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The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) |
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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 (...) |
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Biological regulation is what allows an organism to handle the effects of a perturbation, modulating its own constitutive dynamics in response to particular changes in internal and external conditions. With the central focus of analysis on the case of minimal living systems, we argue that regulation consists in a specific form of second-order control, exerted over the core regime of production and maintenance of the components that actually put together the organism. The main argument is that regulation requires a distinctive (...) |
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In many fields in the life sciences investigators refer to downward or top-down causal effects. Craver and Bechtel defended the view that such cases should be understood in terms of a constitution relation between levels in a mechanism and causation as solely an intra-level relation. Craver and Bechtel, however, provided insufficient specification as to when entities constitute a higher-level mechanism. In this paper I appeal to graph-theoretic representations of networks that are now widely employed in systems biology and neuroscience to (...) |
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Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Critiques of the framework have focused on its lack of empirical support and a failure to generate concrete, falsifiable predictions. I take both positive and negative evaluations of the FEP thus far to have been largely in error, and appeal to a robust literature on scientific modelling to rectify the situation. A (...) |
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Predictive processing approaches to the mind are increasingly popular in the cognitive sciences. This surge of interest is accompanied by a proliferation of philosophical arguments, which seek to either extend or oppose various aspects of the emerging framework. In particular, the question of how to position predictive processing with respect to enactive and embodied cognition has become a topic of intense debate. While these arguments are certainly of valuable scientific and philosophical merit, they risk underestimating the variety of approaches gathered (...) |
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Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of (...) |
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Science is the study of our world, as it is in its messy reality. Nonetheless, science requires idealization to function—if we are to attempt to understand the world, we have to find ways to reduce its complexity. Idealization and the Aims of Science shows just how crucial idealization is to science and why it matters. Beginning with the acknowledgment of our status as limited human agents trying to make sense of an exceedingly complex world, Angela Potochnik moves on to explain (...) |
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The traditional use of ergodic theory in the foundations of equilibrium statistical mechanics is that it provides a link between thermodynamic observables and microcanonical probabilities. First of all, the ergodic theorem demonstrates the equality of microcanonical phase averages and infinite time averages (albeit for a special class of systems, and up to a measure zero set of exceptions). Secondly, one argues that actual measurements of thermodynamic quantities yield time averaged quantities, since measurements take a long time. The combination of these (...) |
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While the fundamental laws of physics are time-reversal invariant, most macroscopic processes are irreversible. Given that the fundamental laws are taken to underpin all other processes, how can the fundamental time-symmetry be reconciled with the asymmetry manifest elsewhere? In statistical mechanics, progress can be made with this question. What I dub the ‘Zwanzig–Zeh–Wallace framework’ can be used to construct the irreversible equations of SM from the underlying microdynamics. Yet this framework uses coarse-graining, a procedure that has faced much criticism. I (...) |
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A proposal for the biological grounding of intrinsic teleology and sense-making through the theory of autopoiesis is critically evaluated. Autopoiesis provides a systemic lan- guage for speaking about intrinsic teleology but its original formulation needs to be elaborated further in order to explain sense-making. This is done by introducing adaptivity, a many-layered property that allows organisms to regulate themselves with respect to their conditions of via- bility. Adaptivity leads to more articulated concepts of behaviour, agency, sense-construction, health, and temporality than (...) |
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In this paper, I compare the use of the thermodynamic limit in the theory of phase transitions with the infinite-time limit in the explanation of equilibrium statistical mechanics. In the case of phase transitions, I will argue that the thermodynamic limit can be justified pragmatically since the limit behavior also arises before we get to the limit and for values of N that are physically significant. However, I will contend that the justification of the infinite-time limit is less straightforward. In (...) |
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In his 1966 paper “The Strategy of model-building in Population Biology”, Richard Levins argues that no single model in population biology can be maximally realistic, precise and general at the same time. This is because these desirable model properties trade-off against one another. Recently, philosophers have developed Levins’ claims, arguing that trade-offs between these desiderata are generated by practical limitations on scientists, or due to formal aspects of models and how they represent the world. However this project is not complete. (...) |
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The life–mind continuity thesis is difficult to study, especially because the relation between life and mind is not yet fully understood, and given that there is still no consensus view neither on what qualifies as life nor on what defines mind. Rather than taking up the much more difficult task of addressing the many different ways of explaining how life relates to mind, and vice versa, this paper considers two influential accounts addressing how best to understand the life–mind continuity thesis: (...) |
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We study the Johansen–Ledoit–Sornette model of financial market crashes :219–255, 2000). On our view, the JLS model is a curious case from the perspective of the recent philosophy of science literature, as it is naturally construed as a “minimal model” in the sense of Batterman and Rice :349–376, 2014) that nonetheless provides a causal explanation of market crashes, in the sense of Woodward’s interventionist account of causation. |
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The free energy principle says that any self-organising system that is at nonequilibrium steady-state with its environment must minimize its free energy. It is proposed as a grand unifying principle for cognitive science and biology. The principle can appear cryptic, esoteric, too ambitious, and unfalsifiable—suggesting it would be best to suspend any belief in the principle, and instead focus on individual, more concrete and falsifiable ‘process theories’ for particular biological processes and phenomena like perception, decision and action. Here, I explain (...) |
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The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from (...) |
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If one formulates Helmholtz's ideas about perception in terms of modern-day theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring what cause our sensory inputs and learning causal regularities in the sensorium can be resolved using exactly the same principles. Furthermore, inference and learning can proceed in a biologically plausible fashion. The ensuing scheme rests on (...) |
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If one formulates Helmholtz’s ideas about perception in terms of modern-day theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring what cause our sensory inputs and learning causal regularities in the sensorium can be resolved using exactly the same principles. Furthermore, inference and learning can proceed in a biologically plausible fashion. The ensuing scheme rests on (...) |
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Gases reach equilibrium when left to themselves. Why do they behave in this way? The canonical answer to this question, originally proffered by Boltzmann, is that the systems have to be ergodic. This answer has been criticised on different grounds and is now widely regarded as flawed. In this paper we argue that some of the main arguments against Boltzmann's answer, in particular, arguments based on the KAM-theorem and the Markus-Meyer theorem, are beside the point. We then argue that something (...) |
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This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey-Smith (...) |
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Some things are living and some are not. Under the heading “living things” come entities at various levels of biological organization. Some are called “organisms.” However, the term “organism” does not pick out organismal entities uniformly—that is, among all the things that are considered to be whole living systems, some are regarded as indisputably organisms, and others are accorded only qualified organismic status. Perhaps this is because it is not clear why some biological systems should count as organisms and others (...) |
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A hallmark of ecological research is dealing with complexity in the systems under investigation. One strategy is to diminish this complexity by constructing models and theories that are general. Alternatively, ecologists can constrain the scope of their generalizations to particular phenomena or types of systems. However, research employing the second strategy is often met with scathing criticism. I offer a theoretical argument in support of moderate generalizations in ecological research, based on the notions of interdependence and causal heterogeneity and their (...) |
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We argue that, contrary to some analyses in the philosophy of science literature, ergodic theory falls short in explaining the success of classical equilibrium statistical mechanics. Our claim is based on the observations that dynamical systems for which statistical mechanics works are most likely not ergodic, and that ergodicity is both too strong and too weak a condition for the required explanation: one needs only ergodic-like behaviour for the finite set of observables that matter, but the behaviour must ensure that (...) |
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A proposal for the biological grounding of intrinsic teleology and sense-making through the theory of autopoiesis is critically evaluated. Autopoiesis provides a systemic language for speaking about intrinsic teleology but its original formulation needs to be elaborated further in order to explain sense-making. This is done by introducing adaptivity, a many-layered property that allows organisms to regulate themselves with respect to their conditions of viability. Adaptivity leads to more articulated concepts of behaviour, agency, sense-construction, health, and temporality than those given (...) |
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In this fascinating read, Kauffman concludes that the development of life on earth is not entirely predictable, because no theory could ever fully account for the limitless variations of evolution. Sure to cause a stir, this book will be discussed for years to come and may even set the tone for the next "great thinker.". |
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Didier Sornette boldly applies his varied experience in many areas to propose a simple, powerful, and general theory of how, why, and when stock markets crash. |
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Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) |
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one takes to be the most salient, any pair could be judged more similar to each other than to the third. Goodman uses this second problem to showthat there can be no context-free similarity metric, either in the trivial case or in a scientifically ... |
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Robert Batterman examines a form of scientific reasoning called asymptotic reasoning, arguing that it has important consequences for our understanding of the scientific process as a whole. He maintains that asymptotic reasoning is essential for explaining what physicists call universal behavior. With clarity and rigor, he simplifies complex questions about universal behavior, demonstrating a profound understanding of the underlying structures that ground them. This book introduces a valuable new method that is certain to fill explanatory gaps across disciplines. |
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This paper considers questions about continuity and discontinuity between life and mind. It begins by examining such questions from the perspective of the free energy principle (FEP). The FEP is becoming increasingly influential in neuroscience and cognitive science. It says that organisms act to maintain themselves in their expected biological and cognitive states, and that they can do so only by minimizing their free energy given that the long-term average of free energy is entropy. The paper then argues that there (...) |
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This work addresses the autonomous organization of biological systems. It does so by considering the boundaries of biological systems, from individual cells to Home sapiens, in terms of the presence of Markov blankets under the active inference scheme—a corollary of the free energy principle. A Markov blanket defines the boundaries of a system in a statistical sense. Here we consider how a collective of Markov blankets can self-assemble into a global system that itself has a Markov blanket; thereby providing an (...) |
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This is an extensive review of recent work on the foundations of statistical mechanics. |
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- A recent debate has touched upon the question of whether diseases can be understood as dysfunctional mechanisms or whether there are "pathological" mechanisms that deserve to be investigated and explained independently (Nervi 2010; Moghaddam Taaheri 2011). Here I suggest that both views tell us something important about disease but that in many instances only a systemic view can shed light on the relationship between physiology and pathology. I provide examples from the literature in systems biology in support of my (...) |
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Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) |
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