. The details reveal a philosophically compelling view. (shrink)

A provocative defense of a forgotten Chinese approach to identity and difference Historically, the Western encounter with difference has been catastrophic: the extermination and displacement of aboriginal populations, the transatlantic slave trade, and colonialism. China, however, took a different historical path. In Chinese Cosmopolitanism, Shuchen Xiang argues that the Chinese cultural tradition was, from its formative beginnings and throughout its imperial history, a cosmopolitan melting pot that synthesized the different cultures that came into its orbit. Unlike the West, which cast (...) its collisions with different cultures in Manichean terms of the ontologically irreconcilable difference between civilization and barbarism, China was a dynamic identity created out of difference. The reasons for this, Xiang argues, are philosophical: Chinese philosophy has the conceptual resources for providing alternative ways to understand pluralism. Xiang explains that “Chinese” identity is not what the West understands as a racial identity; it is not a group of people related by common descent or heredity but rather a hybrid of coalescing cultures. To use the Western discourse of race to frame the Chinese view of non-Chinese, she argues, is a category error. Xiang shows that China was both internally cosmopolitan, embracing distinct peoples into a common identity, and externally cosmopolitan, having knowledge of faraway lands without an ideological need to subjugate them. Contrasting the Chinese understanding of efficacy—described as “harmony”—with the Western understanding of order, she argues that the Chinese sought to gain influence over others by having them spontaneously accept the virtue of one’s position. These ideas from Chinese philosophy, she contends, offer a new way to understand today’s multipolar world and can make a valuable contribution to contemporary discussions in the critical philosophy of race. (shrink)

In this paper, I propose a theory of living organisms that captures the insights of both traditional Aristotelian hylomorphism and John Dupré's “biological processualism”. Like traditional Aristotelian hylomorphism, the proposed theory understands material objects to be comprised of both matter and form. Unlike contemporary structural varieties of hylomorphism, however, it does not understand the form of a material object to be a relation, configuration, or structure exhibited by its parts but an activity or process in which its matter is continuously (...) engaged. Following Mark Steen, I call the proposed theory “Hyloenergeism”. As a version of hylomorphism, hyloenergeism better captures the inherent dynamism of living organisms than contemporary structural approaches. And it does so not by abandoning the substantialist paradigm, as Dupré's biological processualism does, but by reconceptualizing the nature of material substances as possessing a processual core. Hyloenergeism, then, paves a middle way for those looking for a substance view of living organisms sensitive to the concerns raised by contemporary processualist philosophers of biology. (shrink)

In this article, I argue that, for the purpose of developing an effective critical social ontology about gender groups, it is not simply sufficient to carve gender groups at their joints: one must have in view whether the metaphysical categories we use to make sense of gender groups are prone to ideological distortion and vitiation. The norms underpinning a gender group's constitution as a type of social class and the norms involved in gender identity attributions, I propose, provide compelling reason (...) to think critical social ontological discourse is more processist-orientated, rather than substantival-orientated. The advantages of a processist critical social ontology of gender groups are that, unlike substance-discourse, process-discourse recognizes how gender group talk and gender identity talk are often messy and therefore require a conceptual scheme that can transform vocabulary for the emancipatory purpose of ending oppression, domination, and marginalization. (shrink)

There has been much criticism of the idea that Friston's free-energy principle can unite the life and mind sciences. Here, we argue that perhaps the greatest problem for the totalizing ambitions of its proponents is a failure to recognize the importance of evolutionary dynamics and to provide a convincing adaptive story relating free-energy minimization to organismal fitness.

According to process ontology in the philosophy of biology, the living world is better understood as processes rather than as substantial individuals. Within this perspective, an organism does not consist of a hierarchy of structures like a machine, but rather a dynamic hierarchy of processes, dynamically maintained and stabilized at different time scales. With this respect, two processual approaches on enzymes by Stein (Hyle Int J Philos Chem 10(4):5–22, 2004, Process Stud 34:62–80, 2005, Found Chem 8:3–29, 2006) and by Guttinger (...) (Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press, Oxford, 2018) allows to think of macromolecules as relational and processual entities. In this work, I propose to extend their arguments to another case study within the biochemical domain, which is the case of ligand receptors and receptor-mediated biosignaling. The aim of this work is to analyze the case of G Protein-Coupled Receptors and biosignaling under the consideration of a processual ontology. I will defend that the processual ontology framework is adequate for the biochemical domain and that it allows accounting for the current biochemical knowledge related to the case study. (shrink)

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)

Biology seems to present local and transitory regularities rather than immutable laws. To account for these historically constituted regularities and to distinguish them from mathematical invariants, Montévil and Mossio (Journal of Theoretical Biology 372:179–191, 2015) have proposed to speak of constraints. In this article we analyse the causal power of these constraints in the evolution of biodiversity, i.e., their positivity, but also the modality of their action on the directions taken by evolution. We argue that to fully account for the (...) causal power of these constraints on evolution, they must be thought of in terms of normativity. In this way, we want to highlight two characteristics of the evolutionary constraints. The first, already emphasised as reported by Gould (The structure of evolutionary theory, Harvard University Press, 2002), is that these constraints are both produced by and producing biological evolution and that this circular causation creates true novelties. The second is that this specific causality, which generates unpredictability in evolution, stems not only from the historicity of biological constraints, but also from their internalisation through the practices of living beings. (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)

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)

Processes produce changes: rivers erode their banks and thunderstorms cause floods. If I am right that organisms are a kind of process, then the causally efficacious behaviours of organisms are also examples of processes producing change. In this paper I shall try to articulate a view of how we should think of causation within a broadly processual ontology of the living world. Specifically, I shall argue that causation, at least in a central class of cases, is the interaction of processes, (...) that such causation is the exercise of a capacity inherent in that process and, negatively, that causation should not be understood as the instantiation of universal laws. The approach I describe has substantial similarities with the process causality articulated by Wesley Salmon and Phil Dowe for physical causation, making it plausible that the basic approach can be applied equally to the non-living world. It is an approach that builds at crucial points on the criticisms of determinism and universal causality famously articulated by Elizabeth Anscombe. (shrink)

Both concepts of the holobiont and the immune system are at the heart of an ongoing scientific and philosophical examination concerning questions of the organism’s individuality and identity as well as the relations between organisms and their environment. Examining the holobiont, the question of boundaries and individuality is challenging because it is both an assemblage of organisms with physiological cohesive aspects. I discuss the concept of immunity and the immune system function from the holobiont perspective. Because of the host-microbial close (...) relations of codependence and interdependence, the holobiont is more often than not confused with the host, as the host is the domain in which this entity exists. I discuss the holobiont unique ecological characteristics of microbial assemblages connected to a host in a network of interactions in which the host is one of the organisms in the community but also its landscape. Therefore, I suggest viewing the holobiont as a host-ecosystem and discuss the implication of such a view on the concept of immunity and the meaning of protection. Furthermore, I show that viewing the holobiont as a host ecosystem opens the possibility of using the same ecological definition of boundaries and immunity dealing with an ecological system. Thus, the holobiont’s boundaries and immunity are defined by the persistence of its complex system of interactions integrating existing and new interactions. This way of thinking presents a notion of immunity that materializes as the result of the complex interdependence relations between the different organisms composing the holobiont similar to that of an ecosystem. Taking this view further, I discuss the notion of immunogenicity that is ontologically heterogeneous with various causal explanations of the processes of tolerance and targeted immune response. Finally, I discuss the possible conceptualization of already existing and new biomedical practices. (shrink)

An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM argue that applying Woodward’s account to this philosophical problem conflates causation and constitution, thus rendering the account incoherent. These criticisms, we (...) argue, arise from failing to distinguish the semantic, epistemic, and metaphysical aspects of the problem of constitutive relevance. In distinguishing these aspects of the problem and responding to these critics accordingly, we amend MM into a refined epistemic criterion, the “matched interlevel experiments” account. Further, we explain how this epistemological thesis is grounded in the plausible metaphysical thesis that constitutive relevance is causal betweenness. (shrink)

There is not a consensus on the definition of vitality or life yet. Therefore, there are hundreds of definitions and interpretations about life. A number of new or similar definitions have been added in the relevant literature year by year. From this point of view, in this study, it has been examined whether the words canlılık (vitality) and hayat (life) in Turkish can be used as terms equivalent to each other and it has been put forward that it would be (...) more correct to use them separately. The relationship between the parts of an organism’s hierarchy is reviewed, based on the relationships that the cell, as the place where vitality arises, establishes with its similars on the horizontal and with the lineage on the vertical. Based on all of these, a vitality design has been put forward. According to this theoretical design, life has a purpose to continue, and this is possible through an activity of manifestation through the reproduction and diversity of the living beings. It is suggested to use the term homeokinesis instead of homeostasis in order to describe the balance in the living things. Keywords: life, philosophy of biology, relationality, vitality. (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)

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)

Objections to the computational theory of cognition, inspired by twentieth century phenomenology, have tended to fixate on the embodiment and embeddedness of intelligence. In this paper I reconstruct a line of argument that focusses primarily on the abstract nature of scientific models, of which computational models of the brain are one sort. I observe that the critique of scientific abstraction was rather commonplace in the philosophy of the 1920s and 30s and that attention to it aids the reading of The (...) Organism ([1934] 1939) by the neurologist Kurt Goldstein. With this background in place, we see that some brief but spirited criticisms of cybernetics by two later thinkers much influenced by Goldstein, Georges Canguilhem (1963) and Maurice Merleau-Ponty (1961), show continuity with the earlier discussions of abstraction in science. (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)

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)

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)

This paper argues that Confucianism had an antiessentialist conception of selfhood. This understanding of self means that they did not have, and could not have had, a concept of “race” in the sense that one's essence determines one's becoming. In the Confucian canon, the embodiment of cultural norms/performance of culturally appropriate actions defines one's human-ness. This account of human agency in becoming human can be seen in the Confucian explanation of moral failure. This assumption of human agency also means that (...) the Confucian understanding of hierarchy is social as opposed to ontological and that differences between peoples are understood to be a result of culture–custom variation. (shrink)

In this paper we will argue that the identity of the entities that inhabit the nanoworld is a contextual identity. To defend that, we will analyse the so-called “biological” identity and the “synthetic” identity of nanomaterials. From this analysis, we will claim that nano-individuals (entities that show an intermediate nature between individuals and stuff), can be adequately understood from the perspective of a processual ontology. With that, we intend to contribute to the philosophical understanding of the ontology of the nano-domain.

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.

Theological discourse surrounding the environmental crisis has rightly brought to the forefront human agency as a primary causal determinant. However, this article explores a theistic divine action position toward an account of the present global precipice that the earth and all its creatures teeter upon. The first section offers a preferred view of divine action theory, Divine Compositionalism, with explanatory power to account for an ever-changing planet. Furthermore, Divine Compositionalism is used to ground the role of God as Creator and (...) sustainer of all things toward a constructive biotheology. The second section accounts for both human culpability and God’s divine action, retaining human free will and God’s sovereignty within a creation God owns and loves. The final section explores a possible remedy to the environmental precipice through the very elements of human cooperation that ensured the success of our prehistoric ancestors. A cooperative biotheology entails humanity re-claiming its inter-relation with all creatures in a world family while exercising the free will to partner with one another on a spiritual level in accomplishing God’s good and wonderful eternal ideas for the next step in human spiritual development toward earth’s physical evolution.Contribution: Drawing upon Divine Compositionalism as a new view of divine action, this article explores God’s action in the natural world as it is now and offers a biotheology that entails divine–human partnership toward an alternative future outcome. (shrink)

During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that (...) underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process. (shrink)

In this paper, I argue that attempts in the philosophy of biology to show that organisms are processes rather than substances fail. Despite what process ontologists have said, I argue that substance ontology is perfectly able to accommodate the dynamic nature of organisms, their ecological dependence, and their vague boundaries, and that their criticisms are not directed at substance ontology simpliciter, but only at specific (perhaps untenable) characterisations of substances. The paper ends by considering what a processual philosophy of biology (...) that is radically in conflict with an ontology of substances might look like. (shrink)

This article argues that Ernst Cassirer's views about the concept of substance and his views on mythic consciousness are applicable to the concept of race. By analyzing examples from the most influential and representative racial theories, this article shows that the concept of race functions like the concept of substance whereby random, large-scale, and irreducibly complex phenomena is explained through the deterministic behavior of a smaller, material, constituent part. Given that mythic consciousness explains causality in the same way, this substance-mode (...) explanation of becoming can also be termed “mythic.” Further, under this substance/racial understanding of personhood, humans have no agency to determine their own fates. It is this fatalism that Cassirer railed against in The Myth of the State. In place of this substance (racial) understanding of personhood, and as this article will describe, Cassirer argued for a “functional” (cultural) understanding of personhood. (shrink)

The term ‘information’ is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of ‘meaning’ and ‘causation’. While ‘information’ is a term that serves a useful purpose in specific disciplines, there is much to the concept that is problematic. Part 1 is a critique of the stance that information is an independently existing entity. On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, and in so doing, generate (...) meaning. I provide a detailed proposal in Part 2 that supports the claim that it is the dynamic form of a system that qualifies the informational nature of meaningful interactive engagement, that is, that information is dependent on dynamic form rather than that it exists independently. In Part 3, I reflect on the importance of the distinction between the independent and dependent stances by looking specifically at the implications for how we might better interpret causation and emergence. (shrink)

What is it for an individual thing in the natural world—a rock, a mouse, a family or a planet—to be made of other things—crystals, organs, animals, soil, water, or dirt? Rocks, mice, families and planets are composites, but how are we to understand the relation that holds between these composites and their component parts? My aim is to offer a new account of this relation, which I shall call corporeal composition. A central claim of my account is that corporeal composition (...) is grounded in causal relations between components. I will show how this claim, combined with a minimalist approach to causation—that causation is not one thing, but many—entails a position I call compositional minimalism—that composition is not one thing, but many. (shrink)

This paper argues that Confucianism had an antiessentialist conception of selfhood. This understanding of self means that they did not have, and could not have had, a concept of “race” in the sense that one's essence determines one's becoming. In the Confucian canon, the embodiment of cultural norms/performance of culturally appropriate actions defines one's human-ness. This account of human agency in becoming human can be seen in the Confucian explanation of moral failure. This assumption of human agency also means that (...) the Confucian understanding of hierarchy is social as opposed to ontological and that differences between peoples are understood to be a result of culture–custom variation. (shrink)

Substantialism, which is an extremely common paradigm in Western philosophy, has dominated the sciences over time. Arguing that the authentic structure of existence is fixed and unchangeable; over time, with the development of modern physics, this understanding, which was easily adopted due to the precision of mechanical and mathematical explanations and the ease of categorization, created a school of biology that tried to develop through quantitative propositions; thus, living things were considered static entities that could be understood through reverse engineering. (...) Findings regarding evolution, which has continued uninterrupted for millions of years, have led to the gradual abandonment of essentialism. In addition, when many new data were analyzed, such as the transition from genetics to epigenetics and the mutual interaction in nature and niche creation, it was realized that biology in particular and all natural sciences in general needed a new metaphysical approach, thus process philosophy came to the fore. In process philosophy and metaphysics, it is accepted that every structure in nature consists of processual structures, not substances. The living world is fundamentally dynamic, and the existence of things always depends on the existence of processes, the basic assumption of biology is stability, not change; more precisely, it is argued that it is a stability achieved through constant change. By presenting a methodology, metaphysics and perspective from the process perspective of John Dupré, one of today's most important philosophers of biology, it is aimed to draw attention to the flowing of existence and processes of nature, expressed by Heraclitus as panta rhei (everything flows). (shrink)

As this study elucidates, Daoist philosophy provides an account of how and why desires are morally and epistemologically suspect. The Daoist critique of desire is itself informed by a processual un...

According to process ontology in the philosophy of biology, the living world is better understood as processes rather than as substantial individuals. Within this perspective, an organism does not consist of a hierarchy of structures like a machine, but rather a dynamic hierarchy of processes, dynamically maintained and stabilized at different time scales. With this respect, two processual approaches on enzymes by Stein (Hyle Int J Philos Chem 10(4):5–22, 2004, Process Stud 34:62–80, 2005, Found Chem 8:3–29, 2006) and by Guttinger (...) (Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press, Oxford, 2018) allows to think of macromolecules as relational and processual entities. In this work, I propose to extend their arguments to another case study within the biochemical domain, which is the case of ligand receptors and receptor-mediated biosignaling. The aim of this work is to analyze the case of G Protein-Coupled Receptors and biosignaling under the consideration of a processual ontology. I will defend that the processual ontology framework is adequate for the biochemical domain and that it allows accounting for the current biochemical knowledge related to the case study. (shrink)

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the (...) most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics. (shrink)

This paper argues that the ‘processual holism’ of Chinese metaphysics explains its characteristic attitude towards non-humans such as animals and demons. As all things are constantly in process and form a continuum, it follows that ontological distinctions between ‘species’ become impossible to delimit. The distinctions one makes are instead understood as perspectival and provisional. These metaphysical assumptions explain the lack of interest in the Chinese tradition for classifying the distinctions between humans and non-human. We see many examples of the different (...) schools of philosophy espousing the view that the distinction between humans and non-humans is tenuous, precarious and subject to change. A key implication that follows is that the Chinese worldview saw no ontological distinction between those considered as ‘Chinese’ and as ‘non-Chinese.’ The unavailability of ontological distinction as an explanation for the existence of difference means that phenomena that are perceived as anomalous, such as ghosts and spirits, are attributed to the perspective of the human agent; anomaly/difference is not understood as ontological. (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)

This article is concerned with two interrelated questions: what, if anything, distinguishes synthetic from natural organisms, and to what extent, if any, creating the former is of moral significance. These are ontological and ethical questions, respectively. As the title indicates, I address both from a broadly neo-Aristotelian perspective, i.e. a teleological philosophy of life and virtue ethics. For brevity’s sake, I shall not argue for either philosophical position at length, but instead hope to demonstrate their legitimacy through their explanatory power. (...) I firstly argue that synthetic organisms differ in kind from natural organisms and machines, and differ only by degree from genetically modified organisms. I then suggest that this is nevertheless sufficient to give us specific ethical reservations about synthetic biology: namely, that more than any other widely used biotechnology, it is characterised by a drive to mastery that stands opposed to due appreciation of the giftedness of life. (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)

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)

Although the analogy between macroscopic machines and biological molecular devices plays an important role in the conceptual framework of both neo-mechanistic accounts and nanotechnology, it has recently been claimed that certain complex molecular devices cannot be considered machines since they are subject to physicochemical forces that are different from those of macroscopic machines. However, the structural and physicochemical conditions that allow both macroscopic machines and microscopic devices to work and perform new functions, through a combination of elemental functional parts, have (...) not yet been examined. In order to fill this void, this paper has a threefold aim: first, to clarify the structural and organisational conditions of macroscopic machines and microscopic devices; second, to determine whether the machine-like analogy fits nanoscale devices; and third, to assess whether the machine-like analogy is appropriate for describing the behaviour of some biological macromolecules. Finally, the paper gives an account of ‘machine’ which, while acknowledging the physicochemical and organisational differences between man-made machines and biological microscopic devices, nevertheless identifies a common conceptual core that allows us to consider the latter ‘machines’. (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)

In this paper I argue that thinking in terms of process metaphysics and seeing the mind and mental disorders as processual in nature allows for a more complete understanding of mental disorders than is allowed by non-processual frameworks, while it also allows us to incorporate what we currently know about them. In addition, it can address problems in psychiatry that arise when we ask the wrong kinds of questions that naturally arise within a non-processual metaphysical framework. In this paper I (...) address the problems of reductionism, essentialism and dualism. -/- . (shrink)

This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias Uller’s and Kevin Laland’s volume Evolutionary Causation as well as recent reviews of it as a starting point to reflect (...) on the causal role of agency, individuality, and the environment in evolution. In addition, I critically discuss classical philosophical frameworks of theory change used in this debate to understand changing views of evolutionary causation. (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)

This paper attempts to reconcile the conceptual conflict between typological and population thinking to provide a philosophical foundation for extended evolutionary synthesis. Typological thinking has been considered a pre-Darwinian, essentialist dogma incompatible with population thinking, which is the core notion of Darwinism. More recent philosophical and historical studies suggest that a non-essentialist form of typology has some advantages in the study of evolutionary biology. However, even if we adopt such an epistemological interpretation of typological thinking, there still remains an epistemological (...) and methodological conflict between these two styles of thinking. How can we relate typological thinking with population thinking in pursuit of more integrated or interconnected research into evolutionary biology? I propose that homology thinking, which is another style of thinking that recognizes homologous characters, provides a common basis for typological representations of character states and for character dynamics in an evolving population. Good examples of this bridging role are found in teratology and breeding, where variation and novelty are recognized in developmental and morphological traits, gene expression patterns, and so on. Essentialism-free, dynamic views of homology have great potential to reconcile typological and population thinking and to set the stage for the EES. (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)

Biological macromolecules, considered as the items of the biochemical domain, are typically conceived under the ontological category of substantial individuals. In this paper, I will argue that the philosophical framework of process ontology, according to which the living world is not populated by individuals but by a dynamic hierarchy of processes, is more adequate to account for the structure and functioning of macromolecules. In particular, I will analyze its application to the phenomenon of cell signaling and to one of its (...) key concepts, cell receptors. Current knowledge in biochemistry allows us to conceive receptors as processual and dynamic entities, relationally stabilized and not separated from the biochemical phenomenon of which they are part. (shrink)

RÉSUMÉDans cet article, je soutiens que le « manifeste du processus » de John Dupré et Daniel Nicholson est ironiquement plus sympathique à la métaphysique descriptive qu’à la métaphysique révisionniste. En me concentrant sur leur argument selon lequel toute philosophie du processus glisse automatiquement dans l'obscurantisme Whiteheadien lorsqu'elle ne se contente pas de révéler seulement les caractéristiques problématiques du langage ordinaire, je soutiens que leur position dissimule un espace logique dans lequel la métaphysique révisionniste s'articule sans aucun obscurantisme Whiteheadien et (...) n'implique aucun apauvrissement de l'orientation critique/révisionniste. Je soutiens que les caractéristiques clés des ontologies sociales critiques respectives de Judith Butler et Talia Mae Bettcher occupent un tel espace logique. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)