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)

A new layer of complexity, constituted of networks of information token recurrence, has been identified in socio-technical systems such as the Wikipedia online community and the Zooniverse citizen science platform. The identification of this complexity reveals that our current understanding of the actual structure of those systems, and consequently the structure of the entire World Wide Web, is incomplete, which raises novel questions for data science research but also from the perspective of social epistemology. Here we establish the principled foundations (...) and practical advantages of analyzing information diffusion within and across Web systems with Transcendental Information Cascades, and outline resulting directions for future study in the area of socio-technical systems. We also suggest that Transcendental Information Cascades may be applicable to any kind of time-evolving system that can be observed using digital technologies, and that the structures found in such systems comprise properties common to all naturally occurring complex systems. (shrink)

The Visual World Paradigm (VWP) presents listeners with a challenging problem: They must integrate two disparate signals, the spoken language and the visual context, in support of action (e.g., complex movements of the eyes across a scene). We present Impulse Processing, a dynamical systems approach to incremental eye movements in the visual world that suggests a framework for integrating language, vision, and action generally. Our approach assumes that impulses driven by the language and the visual context impinge minutely on a (...) dynamical landscape of attractors corresponding to the potential eye-movement behaviors of the system. We test three unique predictions of our approach in an empirical study in the VWP, and describe an implementation in an artificial neural network. We discuss the Impulse Processing framework in relation to other models of the VWP. (shrink)

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as (...) a kind of material recomposition strategy also points beyond the mechanistic paradigm. (shrink)

Recently, it has been provocatively claimed that dynamical modeling approaches signal the emergence of a new explanatory framework distinct from that of mechanistic explanation. This paper rejects this proposal and argues that dynamical explanations are fully compatible with, even naturally construed as, instances of mechanistic explanations. Specifically, it is argued that the mathematical framework of dynamics provides a powerful descriptive scheme for revealing temporal features of activities in mechanisms and plays an explanatory role to the extent it is deployed for (...) this purpose. It is also suggested that more attention should be paid to the distinctive methodological contributions of the dynamical framework including its usefulness as a heuristic for mechanism discovery and hypothesis generation in contemporary neuroscience and biology. (shrink)

I examine explanations’ realist commitments in relation to dynamical systems theory. First I rebut an ‘explanatory indispensability argument’ for mathematical realism from the explanatory power of phase spaces (Lyon and Colyvan 2007). Then I critically consider a possible way of strengthening the indispensability argument by reference to attractors in dynamical systems theory. The take-home message is that understanding of the modal character of explanations (in dynamical systems theory) can undermine platonist arguments from explanatory indispensability.

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule’s prediction is based on a one-sided understanding of systems biology as a science (...) that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach—which is based on reverse engineering, simulation, and mathematical analysis—the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis. (shrink)

We historically trace various non-conventional explanations for the origin of the cosmic microwave background and discuss their merit, while analyzing the dynamics of their rejection, as well as the relevant physical and methodological reasons for it. It turns out that there have been many such unorthodox interpretations; not only those developed in the context of theories rejecting the relativistic paradigm entirely but also those coming from the camp of original thinkers firmly entrenched in the relativistic milieu. In fact, the orthodox (...) interpretation has only incrementally won out against the alternatives over the course of the three decades of its multi-stage development. While on the whole, none of the alternatives to the hot Big Bang scenario is persuasive today, we discuss the epistemic ramifications of establishing orthodoxy and eliminating alternatives in science, an issue recently discussed by philosophers and historians of science for other areas of physics. Finally, we single out some plausible and possibly fruitful ideas offered by the alternatives. (shrink)

This article describes new aspects of hysteresis dynamics which have been uncovered through computer experiments. There are several motivations to be interested in fast-slow dynamics. For instance, many physiological or biological systems display different time scales. The bursting oscillations which can be observed in neurons, β-cells of the pancreas and population dynamics are essentially studied via bifurcation theory and analysis of fast-slow systems (Keener and Sneyd, 1998; Rinzel, 1987). Hysteresis is a possible mechanism to generate bursting oscillations. A first part (...) of this article presents the computer techniques (the dotted-phase portrait, the bifurcation of the fast dynamics and the wave form) we have used to represent several patterns specific to hysteresis dynamics. This framework yields a natural generalization to the notion of bursting oscillations where, for instance, the active phase is chaotic and alternates with a quiescent phase. In a second part of the article, we emphasize the evolution to chaos which is often associated with bursting oscillations on the specific example of the Hindmarsh–Rose system. This evolution to chaos has already been studied with classical tools of dynamical systems but we give here numerical evidence on hysteresis dynamics and on some aspects of the wave form. The analytical proofs will be given elsewhere. (shrink)

Although there is a substantial philosophical literature on dynamical systems theory in the cognitive sciences, the same is not the case for neuroscience. This paper attempts to motivate increased discussion via a set of overlapping issues. The first aim is primarily historical and is to demonstrate that dynamical systems theory is currently experiencing a renaissance in neuroscience. Although dynamical concepts and methods are becoming increasingly popular in contemporary neuroscience, the general approach should not be viewed as something entirely new to (...) neuroscience. Instead, it is more appropriate to view the current developments as making central again approaches that facilitated some of neuroscience’s most significant early achievements, namely, the Hodgkin–Huxley and FitzHugh–Nagumo models. The second aim is primarily critical and defends a version of the “dynamical hypothesis” in neuroscience. Whereas the original version centered on defending a noncomputational and nonrepresentational account of cognition, the version I have in mind is broader and includes both cognition and the neural systems that realize it as well. In view of that, I discuss research on motor control as a paradigmatic example demonstrating that the concepts and methods of dynamical systems theory are increasingly and successfully being applied to neural systems in contemporary neuroscience. More significantly, such applications are motivating a stronger metaphysical claim, that is, understanding neural systems as being dynamical systems, which includes not requiring appeal to representations to explain or understand those phenomena. Taken together, the historical claim and the critical claim demonstrate that the dynamical hypothesis is undergoing a renaissance in contemporary neuroscience. (shrink)

Microphysical laws are time reversible, but macrophysics, chemistry and biology are not. This paper explores how this asymmetry arises due to the cosmological context, where a non-local Direction of Time is imposed by the expansion of the universe. This situation is best represented by an Evolving Block Universe, where local arrows of time emerge in concordance with the Direction of Time because a global Past Condition results in the Second Law of Thermodynamics pointing to the future. At the quantum level, (...) the indefinite future changes to the definite past due to quantum wave function collapse events. (shrink)

In this paper, we argue for a theoretical separation of the free-energy principle from Helmholtzian accounts of the predictive brain. The free-energy principle is a theoretical framework capturing the imperative for biological self-organization in information-theoretic terms. The free-energy principle has typically been connected with a Bayesian theory of predictive coding, and the latter is often taken to support a Helmholtzian theory of perception as unconscious inference. If our interpretation is right, however, a Helmholtzian view of perception is incompatible with Bayesian (...) predictive coding under the free-energy principle. We argue that the free energy principle and the ecological and enactive approach to mind and life make for a much happier marriage of ideas. We make our argument based on three points. First we argue that the free energy principle applies to the whole animal–environment system, and not only to the brain. Second, we show that active inference, as understood by the free-energy principle, is incompatible with unconscious inference understood as analagous to scientific hypothesis-testing, the main tenet of a Helmholtzian view of perception. Third, we argue that the notion of inference at work in Bayesian predictive coding under the free-energy principle is too weak to support a Helmholtzian theory of perception. Taken together these points imply that the free energy principle is best understood in ecological and enactive terms set out in this paper. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology in (...) order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Self-fulfillment of theories is argued to be a threat to social science in at least two ways. First, a realist might worry that self-fulfillment constitutes a threat to the idea that social science is a proper science consistent with a realist approach that develops true and successful statements about the world. Second, one might argue that the potential self-fulfilling nature of social science theories potentially undermines the ethical integrity of social scientists. We argue that if one accepts that social science (...) theories are not based on laws akin to those that govern natural reality or acknowledges that if one can predict self-fulfillment via a meta-theory that explains the underlying regularities of the self-fulfilling change, the threat to realism is dismantled. Furthermore, on the basis of these arguments, we show that if one is unable to predict the consequences of a theory, it is difficult to ascribe moral responsibility at the individual level. It is, therefore, not the potential self-fulfillment of theories per se that poses an ethical challenge, in contrast to claims in the literature. (shrink)

The dynamical hypothesis states that cognitive systems are dynamical systems. While dynamical systems play an important role in many cognitive phenomena, the dynamical hypothesis as stated applies to every system and so fails both to specify what makes cognitive systems distinct and to distinguish between proposals regarding the nature of cognitive systems. To avoid this problem, I distinguish several different types of dynamical systems, outlining four dimensions along which dynamical systems can vary: total-state versus partial-state, internal versus external, macroscopic versus (...) microscopic, and systemic versus componential, and illustrate these with examples. I conclude with two illustrations of partial-state, internal, microscopic, componential dynamicism. (shrink)

Dynamical systems play a central role in explanations in cognitive neuroscience. The grounds for these explanations are hotly debated and generally fall under two approaches: non-mechanistic and mechanistic. In this paper, I first outline a neurodynamical explanatory schema that highlights the role of dynamical systems in cognitive phenomena. I next explore the mechanistic status of such neurodynamical explanations. I argue that these explanations satisfy only some of the constraints on mechanistic explanation and should be considered pseudomechanistic explanations. I defend this (...) argument against three alternative interpretations of the neurodynamical explanatory schema. The independent interpretation holds that neurodynamical explanations and mechanisms are independent. The constitutive interpretation holds that neurodynamical explanations are constitutive but otherwise non-mechanistic. Both the independent and constitutive interpretations fail to account for all the features of neurodynamical explanations. The partial interpretation assumes that the targets of dynamical systems models are mechanisms and so holds that neurodynamical explanations are incomplete because they lack mechanistic details. I contend instead that the targets of those models are dynamical systems distinct from mechanisms and defend this claim against several objections. I conclude with a defense of the pseudomechanistic interpretation and a discussion of the source of their explanatory power in relation to a causal-mechanical description of the world. (shrink)

Cognitive neuroscientists are turning to an increasingly rich array of neurodynamical systems to explain mental phenomena. In these explanations, cognitive capacities are decomposed into a set of functions, each of which is described mathematically, and then these descriptions are mapped on to corresponding mathematical descriptions of the dynamics of neural systems. In this paper, I outline a novel explanatory schema based on these explanations. I then argue that these explanations present a novel type of dynamicism for the philosophy of mind (...) and neuroscience, componential dynamicism, that focuses on the parts of cognitive systems that fill certain functional roles in producing cognitive phenomena. (shrink)

Observational learning can enhance the acquisition and performance quality of complex motor skills. While an extensive body of research has focused on the benefits of synchronous (i.e., concurrent physical practice) and non-synchronous (i.e., delayed physical practice) observational learning strategies, the question remains as to whether these approaches differentially influence performance outcomes. Accordingly, we investigate the differential outcomes of synchronous and non-synchronous observational training contexts using a novel dance sequence. Using multidimensional cross-recurrence quantification analysis, movement time-series were recorded for novice dancers (...) who either synchronised with (n = 22) or observed and then imitated (n = 20) an expert dancer. Participants performed a 16-count choreographed dance sequence for 20 trials assisted by the expert, followed by one final, unassisted performance trial. Although end-state performance did not significantly differ between synchronous and non-synchronous learners, a significant decline in performance quality from imitation to independent replication was shown for synchronous learners. A non-significant positive trend in performance accuracy was shown for non-synchronous learners. For all participants, better imitative performance across training trials led to better end-state performance, but only for the accuracy (and not timing) of movement reproduction. Collectively, the results suggest that synchronous learners came to rely on a realtime mapping process between visual input from the expert and their own visual and proprioceptive intrinsic feedback, to the detriment of learning. Thus, the act of synchronising alone does not ensure an appropriate training context for advanced sequence learning. (shrink)

When reasoning about dependence relations, philosophers often rely on gradualist assumptions, according to which abrupt changes in a phenomenon of interest can result only from abrupt changes in the low-level phenomena on which it depends. These assumptions, while strictly correct if the dependence relation in question can be expressed by continuous dynamical equations, should be handled with care: very often the descriptively relevant property of a dynamical system connecting high- and low-level phenomena is not its instantaneous behaviour but its stable (...) fixed points (those in the vicinity of which it spends most of the time, after comparatively short transitory periods), and stable fixed points can change abruptly as a result of infinitesimal changes of the low-level phenomenon. We illustrate this potential gradualist trap by showing that Chalmers’ fading qualia argument falls into it. (shrink)

This volume is a collation of original contributions from the key actors of a new trend in the contemporary theory of knowledge and belief, that we call “dynamic epistemology”. It brings the works of these researchers under a single umbrella by highlighting the coherence of their current themes, and by establishing connections between topics that, up until now, have been investigated independently. It also illustrates how the new analytical toolbox unveils questions about the theory of knowledge, belief, preference, action, and (...) rationality, in a number of central axes in dynamic epistemology: temporal, social, probabilistic and even deontic dynamics. (shrink)

In this paper, a HIV-TB co-infection model is explored which incorporates a non-linear treatment rate for TB. We begin with presenting a HIV-TB co-infection model and analyze both HIV and TB sub-models separately. The basic reproduction numbers corresponding to HIV-only, TB-only and the HIV-TB full model are computed. The disease-free equilibrium point of the HIV sub-model is shown to be locally as well as globally asymptotically stable when its corresponding reproduction number is less than unity. The HIV-only model exhibits a (...) transcritical bifurcation. On the other hand, for the TB sub-model, the disease-free equilibrium point is locally asymptotically stable but may not be globally asymptotically stable. We have also analyzed the full HIV-TB co-infection model. Numerical simulations are performed to investigate the effect of treatment rate in the presence of resource limitation for TB infected individuals, which emphasize the fact that to reduce co-infection from the population programs to accelerate the treatment of TB should be implemented. (shrink)

Embodied approaches to cognition conceive of mental life as emerging from the ongoing relationship between neural and extra-neural resources. The latter include, first and foremost, our entire body, but also the activity patterns enacted within a contingent milieu, cultural norms, social factors, and the features of the environment that can be used to enhance our cognitive capacities (e.g., tools, devices, etc.). Recent work in music education and sport psychology has applied general principles of embodiment to a number of social contexts (...) relevant to their respective fields. In particular, both disciplines have contributed fascinating perspectives to our understanding of how skills are acquired and developed in groups; how musicians, athletes, teachers, and coaches experience their interactions; and how empathy and social action participate in shaping effective performance. In this paper, we aim to provide additional grounding for this research by comparing and further developing original themes emerging from this cross-disciplinary literature and empirical works on how performative skills are acquired and optimized. In doing so, our discussion will focus on: (1) the feeling of being together, as meaningfully enacted in collective musical and sport events; (2) the capacity to skillfully adapt to the contextual demands arising from the social environment; and (3) the development of distributed forms of bodily memory. These categories will be discussed from the perspective of embodied cognitive science and with regard to their relevance for music education and sport psychology. It is argued that because they play a key role in the acquisition and development of relevant skills, they can offer important tools to help teachers and coaches develop novel strategies to enhance learning and foster new conceptual and practical research in the domains of music and sport. (shrink)

The concept of time is examined using the second law of thermodynamics that was recently formulated as an equation of motion. According to the statistical notion of increasing entropy, flows of energy diminish differences between energy densities that form space. The flow of energy is identified with the flow of time. The non-Euclidean energy landscape, i.e. the curved space–time, is in evolution when energy is flowing down along gradients and levelling the density differences. The flows along the steepest descents, i.e. (...) geodesics are obtained from the principle of least action for mechanics, electrodynamics and quantum mechanics. The arrow of time, associated with the expansion of the Universe, identifies with grand dispersal of energy when high-energy densities transform by various mechanisms to lower densities in energy and eventually to ever-diluting electromagnetic radiation. Likewise, time in a quantum system takes an increment forwards in the detection-associated dissipative transformation when the stationary-state system begins to evolve pictured as the wave function collapse. The energy dispersal is understood to underlie causality so that an energy gradient is a cause and the resulting energy flow is an effect. The account on causality by the concepts of physics does not imply determinism; on the contrary, evolution of space–time as a causal chain of events is non-deterministic. (shrink)

This paper explains and defends the idea that metaphysical necessity is the strongest kind of objective necessity. Plausible closure conditions on the family of objective modalities are shown to entail that the logic of metaphysical necessity is S5. Evidence is provided that some objective modalities are studied in the natural sciences. In particular, the modal assumptions implicit in physical applications of dynamical systems theory are made explicit by using such systems to define models of a modal temporal logic. Those assumptions (...) arguably include some necessitist principles. -/- Too often, philosophers have discussed ‘metaphysical’ modality — possibility, contingency, necessity — in isolation. Yet metaphysical modality is just a special case of a broad range of modalities, which we may call ‘objective’ by contrast with epistemic and doxastic modalities, and indeed deontic and teleological ones (compare the distinction between objective probabilities and epistemic or subjective probabilities). Thus metaphysical possibility, physical possibility and immediate practical possibility are all types of objective possibility. We should study the metaphysics and epistemology of metaphysical modality as part of a broader study of the metaphysics and epistemology of the objective modalities, on pain of radical misunderstanding. Since objective modalities are in general open to, and receive, natural scientific investigation, we should not treat the metaphysics and epistemology of metaphysical modality in isolation from the metaphysics and epistemology of the natural sciences. -/- In what follows, Section 1 gives a preliminary sketch of metaphysical modality and its place in the general category of objective modality. Section 2 reviews some familiar forms of scepticism about metaphysical modality in that light. Later sections explore a few of the many ways in which natural science deals with questions of objective modality, including questions of quantified modal logic. (shrink)

The future of human computation benefits from examining tasks that agents already perform and designing environments to give those tasks computational significance. We call this natural human computation. We consider the possible future of NHC through the lens of Swarm!, an application under development for Google Glass. Swarm! motivates users to compute the solutions to a class of economic optimization problems by engaging the attention dynamics of crowds. We argue that anticipating and managing economies of attention provides one of the (...) most tantalizing future applications for NHC. (shrink)

Life is supported by a myriad of chemical reactions. To describe the overall process we have formulated entropy for an open system undergoing chemical reactions. The entropy formula allows us to recognize various ways for the system to move towards more probable states. These correspond to the basic processes of life i.e. proliferation, differentiation, expansion, energy intake, adaptation and maturation. We propose that the rate of entropy production by various mechanisms is the fitness criterion of natural selection. The quest for (...) more probable states results in organization of matter in functional hierarchies. (shrink)

Many mechanisms, functions and structures of life have been unraveled. However, the fundamental driving force that propelled chemical evolution and led to life has remained obscure. The second law of thermodynamics, written as an equation of motion, reveals that elemental abiotic matter evolves from the equilibrium via chemical reactions that couple to external energy towards complex biotic non-equilibrium systems. Each time a new mechanism of energy transduction emerges, e.g., by random variation in syntheses, evolution prompts by punctuation and settles to (...) a stasis when the accessed free energy has been consumed. The evolutionary course towards an increasingly larger energy transduction system accumulates a diversity of energy transduction mechanisms, i.e. species. The rate of entropy increase is identified as the fitness criterion among the diverse mechanisms, which places the theory of evolution by natural selection on the fundamental thermodynamic principle with no demarcation line between inanimate and animate. (shrink)

It is becoming ever more accepted that investigations of mind span the brain, body, and environment. To broaden the scope of what is relevant in such investigations is to increase the amount of data scientists must reckon with. Thus, a major challenge facing scientists who study the mind is how to make big data intelligible both within and between fields. One way to face this challenge is to structure the data within a framework and to make it intelligible by means (...) of a common theory. Radical embodied cognitive neuroscience can function as such a framework, with dynamical systems theory as its methodology, and self-organized criticality as its theory. (shrink)

Recent work by Frigg et. al. and Mayo-Wilson have called attention to a particular sort of error associated with attempts to model certain complex systems: structural modeling error. The assessment of the degree of SME in a model presupposes agreement between modelers about the best way to individuate natural systems, an agreement which can be more problematic than it appears. This problem, which we dub “the system individuation problem” arises in many of the same contexts as SME, and the two (...) often compound one another. This paper explores the common roots of the two problems in concerns about the precision of predictions generated by scientific models, and discusses how both concerns bear on the study of complex natural systems, particularly the global climate. (shrink)

The subject of musical emotions has emerged only recently as a major area of research. While much work in this area offers fascinating insights to musicological research, assumptions about the nature of emotional experience seem to remain committed to appraisal, representations, and a rule-based or information-processing model of cognition. Over the past three decades alternative ‘embodied’ and ‘enactive’ models of mind have challenged this approach by emphasising the self-organising aspects of cognition, often describing it as an ongoing process of dynamic (...) interactivity between an organism and its environment. More recently, this perspective has been applied to the study of emotion in general, opening up interesting new possibilities for theory and research. This new approach, however, has received rather limited attention in musical contexts. With this in mind, we critically review the history of music and emotion studies, arguing that many existing theories offer only limited views of what musical-emotional experience entails. We then attempt to provide preliminary grounding for an alternative perspective on music and emotion based on the enactive/dynamic systems approach to the study of mind. (shrink)

Individuals make decisions under uncertainty every day based on incomplete information concerning the potential outcome of the choice or chance levels. The choices individuals make often deviate from the rational or mathematically objective solution. Accordingly, the dynamics of human decision-making are difficult to capture using conventional, linear mathematical models. Here, we present data from a two-choice task with variable risk between sure loss and risky loss to illustrate how a simple nonlinear dynamical system can be employed to capture the dynamics (...) of human decision-making under uncertainty (i.e., multi-stability, bifurcations). We test the feasibility of this model quantitatively and demonstrate how the model can account for up to 86% of the observed choice behavior. The implications of using dynamical models for explaining the nonlinear complexities of human decision-making are discussed, as well as the degree to which nonlinear dynamical systems theory might offer an alternative framework for understanding human decision-making processes. (shrink)

In which respects do modeling and experimenting resemble or differ from each other? We explore this question through studying in detail the combinatorial strategy in synthetic biology whereby scientists triangulate experimentation on model organisms, mathematical modeling, and synthetic modeling. We argue that this combinatorial strategy is due to the characteristic constraints of the three epistemic activities. Moreover, our case study shows that in some cases materiality clearly matters, in fact it provides the very rationale of synthetic modeling. We will show (...) how the materialities of the different kinds of models – biological components versus mathematical symbols – in combination with their different structures – the complexity of biological organisms versus the isolated network structure and its mathematical dynamics - define the spectrum of epistemic possibilities in synthetic biology. Furthermore, our case shows that from the perspective of scientific practice the question of whether or not simulations are like or unlike experiments is often beside the point, since they are used to accomplish different kinds of things. (shrink)

Spontaneous brain activity has received increasing attention as demonstrated by the exponential rise in the number of published papers on this topic over the last thirty years. Such “intrinsic” brain activity, generated in the absence of an explicit task, is frequently associated with resting-state or default-mode networks. The focus on characterizing spontaneous brain activity promises to shed new light on questions concerning the structural and functional architecture of the brain and how they are related to “mind”. However, many critical questions (...) have yet to be addressed. In this review, we focus on a scarcely explored area, specifically the energetic requirements and constraints of spontaneous activity, taking into account both thermodynamical and informational perspectives. We argue that the “classical” definitions of spontaneous activity do not take into account an important feature, that is, the critical thermodynamic energetic differences between spontaneous and evoked brain activity. Spontaneous brain activity is associated with slower oscillations compared with evoked, task-related activity, hence it exhibits lower levels of enthalpy and “free-energy” (i.e. the energy that can be converted to do work), thus supporting noteworthy thermodynamic energetic differences between spontaneous and evoked brain activity. Increased spike frequency during evoked activity has a significant metabolic cost, consequently, brain functions traditionally associated with spontaneous activity, such as mind wandering, require less energy that other nervous activities. We also review recent empirical observations in neuroscience, in order to capture how spontaneous brain dynamics and mental function can be embedded in a non-linear dynamical framework, which considers nervous activity in terms of phase spaces, particle trajectories, random walks, attractors and/or paths at the edge of the chaos. This takes us from the thermodynamic free-energy, to the realm of “variational free-energy”, a theoretical construct pertaining to probability and information theory which allows explanation of unexplored features of spontaneous brain activity. (shrink)

We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called chemical organization theory sheds new light on the longstanding complexity–stability debate. Namely, COT provides a novel conceptual landscape plenty of analytic tools to explore the interplay between structure and stability of ecological systems. Given a large set of species and their interactions, COT identifies, in a computationally feasible way, each and every sub-collection of species that is closed and self-maintaining. These sub-collections, (...) called organizations, correspond to the groups of species that can survive together in the long-term. Thus, the set of organizations contains all the stable regimes that can possibly happen in the dynamics of the ecological system. From here, we propose to conceive the notion of stability from the properties of the organizations, and thus apply the vast knowledge on the stability of reaction networks to the complexity–stability debate. As an example of the potential of COT to introduce new mathematical tools, we show that the set of organizations can be equipped with suitable joint and meet operators, and that for certain ecological systems the organizational structure is a non-boolean lattice, providing in this way an unexpected connection between logico-algebraic structures, popular in the foundations of quantum theory, and ecology. (shrink)

On the observational equivalence of continuous-time deterministic and indeterministic descriptions Content Type Journal Article Pages 193-225 DOI 10.1007/s13194-010-0011-5 Authors Charlotte Werndl, Department of Philosophy, Logic and Scientific Method, London School of Economics, Houghton Street, London, WC2A 2AE UK Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912 Journal Volume Volume 1 Journal Issue Volume 1, Number 2.

Understanding modeling in biology requires understanding how biology is organized as a discipline and how this organization influences the research practices of biologists. Biology includes a wide range of sub-disciplines, such as cell biology, population biology, evolutionary biology, molecular biology, and systems biology among others. Biologists in sub-disciplines such as cell, molecular, and systems biology believe that the use of a few experimental models allows them to discover biological universals, whereas biologists in sub-disciplines such as ecology and evolutionary biology believe (...) that the use of many different experimental and mathematical models is necessary in order to do this. Many practitioners of both approaches misunderstand best practices of modeling, especially those related to model testing. We stress the need for biologists to better engage with best practices and for philosophers of biology providing normative guidance for biologists to better engage with current developments in biology. This is especially important as biology transitions from a “data-poor” to a “data-rich” discipline. If 21st century biology is going to capitalize on the unprecedented availability of ecological, evolutionary, and molecular data, of computational resources, and of mathematical and statistical tools, biologists will need a better understanding of what modeling is and can be. (shrink)

Cybernetics, or self-governance of animal and machine, requires the ability to sense the world and to act on it in an appropriate manner. Likewise, self-governance of a human society requires groups of people to collectively sense and act on their environment. I argue that the evolution of political systems is characterized by a series of innovations that attempt to solve two ‘scalability’ problems: scaling up a group’s ability to make sense of an increasingly complex world, and to cooperate in increasingly (...) larger groups. I then explore some recent efforts toward using the Internet and social media to provide alternative means for addressing these scalability challenges, under the banners of crowdsourcing and computer-supported argumentation. I present some lessons from those efforts about the limits of technology, and the research directions more likely to bear fruit. (shrink)

La resonancia magnética funcional es una de las técnicas de neuroimagen más difundidas en las neurociencias cognitivas. Su influencia tuvo un rol central en la configuración del aspecto experimental de este campo. Frente a esto, consideramos que su estatus como evidencia no ha sido suficientemente discutido en la literatura filosófica. En este trabajo nos centramos sobre este punto abordando el problema clásico de definir el alcance que puede tener la estrategia localizacionista en neurociencias. Atendemos al modo en que este problema (...) se manifiesta hoy, tomando algunos ejemplos recientes de abordajes neurocientíficos caracterizados por estudiar el carácter dinámico de la actividad a gran escala en el cerebro. Tomamos en cuenta un número de limitaciones que presenta la resonancia magnética funcional, distinguiendo aquellas cuyo tratamiento pone en juego problemáticas de una índole no meramente técnica. A partir del análisis de algunas maneras en que los investigadores les hacen frente, sostenemos que existe una medida importante en que este tipo de estudios de neuroimagen pueden ser orientados sobre la base de supuestos y consideraciones teóricas generales. Concluimos que esta particular permeabilidad teórica de la resonancia magnética funcional es un factor central que incide sobre su estatus como evidencia neurocientífica. (shrink)