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

Understanding a normative concept like oppression requires attention to not only its harms but also the causes of those harms. In other words, a complete understanding of such a concept requires a proper causal explanation. This causal explanation can also inform and constrain our moral response to such harms. Therefore, the conceptual explanatory framework that we use to inform our moral diagnosis and our moral response become significant. The first goal of this dissertation is to propose complexity theory as the (...) proper framework for not only explaining a social phenomenon like oppression but also understanding the proper sites for social change. The second goal of this dissertation is to answer three interrelated questions about how we should respond, morally, to a chronic and complex social problem like racial or gender inequality: (1) Why do the current interventions to address these problems fail? (2) Do social movements play any unique role in addressing these problems? (3) What is our individual responsibility to participate in social movements? In response, I argue that the explanatory frameworks that we choose to understand the cause(s) of social problems can be the source of the inadequacy of our intervention. I argue that a proper social and moral intervention needs to capture the complex and dynamic nature of the social world. I also show that changing the explanatory framework allows us to see the unique role social movements play in making effective and sustainable social change possible. Finally, I conclude supporting such movements is a moral imperative. (shrink)

Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion of decomposition, (...) which I call ‘atomism’, and not with decomposition writ large. Atomism posits that function ascriptions must be made to parts with minimal reference to the surrounding system. Complexity does indeed falsify atomism, but I contend that there is a weaker, ‘contextualist’ notion of decomposition that is fully compatible with the properties that holists cite. Contextualism suggests that the function of parts can shift with external context, and that interactions with other parts might help determine their context-appropriate functions. This still admits of functional decomposition within a given context. I will give examples based on the notion of oscillatory multiplexing in systems neuroscience. If contextualism is feasible, then holist inferences are faulty—one cannot infer from the presence of complexity to the failure of decomposition, mechanism, and reductionism. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

Panpsychism is the view that every concrete and unified thing has some form of phenomenal consciousness or experience. It is an age-old doctrine, which, to the surprise of many, has recently taken on new life. In philosophy of mind, it has been put forth as a simple and radical solution to the mind–body problem (Chalmers 1996, 2003;Strawson 2006; Nagel 1979, 2012). In metaphysics and philosophy of science, it has been put forth as a solution to the problem of accounting for (...) the intrinsic nature of the physical itself (Strawson 2006, Seager 2006). In this thesis, I show that panpsychism can also be defended on the basis of an argument from our (arguable) acquaintance with the nature of causation in agency. This argument has made frequent appearances throughout the history of philosophy, with philosophers such as Leibniz, Schopenhauer and James, and I construct and defend an updated version of it. Furthermore, I offer a solution to the combination problem: how can complex (human and animal-type) consciousness result from simple (fundamental particle-type) consciousness? This is generally regarded as the most serious problem facing contemporary panpsychism. I propose that mental combination can be construed as kind causal process culminating in a fusion, and show how this avoids the main difficulties with accounting for mental combination. (shrink)

Emergence is a notorious philosophical term of art. A variety of theorists have appropriated it for their purposes ever since George Henry Lewes gave it a philosophical sense in his 1875 Problems of Life and Mind. We might roughly characterize the shared meaning thus: emergent entities (properties or substances) ‘arise’ out of more fundamental entities and yet are ‘novel’ or ‘irreducible’ with respect to them. (For example, it is sometimes said that consciousness is an emergent property of the brain.) Each (...) of the quoted terms is slippery in its own right, and their specifications yield the varied notions of emergence that we discuss below. There has been renewed interest in emergence within discussions of the behavior of complex systems and debates over the reconcilability of mental causation, intentionality, or consciousness with physicalism. (shrink)

We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...) causes can be translated into mechanistically mediated effects, the posited relationship is intelligible and should raise no special philosophical objections. When they cannot, they are suspect. (shrink)

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European (...) philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.”. (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)

ABSTRACTIs it possible to reconcile the concept of conscious agency with the view that humans are biological creatures subject to material causality? The problem of conscious agency is complicated by the tendency to attribute autonomous powers of control to conscious processes. In this paper, we offer an embodied process model of conscious agency. We begin with the concept of embodied emergence – the idea that psychological processes are higher-order biological processes, albeit ones that exhibit emergent properties. Although consciousness, experience, and (...) representation are emergent properties of higher-order biological organisms, the capacity for hierarchical regulation is a property of all living systems. Thus, while the capacity for consciousness transforms the process of hierarchical regulation, consciousness is not an autonomous center of control. Instead, consciousness functions as a system for coordinating novel representations of the most pressing demands placed on the organism at any given time.... (shrink)

Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by (...) wholly physical properties, e.g., geometrical structures of molecular aggregates (cells). In response, we argue that contrary to his expectations one cannot infer reductionist assumptions even from detailed biological explanations that invoke the molecular level, as interlevel causal reciprocity is essential to these explanations. Recent very detailed explanations that concern the structure and function of chromatin—the intricacies of supposedly basic molecular level—demonstrate this. They show that what seem to be basic physical parameters extend into a more general biological context, thus rendering elusive the concepts of the basic level and causal hierarchy postulated by the reductionists. In fact, relevant phenomena are defined across levels by entangled, extended parameters. Nor can the biological context be explained away by basic physical parameters defining molecular level shaped by evolution as a physical process. Reductionists claim otherwise only because they overlook the evolutionary significance of initial conditions best defined in terms of extended biological parameters. Perhaps the reductionist assumptions (as well as assumptions that postulate any particular levels as causally fundamental) cannot be inferred from biological explanations because biology aims at manipulating organisms rather than producing explanations that meet the coherence requirements of general ontological models. Or possibly the assumptions of an ontology not based on the concept of causal powers stratified across levels can be inferred from biological explanations. The incoherence of downward causation is inevitable, given reductionist assumptions, but an ontological alternative might avoid this. We outline desiderata for the treatment of levels and properties that realize interlevel causation in such an ontology. (shrink)

The concept of emergence is widely used in both the philosophy of mind and in cognitive science. In the philosophy of mind it serves to refer to seemingly irreducible phenomena, in cognitive science it is often used to refer to phenomena not explicitly programmed. There is no unique concept of emergence available that serves both purposes.

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back (...) in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanics modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent. (shrink)

Biochemists often adopt what may be called the “Strategy of Decomposition” for the causal discovery of biochemical pathway dynamic behaviours. This involves decomposing a pathway into a set of isolated parts, which are then analysed separately. It is assumed that knowledge gained of the isolated parts can then be used to explain the dynamic behaviours of the whole pathway. My thesis addresses the extent to which use of the Strategy of Decomposition is warranted. I evaluate two challenges contained in Bechtel (...) and Richardson’s Discovering Complexity. The first challenge is that pathways lack the ‘modular’ structure assumed in the Strategy of Decomposition. Bechtel and Richardson take biochemists to use a concept of modularity called ‘near decomposability’. The second challenge is that pathways have ‘Pathway Emergent’ behaviours. I reject both challenges. I show that near decomposability is the wrong type of modularity to apply to pathways, and that the occurrence of Pathway Emergence has not been established. I argue that an underlying problem with Bechtel and Richardson’s analyses is that they overstate the consequences of feedback and nonlinearity for the Strategy of Decomposition. Instead, the analysis of pathway modularity and emergence needs to be centered on the context-sensitivity of pathways’ ‘local causal laws’. I identify that the type of modularity assumed in the Strategy of Decomposition is ‘causal law modularity’, which requires the invariance of local causal laws. I also identify a necessary condition for Pathway Emergence: a pathway must manifest at least one local causal law that is not manifested by its isolated parts. I argue that the use of the Strategy of Decomposition may often be unwarranted. This is because the local causal laws of pathways are highly context-sensitive, and pathways might often not be causal law modular. This context-sensitivity also leaves open the possibility of Pathway Emergence. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to many other types of (...) formal networks and weakens the emergentist claim attached to bio-molecular networks, and by extension to living systems. (shrink)

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its (...) assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)

Jaegwon Kim’s exclusion argument is a general ontological argument, applicable to any properties deemed supervenient on a microproperty basis, including biological properties. It implies that the causal power of any higher-level property must be reducible to the subset of the causal powers of its lower-level properties. Moreover, as Kim’s recent version of the argument indicates, a higher-level property can be causally efficient only to the extent of the efficiency of its micro-basis. In response, I argue that the ontology that aims (...) to capture experimentally based explanations of metabolic control systems and morphogenetic systems must involve causally relevant contextual properties. Such an ontology challenges the exclusiveness of micro-based causal efficiency that grounds Kim’s reductionism, since configurations themselves are inherently causally efficient constituents. I anticipate and respond to the reductionist’s objection that the nonreductionist ontology’s account of causes and inter-level causal relations is incoherent. I also argue that such an ontology is not open to Kim’s overdetermination objection. (shrink)

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)

A critical review of Frans de Waal's book on evolution of morality (Frans de Waal, Primates and Philosophers: How Morality Evolved, Princeton, NJ: Princeton University Press, 2006).

Weak emergence is the view that a system’s macro properties can be explained by its micro properties but only in an especially complicated way. This paper explains a version of weak emergence based on the notion of explanatory incompressibility and “crawling the causal web.” Then it examines three reasons why weak emergence might be thought to be just in the mind. The first reason is based on contrasting mere epistemological emergence with a form of ontological emergence that involves irreducible downward (...) causation. The second reason is based on the idea that attributions of emergence are always a reflection of our ignorance of non-emergent explanations. The third reason is based on the charge that complex explanations are anthropocentric. Rather than being just in the mind, weak emergence is seen to involve a distinctive kind of complex, macro-pattern in the mind-independent objective micro-causal structure that exists in nature. The paper ends by addressing two further questions. One concerns whether weak emergence applies only or mainly to computer simulations and computational systems. The other concerns the respect in which weak emergence is dynamic rather than static. (shrink)

Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be (...) applied to establish, in a general sense, a set of theoretical constraints for explaining the instantiation of different kinds of meaning processes (iconic, indexical, symbolic) in semiotic systems. We use it to model a semiotic process in the immune system, namely, B-cell activation, in order to offer insights into the heuristic role it can play in the development of explanations for specific semiotic processes. (shrink)

The philosophical discussion of emergence is often focused on properties of ‘wholes’ that are evaluated as emergent with respect to the properties of ‘parts’. Downward causation is, consequently, evaluated as some kind of causal influence of whole properties over parts properties. Yet, several important cases in scientific practice seem to be pursuing hypotheses of parts properties emerging from wholes properties, inverting the instinctive association of emergence with wholes. Furthermore, some areas of reflection which are very important for emergence, e.g., the (...) philosophy of consciousness, do not allow mapping properties onto part-whole organizations. The conceptual puzzle is solved by constructing a framework that disentangles the mereological dimension from the superventional dimension. By liberalizing the spatio-temporal allocation of emergent properties, the proposed dual framework could better capture the way in which emergence and downward causation are addressed in scientific practice. (shrink)

Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that (...) is incompressible and its behavior cannot be derived except by crawling through all of the gory details of the interactions in the web. The central thesis of this article is that synthetic biology centrally is the activity of engineering the desired weak emergent properties of synthetic cells. Synthetic biology has many different ways to engineer desired weak emergent properties of synthetic cells, including Edisonian trial and error, standardized parts, refactoring, and reprogramming synthetic genomes. The article ends by noting two philosophical consequences of engineering weak emergence. One is epistemological: synthesis is crucial for discovering weak emergent properties. The other is metaphysical: simple life forms are nothing but complex chemical mechanisms. (shrink)

I defend a physicalistic version of ontological emergence; qualia emerge from the brain, but are physical properties nevertheless. First, I address the following questions: what are the central tenets of physicalistic ontological emergentism; what are the relationships between these tenets; what is the relationship between physicalistic ontological emergentism and non-reductive physicalism; and can there even be a physicalistic version of ontological emergentism? This discussion is merely an attempt to clarify exactly what a physicalistic version of ontological emergentism must claim, and (...) to show that the view is at least coherent. I then defend the view from objections, for example, Kim’s (Philos Stud 95:3–36, 1999) attempt to apply a version of his exclusion argument to ontological emergentism. I conclude by offering a positive argument for the view: given certain empirical evidence concerning the organization of the brain, physicalism might have to endorse ontological emergentism to avoid epiphenomenalism. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...) broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

Accounts of mechanistic explanation have emphasized the importance of looking down—decomposing a mechanism into its parts and operations. Using research on visual processing as an exemplar, I illustrate how productive such research has been. But once multiple components of a mechanism have been identified, researchers also need to figure out how it is organized—they must look around and determine how to recompose the mechanism. Although researchers often begin by trying to recompose the mechanism in terms of sequential operations, they frequently (...) find that the components of a mechanism interact in complex ways involving positive and negative feedback and that the organization often exhibits highly interactive local networks linked by a few long-range connections (small-worlds organization) and power law distributions of connections. The mechanisms are themselves active systems that are perturbed by inputs but not set in motion by them. Researchers also need to look up —situate a mechanism in its context, which may be a larger mechanism that modulates its behavior. When looking down is combined with looking around and up, mechanistic research results in an integrated, multi-level perspective. (shrink)

The work is the presentation of a logical theory - Logic in Reality (LIR) - and of applications of that theory in natural science and philosophy, including ...

Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using concept maps and reasoning questions. The context of this study was a computational learning environment developed specifically to foster this ability. This environment presents proteins as the mechanism-mediating genetic phenomena. (...) We found that students’ ability to connect genes, proteins, and traits, or to reason using this connection, was initially poor. However, significant improvement was obtained when using the learning environment. Our results suggest that visual representations of proteins’ functions in the context of a specific trait contributed to this improvement. One significant aspect of these results is the indication that 10th graders are capable of accurately describing genetic phenomena and their underlying mechanisms, a task that has been shown to raise difficulties, even in higher grades of high school. (shrink)

It is argued that once biological systems reach a certain level of complexity, mechanistic explanations provide an inadequate account of many relevant phenomena. In this article, I evaluate such claims with respect to a representative programme in systems biological research: the study of regulatory networks within single-celled organisms. I argue that these networks are amenable to mechanistic philosophy without need to appeal to some alternate form of explanation. In particular, I claim that we can understand the mathematical modelling techniques of (...) systems biologists as part of a broader practice of constructing and evaluating mechanism schemas. This argument is elaborated by considering the case of bacterial chemotactic networks, where some research has been interpreted as explaining phenomena by means of abstract design principles. (shrink)

In recent years, many philosophers of science have attempted to articulate a theory of non-epistemic emergence that is compatible with mechanistic explanation and incompatible with reductionism. The 2005 account of Fred C. Boogerd et al. has been particularly influential. They argued that a systemic property was emergent if it could not be predicted from the behaviour of less complex systems. Here, I argue that Boogerd et al.'s attempt to ground emergence in complexity guarantees that we will see emergence, but at (...) the cost of rendering it either trivial or epistemic. There are three basic problems. First, neither the measures of complexity explicitly mentioned by Boogerd et al. nor the most popular measures in the literature can do the practical and theoretical work that they assign to complexity. Second, I argue that while the success of their view depends on restricting the base of information available to the reductionist, this cannot be done in a way that is metaphysically neutral with respect to emer.. (shrink)

Most philosophical accounts of emergence are based on supervenience, with supervenience being an ontologically synchronic relation of determination. This conception of emergence as a relation of supervenience, I will argue, is unable to make sense of the kinds of emergence that are widespread in self-organizing and nonlinear dynamical systems, including distributed cognitive systems. In these dynamical systems, an emergent property is ontological and diachronic.

There is a trend within philosophy of biology to concentrate on questions that are strongly related to particular biological research programs rather than on the general scope of the field and its relation to other sciences. Projects of the latter kind, of course, are followed as well but will not be the topic of this review. Shifting the focus to particular research programs reflects philosophers’ increased interest in knowledge of, and contribution to, actual biological research, which is organized in such (...) programs. It is accompanied by the increasing enthusiasm of biologists to involve philosophers in the conceptual work of theoretical biology. I concentrate on the philosophies of four biological research programs, three of which are devoted to evolutionary biology, which is still the main field of interest among philosophers of biology: adaptationism, EvoDevo, and the developmental systems approach. In addition, a short sketch of the newly emerging philosophy of systems biology is given. Several lines of philosophical inquiry can be found in all of the fields considered here: philosophy contributes to the conceptual development of biological research programs, it analyzes structures and delineations of particular research programs, and sometimes it is involved in a comparative assessment of biological programs as well. Philosophical projects that start from the level of a particular research program may give rise to a bottom-up perspective on biology and allow for an integrative view of biological research. This may open up the opportunity to tackle “larger” questions again in an altered and fruitful manner. (shrink)

The first part of this paper deals with the relations between mechanistic explanation and reduction. It is argued that there is no insuperable conflict between the two, but that the mechanistic framework adds requirements that are not acknowledged in the model of property reduction. The second part concerns the relations between organization and environmental factors. Internal organization may be so tightly linked to external context that both have to be considered together.

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)

Ioannidis [Why most published research findings are false. PLoS Med 2: e124 ] identifies six factors that contribute to explaining why most of the current published research findings are more likely to be false than true, and argues that for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this article, we argue that three “hot” areas in current biological research, viz., agent-based modeling, evolutionary developmental biology, and systems biology, are especially (...) prone to the flaws. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)