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)

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)

The paper approximates Jakob von Uexküll’s theory of meaning and the process-thought in Alfred Whitehead’s philosophy. As the main idea, the paper points at the compatibility of meaning and process according to the perspectives of Uexküll and Whitehead. It suggests that Uexküll’s common meaning rule can describe the processes of novelty in the world as does Whitehead’s principle of creativity. It is also suggested that Uexküll and Whitehead abandon a substantialist view of the organism – the organism means much more (...) process, activity and creation than anything thing-like. In approaching Uexküll’s theory of meaning, a semiotic interpretation of Whitehead’s principle of creativity is proposed in which the concept of the threshold is fundamental to defining the boundary between the semiotic and the non-semiotic areas corresponding to the living and the non-living. In conclusion, the paper suggests that the activity of meaning distinguishes animate entities from inanimate ones in the sense that meaning and life overlap – meaning could not have existed prior to life. (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)

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)

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)

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)

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 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)

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)

Journal Name: Semiotica Issue: Ahead of print.

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)

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)

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)

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

“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 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)