Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to (...) simulate human disease? I argue that, unless three requirements are met in the process of humanizing mice, very little does. My requirements are not meant to provide necessary and sufficient conditions that guarantee a particular outcome. Instead, they serve as a heuristic for guiding scientific judgments involving extrapolation. In developing each requirement, I engage with philosophical issues concerning the nature of model-based science and the mechanistic approach (and its limits) to making generalizations in the life sciences. (shrink)

Defending or attacking either functionalism or computationalism requires clarity on what they amount to and what evidence counts for or against them. My goal here is not to evaluate their plausibility. My goal is to formulate them and their relationship clearly enough that we can determine which type of evidence is relevant to them. I aim to dispel some sources of confusion that surround functionalism and computationalism, recruit recent philosophical work on mechanisms and computation to shed light on them, and (...) clarify how functionalism and computationalism may or may not legitimately come together. (shrink)

We begin by distinguishing computationalism from a number of other theses that are sometimes conflated with it. We also distinguish between several important kinds of computation: computation in a generic sense, digital computation, and analog computation. Then, we defend a weak version of computationalism—neural processes are computations in the generic sense. After that, we reject on empirical grounds the common assimilation of neural computation to either analog or digital computation, concluding that neural computation is sui generis. Analog computation requires continuous (...) signals; digital computation requires strings of digits. But current neuroscientific evidence indicates that typical neural signals, such as spike trains, are graded like continuous signals but are constituted by discrete functional elements (spikes); thus, typical neural signals are neither continuous signals nor strings of digits. It follows that neural computation is sui generis. Finally, we highlight three important consequences of a proper understanding of neural computation for the theory of cognition. First, understanding neural computation requires a specially designed mathematical theory (or theories) rather than the mathematical theories of analog or digital computation. Second, several popular views about neural computation turn out to be incorrect. Third, computational theories of cognition that rely on non-neural notions of computation ought to be replaced or reinterpreted in terms of neural computation. (shrink)

We sketch a framework for building a unified science of cognition. This unification is achieved by showing how functional analyses of cognitive capacities can be integrated with the multilevel mechanistic explanations of neural systems. The core idea is that functional analyses are sketches of mechanisms , in which some structural aspects of a mechanistic explanation are omitted. Once the missing aspects are filled in, a functional analysis turns into a full-blown mechanistic explanation. By this process, functional analyses are seamlessly integrated (...) with multilevel mechanistic explanations. (shrink)

Computationalism has been the mainstream view of cognition for decades. There are periodic reports of its demise, but they are greatly exaggerated. This essay surveys some recent literature on computationalism. It concludes that computationalism is a family of theories about the mechanisms of cognition. The main relevant evidence for testing it comes from neuroscience, though psychology and AI are relevant too. Computationalism comes in many versions, which continue to guide competing research programs in philosophy of mind as well as psychology (...) and neuroscience. Although our understanding of computationalism has deepened in recent years, much work in this area remains to be done. (shrink)

I offer an explication of the notion of computer, grounded in the practices of computability theorists and computer scientists. I begin by explaining what distinguishes computers from calculators. Then, I offer a systematic taxonomy of kinds of computer, including hard-wired versus programmable, general-purpose versus special-purpose, analog versus digital, and serial versus parallel, giving explicit criteria for each kind. My account is mechanistic: which class a system belongs in, and which functions are computable by which system, depends on the system's mechanistic (...) properties. Finally, I briefly illustrate how my account sheds light on some issues in the history and philosophy of computing as well as the philosophy of mind. (shrink)

Some recent arguments defending the genuine causal efficacy of the mental have been relying on empirical research on neuroprosthetics. This essay presents a critical analysis of these arguments. The problem of mental causation, and the basic idea and results of neuroprosthetics are reviewed. It is shown how appealing to the research on neuroprosthetics can be interpreted to give support to the idea of mental causation. However, it does so only in a rather deflationary sense: by holding the mental identical with (...) the neural. So contrary to what the arguments have been assuming, neuroprosthetics cannot be used to argue for nonreductive physicalism. It can rather be taken to illustrate just the opposite: how the mental and the physical are identical. (shrink)

In this essay, we set out to survey and critically assess various attitudes and understandings of reductionism as it appears in discussions regarding the scientific study of religion. Our objective in the essay is twofold. First, we articulate what we will refer to as three ‘meta-interpretative’ frameworks, which summarize the distinct positions one can witness in response to the explanations coming out of research within the new science of religion. Second, and more importantly, we seek to demonstrate that under no (...) sensible interpretation of the notion of ‘reduction’ do the explanations provide a basis for defending one of the meta-interpretative frameworks rather than another. (shrink)

Psychoneural reduction has been debated extensively in the philosophy of neuroscience. In this article I will evaluate metascientific approaches that claim direct molecular and cellular explanations of cognitive functions. I will initially consider the issues involved in linking cellular properties to behaviour from the general perspective of neural circuits. These circuits that integrate the molecular and cellular components underlying cognition and behaviour, making consideration of circuit properties relevant to reductionist debates. I will then apply this general perspective to specific systems (...) where psychoneural reduction has been claimed, namely hippocampal long-term potentiation and the Aplysia gill-withdrawal reflex. (shrink)

This article considers interventionist arguments for downward causation and non-fundamental level causal explanation from the point of view of inferring causation from experiments. Several authors have utilised the interventionist theory of causal explanation to argue that the causal exclusion argument is moot and that higher-level as well as downward causation is real. I show that this argument can be made when levels are understood as levels of grain, leaving us with a choice between causal explanations pitched at different levels. Causal (...) proportionality has been suggested as a principle for choosing the correct level of description for causal explanations, but this suggestion has serious problems. I offer an alternative principle, based on the idea that explanations should track actual difference-makers. I then consider claims about systems causally influencing their own parts. Such claims risk conceptual confusion for the same reason as the exclusion argument, by conflating causal and constitutive dependencies. The distinction between causation and constitution is used to give criteria for the correct use of the idea of downward causation. (shrink)

It is often indeterminate what function a given computational system computes. This phenomenon has been referred to as “computational indeterminacy” or “multiplicity of computations.” In this paper, we argue that what has typically been considered and referred to as the challenge of computational indeterminacy in fact subsumes two distinct phenomena, which are typically bundled together and should be teased apart. One kind of indeterminacy concerns a functional characterization of the system’s relevant behavior. Another kind concerns the manner in which the (...) abstract states are interpreted. We discuss the similarities and differences between the two kinds of computational indeterminacy, their implications for certain accounts of “computational individuation” in the literature, and their relevance to different levels of description within the computational system. We also examine the inter-relationships between our proposed accounts of the two kinds of indeterminacy and the main accounts of “computational implementation.”. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

One of the most widely used procedures applied to non-human animals or pre-linguistic humans is the “violation of expectation paradigm”. Curiously there is almost no discussion in the philosophical literature about it. Our objective will be to provide a first approach to the meta-theoretical nature of the assumptions behind the procedure that appeals to the violation of expectation and to extract some consequences. We show that behind them exists an empirical principle that affirms that the violation of the expectation of (...) certain mental rules generates surprise. We then proceeded to discuss the nature of these “mental rules”. We show that, as is often the case with theoretical concepts proposed by theories, they do not have a fixed interpretation. This will allow us to show that the usual relationship found in the developmental psychology literature between this experimental paradigm and cognitive approaches (which interpret experimental results in terms of higher-level mental activities) is not necessary. Finally, we relate this experimental design with the mark test and the inequity aversion test and discuss the possible ampliation of the application of the empirical principle of violation of expectation. (shrink)

This paper investigates the interaction between semantic theories for cp-laws (roughly, laws that hold “all things equal”) and metaphysical theories of kinds in the special sciences. Its central conclusion is that cp-laws concerning kinds behave differently from cp-laws concerning non-kinds: “ravens are black” which concerns the kind corvus corax, behaves differently from from “albino ravens are white” which concerns the non-kind grouping of albino ravens. I argue that this difference is in the first instance logical: the two sorts of cp-laws (...) give rise to different inferential patterns. I draw two further conclusions. The difference in logical behavior poses a severe problem for extant semantic theories of cp-laws, and: we cannot elucidate the distinction between kinds and non-kinds by suggesting that only kinds can appear in laws. (shrink)

This chapter contains sections titled: References.

Philosophy of psychiatry has boomed in the last few years. We are now seeing a growing literature on the nature of psychiatric explanation, including work that makes contact with longstanding disputes in the philosophy of science as well as more specific work on mental disorders. This paper looks at some recent work on both representing and explaining mental illness. An emerging picture sees explanation of mental disorder as first constructing causal-statistical networks that represent disease pathways as they unfold in time, (...) and then choosing strategies for causal explanation. The epistemic problems in psychiatry are huge, and they arise from the extreme variety in the causes and trajectories of mental disorders across patients. Existing concepts of levels of explanation and mechanism may seem like an obvious epistemic armoury, but they may not fit psychiatry very well, and philosophical theories of psychiatric explanation stress different ways of trying to understand robust patterns amid the individual variation. (shrink)

Dead reckoning is a feature of the navigation behaviour shown by several creatures, including the desert ant. Recent work by C. Randy Gallistel shows that some connectionist models of dead reckoning face important challenges. These challenges are thought to arise from essential features of the connectionist approach, and have therefore been taken to show that connectionist models are unable to explain even the most primitive of psychological phenomena. I show that Gallistel’s challenges are successfully met by one recent connectionist model, (...) proposed by Ulysses Bernardet, Sergi Bermúdez i Badia, and Paul F.M.J. Verschure. The success of this model suggests that there are ways to implement dead reckoning with neural circuits that fall within the bounds of what many people regard as neurobiologically plausible, and so that the wholesale dismissal of the connectionist modelling project remains premature. (shrink)

In this study the notion of mechanistic entities is analyzed as it has been conceptualized by Hermann Lotze in his article Life. Vital Force (1842), the metaphysical foundation of which has recourse to his Metaphysik (1841) and Logik (1843). According to Lotze, explanations in the sciences are arguments which have a syntactic and a semantic structure—similar to that which became later known as the DN-model of explanation. The syntactic structure is delineated by ontological forms, the semantic by cosmological ones; the (...) latter comprise the preconditions for the construction of appearances in accord with the ontological forms. Mechanisms are embedded into this logical framework by representing the more complex spatio-temporal arrangements of cosmological entities. The coordinated model of a mechanism is a reductive type of explanation. This study also demonstrates how Lotze made use of his concept of mechanisms in order to explain law-like and probabilistic events in organic and inorganic nature, thereby establishing an original ‘oligomeric’ (i. e., a fraction of the parts of a system determines its development) variant of a preformative theory of ontogenesis which anticipates modern concepts of genetic determination. In this context, Lotze alludes to paradigms of dissipative structures. The relevance of these reflections for subsequent theories is shown by contrasting them with Schrödinger’s theory of organisms. Finally, a comparison of some aspects of Lotze’s concept of mechanisms with equivalent aspects of current normative approaches confirms that essential elements of the latter versions can be retrieved in the former one. Above that, Lotze employs the teleological aspect of ontological forms in order to determine the extent of the mechanistic system under consideration. He further differentiates three modal states of mechanisms and includes a concept to explain exceptions or irregularities. The concept of ‘activity’ is strictly excluded from his account and shown to be a metaphysical illusion. (shrink)

Cognitive science is an interdisciplinary conglomerate of various research fields and disciplines, which increases the risk of fragmentation of cognitive theories. However, while most previous work has focused on theoretical integration, some kinds of integration may turn out to be monstrous, or result in superficially lumped and unrelated bodies of knowledge. In this paper, I distinguish theoretical integration from theoretical unification, and propose some analyses of theoretical unification dimensions. Moreover, two research strategies that are supposed to lead to unification are (...) analyzed in terms of the mechanistic account of explanation. Finally, I argue that theoretical unification is not an absolute requirement from the mechanistic perspective, and that strategies aiming at unification may be premature in fields where there are multiple conflicting explanatory models. (shrink)

In this paper, we defend a novel, multidimensional account of representational unification, which we distinguish from integration. The dimensions of unity are simplicity, generality and scope, non-monstrosity, and systematization. In our account, unification is a graded property. The account is used to investigate the issue of how research traditions contribute to representational unification, focusing on embodied cognition in cognitive science. Embodied cognition contributes to unification even if it fails to offer a grand unification of cognitive science. The study of this (...) failure shows that unification, contrary to what defenders of mechanistic explanation claim, is an important mechanistic virtue of research traditions. (shrink)

Is there a field of social intelligence? Many various disciplines approach the subject and it may only seem natural to suppose that different fields of study aim at explaining different phenomena; in other words, there is no special field of study of social intelligence. In this paper, I argue for an opposite claim. Namely, there is a way to integrate research on social intelligence, as long as one accepts the mechanistic account to explanation. Mechanistic integration of different explanations, however, comes (...) at a cost: mechanism requires explanatory models to be fairly complete and realistic, and this does not seem to be the case for many models concerning social intelligence, especially models of economical behavior. Such models need either be made more realistic, or they would not count as contributing to the same field. I stress that the focus on integration does not lead to ruthless reductionism; on the contrary, mechanistic explanations are best understood as explanatorily pluralistic. (shrink)

In this paper, an account of theoretical integration in cognitive (neuro)science from the mechanistic perspective is defended. It is argued that mechanistic patterns of integration can be better understood in terms of constraints on representations of mechanisms, not just on the space of possible mechanisms, as previous accounts of integration had it. This way, integration can be analyzed in more detail with the help of constraintsatisfaction account of coherence between scientific representations. In particular, the account has resources to talk of (...) idealizations and research heuristics employed by researchers to combine separate results and theoretical frameworks. The account is subsequently applied to an example of successful integration in the research on hippocampus and memory, and to a failure of integration in the research on mirror neurons as purportedly explanatory of sexual orientation. (shrink)

The claim defended in the paper is that the mechanistic account of explanation can easily embrace idealization in big-scale brain simulations, and that only causally relevant detail should be present in explanatory models. The claim is illustrated with two methodologically different models: Blue Brain, used for particular simulations of the cortical column in hybrid models, and Eliasmith’s SPAUN model that is both biologically realistic and able to explain eight different tasks. By drawing on the mechanistic theory of computational explanation, I (...) argue that large-scale simulations require that the explanandum phenomenon is identified; otherwise, the explanatory value of such explanations is difficult to establish, and testing the model empirically by comparing its behavior with the explanandum remains practically impossible. The completeness of the explanation, and hence of the explanatory value of the explanatory model, is to be assessed vis-à-vis the explanandum phenomenon, which is not to be conflated with raw observational data and may be idealized. I argue that idealizations, which include building models of a single phenomenon displayed by multi-functional mechanisms, lumping together multiple factors in a single causal variable, simplifying the causal structure of the mechanisms, and multi-model integration, are indispensable for complex systems such as brains; otherwise, the model may be as complex as the explanandum phenomenon, which would make it prone to so-called Bonini paradox. I conclude by enumerating dimensions of empirical validation of explanatory models according to new mechanism, which are given in a form of a “checklist” for a modeler. (shrink)

The debate between the defenders of explanatory unification and explanatory pluralism has been ongoing from the beginning of cognitive science and is one of the central themes of its philosophy. Does cognitive science need a grand unifying theory? Should explanatory pluralism be embraced instead? Or maybe local integrative efforts are needed? What are the advantages of explanatory unification as compared to the benefits of explanatory pluralism? These questions, among others, are addressed in this Synthese’s special issue. In the introductory paper, (...) we discuss the background of the questions, distinguishing integrative theorizing from building unified theories. On the one hand, integrative efforts involve collaboration between various disciplines, fields, approaches, or theories. These efforts could even be quite temporary, without establishing any long-term institutionalized fields or disciplines, but could also contribute to developing new interfield theories. On the other hand, unification can rely on developing complete theories of mechanisms and representations underlying all cognition, as Newell’s “unified theories of cognition”, or may appeal to grand principles, as predictive coding. Here, we also show that unification in contemporary cognitive science goes beyond reductive unity, and may involve various forms of joint efforts and division of explanatory labor. This conclusion is one of the themes present in the content of contributions constituting the special issue. (shrink)

In this paper, I argue that computationalism is a progressive research tradition. Its metaphysical assumptions are that nervous systems are computational, and that information processing is necessary for cognition to occur. First, the primary reasons why information processing should explain cognition are reviewed. Then I argue that early formulations of these reasons are outdated. However, by relying on the mechanistic account of physical computation, they can be recast in a compelling way. Next, I contrast two computational models of working memory (...) to show how modeling has progressed over the years. The methodological assumptions of new modeling work are best understood in the mechanistic framework, which is evidenced by the way in which models are empirically validated. Moreover, the methodological and theoretical progress in computational neuroscience vindicates the new mechanistic approach to explanation, which, at the same time, justifies the best practices of computational modeling. Overall, computational modeling is deservedly successful in cognitive science. Its successes are related to deep conceptual connections between cognition and computation. Computationalism is not only here to stay, it becomes stronger every year. (shrink)

In this paper, we argue that several recent ‘wide’ perspectives on cognition (embodied, embedded, extended, enactive, and distributed) are only partially relevant to the study of cognition. While these wide accounts override traditional methodological individualism, the study of cognition has already progressed beyond these proposed perspectives towards building integrated explanations of the mechanisms involved, including not only internal submechanisms but also interactions with others, groups, cognitive artifacts, and their environment. The claim is substantiated with reference to recent developments in the (...) study of “mindreading” and debates on emotions. We claim that the current practice in cognitive (neuro)science has undergone, in effect, a silent mechanistic revolution, and has turned from initial binary oppositions and abstract proposals towards the integration of wide perspectives with the rest of the cognitive (neuro)sciences. (shrink)

In most accounts of realization of computational processes by physical mechanisms, it is presupposed that there is one-to-one correspondence between the causally active states of the physical process and the states of the computation. Yet such proposals either stipulate that only one model of computation is implemented, or they do not reflect upon the variety of models that could be implemented physically. In this paper, I claim that mechanistic accounts of computation should allow for a broad variation of models of (...) computation. In particular, some non-standard models should not be excluded a priori. The relationship between mathematical models of computation and mechanistically adequate models is studied in more detail. (shrink)

Some proponents of the Integrated Information Theory of consciousness profess strong views on the Neural Correlates of Consciousness, namely that large swathes of the neocortex, the cerebellum, at least some sensory cortices, and the so-called limbic system are all not essential for any form of conscious experiences. We argue that this connection is not incidental. Conflation between strong and weak versions of the theory has led these researchers to adopt definitions of NCC that are inconsistent with their own previous definitions, (...) inadvertently betraying the promises of an otherwise fruitful empirical endeavour. (shrink)

This article demonstrates that non-mechanistic, dynamical explanations are a viable approach to explanation in the special sciences. The claim that dynamical models can be explanatory without reference to mechanisms has previously been met with three lines of criticism from mechanists: the causal relevance concern, the genuine laws concern, and the charge of predictivism. I argue, however, that these mechanist criticisms fail to defeat non-mechanistic, dynamical explanation. Using the examples of Haken et al.’s model of bimanual coordination, and Thelen et al.’s (...) dynamical field model of infant perseverative reaching, I show how each mechanist criticism fails once the standards of Woodward’s interventionist framework are applied to dynamical models. An even-handed application of Woodwardian interventionism reveals that dynamical models are capable of producing genuine explanations without appealing to underlying mechanistic details. 1Introduction2Interventionism and Mechanistic Explanation 2.1Causal relevance and ideal interventions2.2Invariance2.3Explanation3Covering-Laws and Dynamical Explanation 3.1Dynamical models3.2Covering-law explanation3.3Prediction4Causal Relevance 4.1The causal relevance concern4.2Intervening on dynamical models4.3Test case I: The Haken–Kelso–Bunz model4.4Test case II: Dynamical field model5Genuine Laws 5.1The genuine laws concern5.2Using invariance in place of laws5.3Test case I: The Haken–Kelso–Bunz model5.4Test case II: Dynamical field model6Prediction 6.1Predictivism6.2Crude and invariant prediction7Interventionist Criticism of the Haken–Kelso–Bunz Model8Dynamical Explanation8Conclusion. (shrink)

Enactivists frequently argue their account heralds a revolution in cognitive science: enactivism will unseat cognitivism as the dominant paradigm. We examine the lines of reasoning enactivists employ in stirring revolt, but show that none of these prove compelling reasons for cognitivism to be replaced by enactivism. First, we examine the hard sell of enactivism: enactivism reveals a critical explanatory gap at the heart of cognitivism. We show that enactivism does not meet the requirements to incite a paradigm shift in the (...) Kuhnian sense—there is no internal crisis in cognitivism. Nor does it provide inherently better explanations of cognition as some have claimed. Second, we consider the soft sell of enactivism: enactivism provides a more attractive, parsimonious, or clear-eyed lens on cognition. This move proves to boil down to a misunderstanding of how theories are selected in science. Instead we lend support to a broader and more desirable way to conceive of enactivism, the recent proposal that enactivism is a philosophy of nature. We explain how a philosophy of nature does more than support a single research paradigm by integrating scientific questions into a cohesive picture. (shrink)

In line with proponents of 4E cognition, Gallagher [2019] is concerned that many cognitive phenomena are not amenable to decomposition strategies since their very nature is to be constituted extensively. By contrast the received view on causal explanation—the mechanistic account [Craver 2007]—emphasises the necessity for decomposition in explaining natural phenomena and insists on a sharp distinction between causal versus constitutive relations. I propose that removing the requirement that constitutive relations cannot also be causes helps to ease this tension between explanation (...) and Gallagher’s non-decompositional stance, per Leuridan [2012]. Further, I draw on Froese et al.’s [2013] minimal model of social cognition to argue that constitutive relations can and do act as causal difference-makers in the Woodwardian sense [Woodward 2003]. (shrink)

Mechanistic explanations are often said to explain because they reveal the causal structure of the world. Conversely, dynamical models supposedly lack explanatory power because they do not describe causal structure. The only way for dynamical models to produce causal explanations is via the 3M criterion: the model must be mapped onto a mechanism. This framing of the situation has become the received view around the viability of dynamical explanation. In this paper, I argue against this position and show that dynamical (...) models can themselves reveal causal structure and consequently produce nonmechanistic, dynamical explanations. Taking the example of cell fates from systems biology, I show how dynamical models, and specifically the attractor landscapes they describe, identify the causes of cell differentiation and explain why cells select particular fates. These dynamical features of the system better fit Woodward’s (2010, 2018) criteria of specificity and proportionality and make them the best candidate causes of cell fates than mechanisms. I also show how these causes are irreducible and inaccessible to mechanistic models, making 3M unworkable and counterproductive in this case. Dynamical models can reveal dynamical causes and thereby provide causal explanations. (shrink)

Mechanistic explanations, according to one prominent account, are derived from objective explanations (Craver 2007, 2014 ). Mechanistic standards of explanation are in turn pulled from nature, and are thereby insulated from the values of investigators, since explanation is an objectively defined achievement grounded in the causal structure of the world (Craver 2014 ). This results in the closure of mechanism’s explanatory standards—it is insulated from the values, norms and goals of investigators. I raise two problems with this position. First, it (...) relies on several ontological claims which, while plausible, fail to guarantee the objectivity of mechanistic explanatory standards to the degree of certainty required. Second, Craver’s position itself introduces a value–laden explanatory standard—the 3M requirement (Kaplan & Craver 2011 )—which undermines the closure of explanatory standards. I show how in practice mechanistic explanation is in part guided by explanatory taste, shorthand for background contextual values that influence our standards of explanation. Mechanism often has a particular pragmatically-oriented taste for control, and gerrymanders explanatory standards in order to obtain it. I conclude by arguing that objectivity, rather than being obtained through the right set of explanatory standards, is better thought of as the result of processes of intersubjective criticism, which renders visible the contextual values of communities of investigators and allows them to be controlled for (Longino 1990 ). (shrink)

Much contemporary debate on the nature of mechanisms centers on the issue of modulating negative causes. One type of negative causability, which I refer to as "causation by absence," appears difficult to incorporate into modern accounts of mechanistic explanation. This paper argues that a recent attempt to resolve this problem, proposed by Benjamin Barros, requires improvement as it overlooks the fact that not all absences qualify as sources of mechanism failure. I suggest that there are a number of additional types (...) of effects caused by absences that need to be incorporated to account for the diversity of causal connections in the biological sciences. Furthermore, it is argued that recognizing natural variability in mechanisms, such as attenuation, leads to some interesting line-drawing issues for contemporary philosophy of mechanisms. (shrink)

Proponents of evidence-based medicine have argued convincingly for applying this scientific method to medicine. However, the current methodological framework of the EBM movement has recently been called into question, especially in epidemiology and the philosophy of science. The debate has focused on whether the methodology of randomized controlled trials provides the best evidence available. This paper attempts to shift the focus of the debate by arguing that clinical reasoning involves a patchwork of evidential approaches and that the emphasis on evidence (...) hierarchies of methodology fails to lend credence to the common practice of corroboration in medicine. I argue that the strength of evidence lies in the evidence itself, and not the methodology used to obtain that evidence. Ultimately, when it comes to evaluating the effectiveness of medical interventions, it is the evidence obtained from the methodology rather than the methodology that should establish the strength of the evidence. (shrink)

A strong case has been made for the role and value of mechanistic reasoning in process-oriented sciences, such as molecular biology and neuroscience. This paper shifts focus to assess the role of mechanistic reasoning in an area where it is neither obvious nor expected: population genetics. Population geneticists abstract away from the causal-mechanical details of individual organisms and, instead, use mathematics to describe population-level, statistical phenomena. This paper, first, develops a framework for the identification of mechanistic reasoning where it is (...) not obvious: mathematical and mechanistic styles of scientific reasoning. Second, it applies this framework to demonstrate that both styles are integrated in modern investigations of evolutionary biology. Characteristic of the former, applied population genetic techniques provide statistical evidence for associations between genotype, phenotype, and fitness. Characteristic of the latter, experimental interventions provide causal-mechanical evidence for associations between the very same relationships, often in the same model organisms. The upshot is a richer perspective of how evolutionary biologists build evidence for hypotheses regarding adaptive evolution and a general framework for assessing the scope of mechanistic reasoning across the sciences. (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)

The aim of this thesis is to argue in favour of the embodied music cognition paradigm, as opposed to traditional theories of musical mind. The thesis consists of three chapters. The goal of the first chapter is to examine computational music cognition, focusing on the main problem of this approach. In the second chapter, I will present and discuss Marc Leman’s EMC, that may serve as a response to the problems of the computational view of the musical mind. Although this (...) framework is interesting, it is unclear in several places. For that reason, I intend to enrich it with the references to the recent works on human mirror neuron system and enactivist views on music cognition. Given that, in the last chapter, I will answer the question, whether mental representations are necessary in music cognition. (shrink)

In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is guided (...) by an interventionist conception of causal structure. While doubts have been raised about the applicability of this notion of causality to complex biological systems, it is here seen to be an adequate guide to inquiry. (shrink)

In an instant classic paper ; 2002: 179–182) biologist Yuri Lazebnik deplores the poor effectiveness of the approach adopted by biologists to understand and “fix” biological systems. Lazebnik suggests that to remedy this state of things biologist should take inspiration from the approach used by engineers to design, understand, and troubleshoot technological systems. In the present paper I substantiate Lazebnik’s analysis by concretely showing how to apply the engineering approach to biological problems. I use an actual example of electronic circuit (...) troubleshooting to ground the thesis that, in engineering, the crucial phases of any non-trivial troubleshooting process are aimed at generating a mechanistic explanation of the functioning of the system, which makes extensive recourse to problem-driven qualitative reasoning possibly based on cognitive artifacts applied to systems that are known to have been designed for function. To show how to translate these findings into biological practice I consider a concrete example of biological model building and “troubleshooting”, aimed at the identification of a “fix” for the human immune system in presence of progressing cancer, autoimmune disease, and transplant rejection. The result is a novel immune system model—the danger model with regulatory cells— and new, original hypotheses concerning the development, prophylaxis, and therapy of these unwanted biological processes. Based on the manifest efficacy of the proposed approach, I suggest a refocusing of the activity of theoretical biologists along the engineering-inspired lines illustrated in the paper. (shrink)

Network theory is applied across the sciences to study phenomena as diverse as the spread of SARS, the topology of the cell, the structure of the Internet and job search behaviour. Underlying the study of networks is graph theory. Whether the graph represents a network of neurons, cells, friends or firms, it displays features that exclusively depend on the mathematical properties of the graph itself. However, the way in which graph theory is implemented to the modelling of networks differs significantly (...) across scientific fields. This article compares the economics variant of network theory with those of other fields. It shows how the methodology employed by economists to model networks is shaped by two explanatory desiderata: that the explanandum phenomenon is based on micro-economic foundations and that the explanation is general. (shrink)

Social scientists associate agent-based simulation (ABS) models with three ideas about explanation: they provide generative explanations, they are models of mechanisms, and they implement methodological individualism. In light of a philosophical account of explanation, we show that these ideas are not necessarily related and offer an account of the explanatory import of ABS models. We also argue that their bottom-up research strategy should be distinguished from methodological individualism.

Some psychologists aim to secure a role for psychological explanations in understanding contemporary social disparities, a concern that plays out in debates over the relevance of the Implicit Association Test. Meta-analysts disagree about the predictive validity of the IAT and about the importance of implicit attitudes in explaining racial disparities. Here, I use the IAT to articulate and explore one route to establishing the relevance of psychological attitudes with small effects: an appeal to a process of “accumulation” that aggregates small (...) effects into large harms. After characterizing mechanisms of accumulation and considering some candidate examples, I argue that such mechanisms suggest how a contemporary attitude with small effects could figure in the explanation of large disparities, but they do not vindicate the importance of such an attitude since such mechanisms are typically also determined by competing causes. I close by sketching several strategies for advancing a defense of the relevance of attitudes with small effects. (shrink)

Proponents of mechanistic explanations have recently proclaimed that all explanations in the neurosciences appeal to mechanisms. The purpose of the paper is to critically assess this statement and to develop an integrative account that connects a large range of both mechanistic and dynamical explanations. I develop and defend four theses about the relationship between dynamical and mechanistic explanations: that dynamical explanations are structurally grounded, that they are multiply realizable, possess realizing mechanisms and provide a powerful top-down heuristic. Four examples shall (...) support my points: the harmonic oscillator, the Haken–Kelso–Bunz model of bimanual coordination, the Watt governor and the Gierer–Meinhardt model of biological pattern formation. I also develop the picture of “horizontal” and “vertical” directions of explanations to illustrate the different perspectives of the dynamical and mechanistic approach as well as their potential integration by means of intersection points. (shrink)