Immunology — though deeply experimental in everyday practice — is also a theoretical discipline. Recent advances in the understanding of innate immunity, how it is triggered and how it shares features that have previously been uniquely ascribed to the adaptive immune system, can contribute to the refinement of the theoretical framework of immunology. In particular, natural killer cells and macrophages are activated by transient modifications, but adapt to long-lasting modifications that occur in the surrounding tissue environment. This process facilitates the (...) maintenance of self-tolerance while permitting efficient immune responses. In this Essay we extend this idea to other components of the immune system and we propose some general principles that lay the foundations for a unifying theory of immunity — the discontinuity theory. According to this theoretical framework, effector immune responses (namely, activated responses that lead to the potential elimination of the target antigen) are induced by an antigenic discontinuity; that is, by the sudden modification of molecular motifs with which immune cells interact. (shrink)

I present a reconstruction of F.H.C. Crick's two 1957 hypotheses "Sequence Hypothesis" and "Central Dogma" in terms of a contemporary philosophical theory of causation. Analyzing in particular the experimental evidence that Crick cited, I argue that these hypotheses can be understood as claims about the actual difference-making cause in protein synthesis. As these hypotheses are only true if restricted to certain nucleic acids in certain organisms, I then examine the concept of causal specificity and its potential to counter claims about (...) causal parity of DNA and other cellular components. I first show that causal specificity is a special kind of invariance under interventions, namely invariance of generalizations that range over finite sets of discrete variables. Then, I show that this notion allows the articulation of a middle ground in the debate over causal parity. (shrink)

Eric Olson distinguishes his animalistic account of transtemporal personal identity from the apparently similar Bodily Criterion, among other things, by accusing the latter of being contaminated with Cartesian implications owing to its usage of the term ‚body‘. In contrast, Olson argues, Animalism is able to avoid these implications by substituting the concept of body for the concept of organism, which makes Animalism not only a distinct position, but also the better alternative to the Bodily Criterion. The paper critically reconstructs Olson’s (...) charge of Cartesianism against the Bodily Criterion, thereby differentiating between several variants of it. This eventually adds up to an evaluation of how suitable these criticisms are for defending Animalism at the expense of the Bodily Criterion. (shrink)

The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified ‘levels’ of organization and suggests that (...) attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily ‘local’ and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended—many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry. (shrink)

According to the standard view of particularity, an entity is a particular just in case it necessarily has a unique spatial location at any time of its existence. That the basic entities of the world we speak about in common sense and science are particular entities in this sense is the thesis of “foundational particularism,” a theoretical intuition that has guided Western ontological research from its beginnings to the present day. The main aim of this paper is to review the (...) notion of particularity and its role in ontology. I proceed in four steps. First, I offer a brief reconstruction of the tasks of ontology as “theory of categorial inference in L”. An ontological theory states which (combinations of) entity types or categories make true L-sentences true; the features of the stipulated categories explain why L-speakers are entitled to draw certain material inferences from the classificatory expressions of L. Second, I draw attention to the fact that since Aristotle this theoretical program typically has been implemented with peculiar restrictions prescribing certain combinations of category features, e.g., the combination of particularity, concreteness, individuality, and subjecthood. I briefly sketch how these restrictions of the “substance paradigm” or “myth of substance” are reinforced by the standard readings of predicate-logical constants, viz. the existential quantifier and the identity sign. Third, I argue that in the context of the substance paradigm foundational particularism is incoherent. I discuss the current standard conceptions of particulars as developed in the debate about individuation (bare particulars, nude particulars, tropes) and show that their main difficulties derive from the traditional restriction that particulars are so also logical subjects and/or individuals. Fourth, to show that the traditional linkages of category features are not conceptual necessities, I sketch the outlines of an ontology (General Process Theory) based on non-particular individuals. For ontologists in computer science working with description logic this monocategoreal ontology based on more or less generic ‘dynamics’ may hold special interest. As General Process Theory documents, ontologists may well abandon the notion of particularity: in common sense and science we do reason about items that have a unique spatial location at any time, but the uniqueness of their location can be taken to be a contingent affair. (shrink)

Molecular change is central to chemistry and has traditionally been interpreted within a metaphysical framework that places emphasis on things and substance. This paper seeks an alternative view based on process metaphysics. The core doctrines of process thought, which give ontological priority to becoming over being, cohere well with modern chemical thinking and support a view of molecules as dynamic systems whose identities endure through time as patterns of stability. Molecular change is then seen as excursions to new stability patterns. (...) Finally, when molecular change is viewed as foundational to emergent complexity, process metaphysics allows evolution to be seen as creative molecular advance. (shrink)

Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on (...) the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise. (shrink)

Since the origins of the notion of emergence in attempts to recover the content of vitalistic anti-reductionism without its questionable metaphysics, emergence has been treated in terms of logical properties. This approach was doomed to failure, because logical properties are either sui generis or they are constructions from other logical properties. If the former, they do not explain on their own and are inevitably somewhat arbitrary (the problem with the related concept of supervenience, Collier, 1988a), but if the latter, reducibility (...) is assured because logical constructs are reducible, by definition, to their logical components. A satisfactory account of emergence must recognise that it is a dynamical, not a logical property of property of natural systems, and that its basis is dynamical rather than logical composition. Collier (1988a) introduced the concept of cohesion as the closure of the causal relations among the dynamical parts of a dynamical particular that determine its resistance to external and internal fluctuations that might disrupt its integrity. Cohesion is an equivalence relation that partitions a set of dynamical particulars into unified and distinct entities, providing the identity conditions for such particulars. Cohesion blocks reduction of dynamical particulars, and is necessary for dynamical emergence. We will give reasons for thinking that cohesion might be sufficient for emergence as well. (shrink)

Cancer research has been at the forefront of biomedical activity in recent decades, and advances in molecular biology have provided a growing amount of information on the mechanisms involved in the etiopathogenesis of tumors. Nevertheless, despite these advances, the complexity of cancer is more evident, especially as different levels of phenomena are considered to explain the heterogeneity of the neoplastic process. A synthetic analysis of advances in cancer research illustrates these changes. In attempting to overcome the limits of epistemological reductionism, (...) there is a move from a view of a genetic basis for cancer to a more comprehensive perspective aiming to integrate a large amount of information and to understand the neoplastic phenomenon at higher levels of biological complexity through a new interpretative framework. (shrink)

Even the simplest cell exhibits a high degree of functional differentiation (FD) realized through several mechanisms and devices contributing differently to its maintenance. Searching for the origin of FD, we briefly argue that the emergence of the respective organizational complexity cannot be the result of either natural selection (NS) or solely of the dynamics of simple self-maintaining (SM) systems. Accordingly, a highly gradual and cumulative process should have been necessary for the transition from either simple self-assembled or self-maintaining systems of (...) functionless structural components to systems with FD. We follow results of recent in vitro experiments with respect to competition among protocells, where a primitive type of selection begins to operate among them accompanied by a parallel evolution of their functional domain. We argue that minimal forms of FD should be established within the evolution of SM processes in protocells as they undergo a simpler selection process for stability and persistence in a prebiotic environment. We then suggest the concept of closure of constraints (CoC) as a way to identify and describe minimal FD in a far-from-equilibrium SM organization. We show in detail how the concept of CoC together with the conditions for its fulfillment can be applied in the case of a simple protocellular system that begins to couple internal chemical reactions with the formation of its membrane components. Finally, we discuss how such SM systems can evolve towards significantly higher levels of FD, suggesting this is mainly the result of functional recombination (formation of mechanisms) in the context of a modular SM organization. (shrink)

The existence claim of a "genetic program" encoded in the DNA molecule which controls biological processes such as development has been examined. Sources of belief in such an entity are found in the rhetoric of Mendelian genetics, in the informationist speculations of Schrodinger and Delbruck, and in the instrumental efficacy found in the use of certain viral, and molecular genetic techniques. In examining specific research models, it is found that attempts at tracking the source of biological control always leads back (...) to the complex state of a cell as a whole, the organizational structure of which is not itself encoded in the DNA. It is argued that the "genetic program" is not an existing biological entity and its philosophical and heuristic status is challenged. (shrink)