This paper compares the two known logical forms of hierarchy, both of which have been used in models of natural phenomena, including the biological. I contrast their general properties, internal formal relations, modes of growth (emergence) in applications to the natural world, criteria for applying them, the complexities that they embody, their dynamical relations in applied models, and their informational relations and semiotic aspects.

Hierarchical organization is an essential characteristic of living things. Although most biologists affirm the concept of living things as hierarchically organized structures, there are widespread differences of interpretation in the meaning of hierarchy and of how the concept of hierarchy applies to living things. One such basic difference involves the distinction between the concept of control hierarchy and classification hierarchy. It is suggested that control hierarchies are distinguished from classification hierarchies in that while the former involve authority relationships between levels, (...) the latter do not. This is illustrated in an analysis of proposed hierarchies of replicators and interactors.The analysis of levels of hierarchies and their relationships also brings up the part-whole problem. An authority relationship between levels implies that the whole has a determining influence on the parts that make up the whole, and that parts have no independent, meaningful existence apart from the whole. The concept of an authority relationship in a part-whole relationship introduces the question of the independence or sovereignty of the components of the subordinate levels in a hierarchically organized living thing. This problem is discussed along with an analysis of the rather novel theory of enkapsis proposed by H. Dooyeweerd, in which he distinguishes part-whole relationships from enkaptic relationships. (shrink)

In a reply to Marga Vicedo the philosophical inconsistency of Morgan is emphasized. It is argued that even if a strict classification of scientists according to their philosophical position is not possible, their science may still be influenced by their philosophical ideas. Finally it is suggested that philosophical ideas influence science less by a direct effect on the scientists than indirectly through science policy and administration.

The founding of the Carnegie Institute’s Department of Embryology in 1913, alongside its systematization of embryo staging, contributed to the mechanization of developmental stages of embryo growth in the early 20th century. For a brief period in the middle of the century, attention to the detailed interrelation between embryo development and time made pre-existing ideas about pregnancy ends less determinative of ideas about that developmental course. However, the turn to the genetic scale led to the disappearance of this attention, replaced (...) by a sense of biological life as seamlessly scripted. This study examines the history of what I refer to as temporal attention: attention to the live, unfolding potentialities within vital matter. The reintroduction of temporal attention to discussions of development allows us to more fully consider non-human vitality and the experiences of beings that house or otherwise intimately intersect with that vital tissue, regardless of outcomes. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...) this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

Levels of organization are structures in nature, usually defined by part-whole relationships, with things at higher levels being composed of things at the next lower level. Typical levels of organization that one finds in the literature include the atomic, molecular, cellular, tissue, organ, organismal, group, population, community, ecosystem, landscape, and biosphere levels. References to levels of organization and related hierarchical depictions of nature are prominent in the life sciences and their philosophical study, and appear not only in introductory textbooks and (...) lectures, but also in cutting-edge research articles and reviews. In philosophy, perennial debates such as reduction, emergence, mechanistic explanation, interdisciplinary relations, natural selection, and many other topics, also rely substantially on the notion. -/- Yet, in spite of the ubiquity of the notion, levels of organization have received little explicit attention in biology or its philosophy. Usually they appear in the background as an implicit conceptual framework that is associated with vague intuitions. Attempts at providing general and broadly applicable definitions of levels of organization have not met wide acceptance. In recent years, several authors have put forward localized and minimalistic accounts of levels, and others have raised doubts about the usefulness of the notion as a whole. -/- There are many kinds of ‘levels’ that one may find in philosophy, science, and everyday life—the term is notoriously ambiguous. Besides levels of organization, there are levels of abstraction, realization, being, analysis, processing, theory, science, complexity, and many others. In this article, the focus will be on levels of organization and debates associated with them, and other kinds of levels will only be discussed when they are relevant to this main topic. (shrink)

Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, and as (...) a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

This paper advances the thesis of methodological mechanism, the claim that to be committed to mechanism is to adopt a certain methodological postulate, i.e. to look for causal pathways for the phenomena of interest. We argue that methodological mechanism incorporates a minimal account of understanding mechanisms, according to which a mechanism just is a causal pathway described in the language of theory. In order to argue for this position we discuss a central example of a biological mechanism, the mechanism of (...) cell death, known as apoptosis. We argue that this example shows that our philosophically deflationary account is sufficient in order to have an illuminating account of mechanisms as the concept is used in biology. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the limits of (...) reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

Critical realism, especially as developed by Roy Bhaskar, embodies at its heart systemic and holistic concepts such as totality, emergence, open systems, stratification, autopoiesis and holistic causality. These concepts have their own long history of development in disciplines such as systems thinking and cybernetics, but there is an absence in Bhaskar’s writings, and that absence is a lack of any reference to the corresponding systems literature. The purpose of this paper is threefold: (i) to demonstrate the extent of this correspondence; (...) (ii) to show that critical realism can benefit from an exposure to these other discourses; and (iii) to show that systems thinking too can gain philosophically from critical realism. (shrink)

In biology the term “vitalism” is usually associated with Hans Driesch’s doctrine of the entelechy: entelechies were nonmaterial, bio-specific agents responsible for governing a few peculiar biological phenomena. Since vitalism defined as such violates metaphysical materialism, the received view refutes the doctrine of the entelechy as a metaphysical heresy. But in the early twentieth century, a different, non-metaphysical evaluation of vitalism was endorsed by some biologists and philosophers, which finally led to a logical refutation of the doctrine of the entelechy. (...) In this non-metaphysical evaluation, first, vitalism was not treated as a metaphysical heresy but a legitimate response to the inadequacy of mechanistic explanations in biology. Second, the refutation of vitalism was logically rather than metaphysically supported by contemporary biological knowledge. The entelechy was not a valid concept, because vitalists could neither formulate vital laws, nor offer convincing examples of experimental indeterminism. (shrink)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

In this article we argue that the classical—linear and bottom-up directed—models of causation in biology, and the ‘‘proximate/ultimate’’ dichotomy, are inappropriate to capture the complexity inherent to biological processes. We introduce a new notion of ‘‘multilevel causation’’ where old dichotomies such as proximate/ultimate and bottom-up/ top-down are reinterpreted within a multilevel, web-like, approach. In briefly reviewing some recent work on complexity, EvoDevo, carcinogenesis, autocatalysis, comparative genomics, animal regeneration, phenotypic plasticity, and niche construction, we will argue that such reinterpretation is a (...) necessary step for the advancement of the ‘‘Extended Synthesis.’’. (shrink)

Several important analyses of the structure of evolutionary explanation have explicitly or implicitly required that historical laws be among the explanans statements. The required historical laws take the form of a generalization which relates some property or event to a developmental sequence of properties or events. The thesis of this paper is that historical laws of this kind are precluded by modern biological theory and, hence, analysis of evolutionary explanation within modern biology that require such laws are defective.

Starting with the observation that there exist contradictory claims in the literature about the relationship between vitalism and emergentism—be it one of inclusion or, on the contrary, exclusion–, this paper aims at disentangling the vitalism–emergentism knot. To this purpose, after having described a particular form of emergentism, namely Lloyd Morgan’s emergent evolutionism, I develop a conceptual analysis on the basis of a distinction between varieties of monism and pluralism. This analysis allows me to identify and characterize several forms of vitalism (...) and emergentism, and a subsequent comparison between these forms constitutes the occasion for a clarification of the relationship between both doctrines. (shrink)

An interdisciplinary fusion between the philosophy of science and the teaching of science can help to eradicate the disciplinary rigidity entrenched in both. In this paper I approach the history of sciencethematically, identifying general themes which transcend the boundaries of individual disciplines. Such conceptual themes can be used as a basis for an interdisciplinary introduction to university science, encouraging certain important cognitive skills not exercised during the disciplinary training emphasised in traditional approaches. Courses which teach themes such as conservation, randomness, (...) and holism/reductionism have already proved successful, and these innovations should encourage philosophers and historians to explore the exciting new possibilities which arise from stepping outside the confines of a single discipline. (shrink)

According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy . While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. (...) Organicists hold that organisms unlike machines are ‘more than the sum of their parts’ and predict that the vital properties of living things can never be explained in terms of mechanical analogies and that the reductionist agenda is doomed to failure. Here we review the current status of the mechanist and organicist conceptions of life particularly as they apply to the cell. We argue that despite the advances in biological knowledge over the past six decades since the molecular biological revolution, especially in the fields of genetics and cell biology the unique properties of living cells have still not been simulated in mechanical systems nor yielded to reductionist—analytical explanations. And we conclude that despite the dominance of the mechanistic–reductionist paradigm through most of the past century the possibility of a twentyfirst century organicist revival cannot be easily discounted. (shrink)