Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of specific traits. (...) Next, these tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation. (shrink)

The goal of this paper is to show how scientific explanation functions in the context of idealized models. It argues that the aspect of explanation most urgently requiring investigation is the nature of the connection between global theories and explanatory local models. This aspect is neglected in traditional accounts of explanation. The paper examines causal, minimal model, and structural accounts of model-based explanation. It argues that they too fail to offer an account of the connection with global theory that (...) can justify the explanatory power of an idealized local model, and consequently these accounts are unable effectively to distinguish explanatory from non-explanatory models. On the account proposed here, scientific explanation requires theoretical integration between the local model described in the explanation and a global theory with independent explanatory power. (shrink)

The goal of this paper is to show how scientific explanation functions in the context of idealized models. It argues that the aspect of explanation most urgently requiring investigation is the nature of the connection between global theories and explanatory local models. This aspect is neglected in traditional accounts of explanation. The paper examines causal, minimal model, and structural accounts of model-based explanation. It argues that they too fail to offer an account of the connection with global theory that (...) can justify the explanatory power of an idealized local model, and consequently these accounts are unable effectively to distinguish explanatory from non-explanatory models. On the account proposed here, scientific explanation requires theoretical integration between the local model described in the explanation and a global theory with independent explanatory power. (shrink)

Some philosophers argue that we should eschew cross-explanatory integrations of mechanistic, dynamicist, and psychological explanations in cognitive science, because, unlike integrations of mechanistic explanations, they do not deliver genuine, cognitive scientific explanations. Here I challenge this claim by comparing the theoretical virtues of both kinds of explanatory integrations. I first identify two theoretical virtues of integrations of mechanistic explanations—unification and greater qualitative parsimony—and argue that no cross-explanatory integration could have such virtues. However, I go on to (...) argue that this is only a problem for those who think that cognitive science aims to specify one fundamental structure responsible for cognition. For those who do not, cross-explanatory integration will have at least two theoretical virtues to a greater extent than integrations of mechanistic explanations: explanatory depth and applicability. I conclude that one’s views about explanatory integration in cognitive science cannot be segregated from one’s views about the explanatory task of cognitive science. (shrink)

Recently, two research traditions that bring together evolutionary biology and medicine, that is to say, Darwinian medicine and evolutionary medicine, have been identified. In this paper, I analyse these two research traditions with respect to explanatory and interdisciplinary integration. My analysis shows that Darwinian medicine does not integrate medicine and evolutionary biology in any strong sense but does incorporate evolutionary concepts into medicine. I also show that backward-looking explanations in Darwinian medicine are not integrated proximate-and-ultimate explanations but functional (...) explanations that include reference to evolutionary concepts. Nevertheless, explanations in Darwinian medicine have heuristic roles as they potentially contribute to conceptual change and tie pieces of knowledge from different fields of medical research together. I argue that Darwinian medicine is an “interfield” that fosters cross-disciplinary exchange between evolutionary biologists and medical researchers and practitioners based on division of labour and separation, rather than unity. Research in evolutionary medicine, on the other hand, happens at the intersection of evolutionary biology and medicine where the two disciplines are already integrated and is designed to produce entangled proximate-evolutionary explanations. My analysis thus adds another important aspect to the philosophical discussion on the distinction between Darwinian medicine and evolutionary medicine. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with (...) the problem pursued. Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

One of the central aims of the neo-mechanistic framework for the neural and cognitive sciences is to construct a pluralistic integration of scientific explanations, allowing for a weak explanatory autonomy of higher-level sciences, such as cognitive science. This integration involves understanding human cognition as information processing occurring in multi-level human neuro-cognitive mechanisms, explained by multi-level neuro-cognitive models. Strong explanatory neuro-cognitive reduction, however, poses a significant challenge to this pluralist ambition and the weak autonomy of cognitive science (...) derived therefrom. Based on research in current molecular and cellular neuroscience, the framework holds that the best strategy for integrating human neuro-cognitive theories is through direct reductive explanations based on molecular and cellular neural processes. It is my aim to investigate whether the neo-mechanistic framework can meet the challenge. I argue that leading neo-mechanists offer some significant replies; however, they are not able yet to completely remove strong explanatory reductionism from their own framework. (shrink)

Philosophers of the social sciences are increasingly convinced that macro-and micro-explanations are complementary. Whereas macro-explanations are broad, micro-explanations are deep. I distinguish between weak and strong complementarity: Strongly complementary explanations improve one another when integrated, weakly complementary explanations do not. To demonstrate the explanatory autonomy of different levels of explanation, explanatory pluralists mostly presuppose the weak form of complementarity. By scrutinizing the notions of explanatory depth and breadth, I argue that macro- and micro-accounts of the same phenomenon (...) are more often strongly complementary. This invites a revision of the pluralist position in which integration promotes explanatory progress. Key Words: explanatory pluralism • social science • explanatory depth • explanatory breadth • mechanism. (shrink)

Philosophers of the social sciences are increasingly convinced that macro-and micro-explanations are complementary. Whereas macro-explanations are broad, micro-explanations are deep. I distinguish between weak and strong complementarity: Strongly complementary explanations improve one another when integrated, weakly complementary explanations do not. To demonstrate the explanatory autonomy of different levels of explanation, explanatory pluralists mostly presuppose the weak form of complementarity. By scrutinizing the notions of explanatory depth and breadth, I argue that macro- and micro-accounts of the same phenomenon (...) are more often strongly complementary. This invites a revision of the pluralist position in which integration promotes explanatory progress. (shrink)

Resumen A través del estudio de los linchamientos, el artículo explora en la capacidad explicativa de algunas de las principales teorías sociológicas sobre integración, dominación e interdependencia para comprender la acción, sin que ello implique interpretaciones totales y recíprocamente excluyentes sobre esas acciones. Por el contrario, se trata de buscar distintas entradas parciales, fragmentos de lo que no son y/o de lo que parcialmente son los linchamientos. El texto observa que la disruptividad de estas acciones respecto de las teorías examinadas (...) podría explicarse en tanto en ellas conciencia y práctica fueron pensadas como oposiciones binarias, que en el mejor de los casos operarían en momentos sucesivos. En estas teorías sociológicas la acción podría explicarse por uno de estos planos o por el otro. Sin embargo, en el caso de los linchamientos es posible que estos dos estratos concurran a explicar la acción de manera conjunta.The article explores in the explanatory capacity of some of the main sociological theories on integration, domination and interdependence, to understand the action, specifically lynching, without implying total and reciprocally exclusive interpretations of these actions. On the contrary, it tries to look for different partial entries to its explanation, fragments of what lynching are not and/or what they partially are. The text notes that the disruption of these actions in relation with the theories examined could be explained considering that in them, consciousness and practice were developed as binary oppositions. This would at best operate in successive moments, but in these cases the action could be explained by either one of these levels. In the lynching case, it is possible that these two strata explain the action jointly. (shrink)

This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...) themes discussed. (shrink)

Comparisons of rival explanations or theories often involve vague appeals to explanatory power. In this paper, we dissect this metaphor by distinguishing between different dimensions of the goodness of an explanation: non-sensitivity, cognitive salience, precision, factual accuracy and degree of integration. These dimensions are partially independent and often come into conflict. Our main contribution is to go beyond simple stipulation or description by explicating why these factors are taken to be explanatory virtues. We accomplish this by using (...) the contrastive-counterfactual approach to explanation and the view of understanding as an inferential ability. By combining these perspectives, we show how the explanatory power of an explanation in a given dimension can be assessed by showing the range of answers it provides to what-if-things-had-been-different questions and the theoretical and pragmatic importance of these questions. Our account also explains intuitions linking explanation to unification or to exhibition of a mechanism. (shrink)

Epidemics, the medical historian Charles Rosenberg argued, typically have four Acts, as in a play. In Act I, which he termed ‘Progressive revelation’, ‘merchants’, ‘municipal authorities’ and ‘the complacency of ordinary men and women’, alike are reluctant to acknowledge an epidemic because of its threat to their ‘economic and institutional interests’ and to ‘their accustomed way of doing things’: gradually however, ‘inexorably accumulating deaths and sicknesses’ bring ‘ultimate, if unwilling, recognition’. In Act II, ‘Managing randomness’, ‘collective agreement’ is sought on (...) an ‘explanatory framework’ to manage the epidemic’s ‘dismaying arbitrariness’. Such frameworks, in previous centuries mainly religious, are now more ‘secular and mechanistic’, but again also moral and social: explanation for example of the ‘differential susceptibility of particular individuals’ is sought in terms of ‘risk-enhancing behaviour’ and ‘style of life’, but also of environmental and social factors, such as ‘residence and occupation’, providing ‘a vehicle for social criticism as well as a rationale for social control’. In Act III, ‘Negotiating public response’, pressure is generated for ‘decisive and visible community response’, often taking the form of ‘collective rites integrating cognitive and emotional elements’. Such rites, including not only ‘the imposition of a quarantine’ and ‘procedures to cleanse and disinfect’, but also religious, or now more often moral or social rituals, afford ‘the reassurance of familiar frames of explanation and logically consequent policies that provide both meaning and the promise of efficacy’. Finally, In Act IV, ‘Subsidence and retrospection’, ‘incidence of the disease gradually declines’, and questions are raised ‘for retrospective moral judgement’ about ‘what “lasting impact” particular incidents have had and what “lessons” have been learnt. Have the dead died in vain? Has a heedless society reverted to its accustomed ways of doing things as soon as denial became once more a …. (shrink)

This target article presents a new computational theory of explanatory coherence that applies to the acceptance and rejection of scientific hypotheses as well as to reasoning in everyday life, The theory consists of seven principles that establish relations of local coherence between a hypothesis and other propositions. A hypothesis coheres with propositions that it explains, or that explain it, or that participate with it in explaining other propositions, or that offer analogous explanations. Propositions are incoherent with each other if (...) they are contradictory, Propositions that describe the results of observation have a degree of acceptability on their own. An explanatory hypothesis is acccpted if it coheres better overall than its competitors. The power of the seven principles is shown by their implementation in a connectionist program called ECHO, which treats hypothesis evaluation as a constraint satisfaction problem. Inputs about the explanatory relations are used to create a network of units representing propositions, while coherende and incoherence relations are encoded by excitatory and inbihitory links. ECHO provides an algorithm for smoothly integrating theory evaluation based on considerations of explanatory breadth, simplicity, and analogy. It has been applied to such important scientific cases as Lovoisier's argument for oxygen against the phlogiston theory and Darwin's argument for evolution against creationism, and also to cases of legal reasoning. The theory of explanatory coherence has implications for artificial intelligence, psychology, and philosophy. (shrink)

Starting from the plurality of explanatory strategies in the actual practice of socialscientists, I introduce a framework for explanatory pluralism – a normative endorsement of the plurality of forms and levels of explanation used by social scientists. Equipped with thisframework, central issues in the individualism/holism debate are revisited, namely emergence,reduction and the idea of microfoundations. Discussing these issues, we notice that in recentcontributions the focus has been shifting towards relationism, pluralism and interaction, awayfrom dichotomous individualism/holism thinking and a (...) winner-takes-all approach. Then, thechallenge of the debate is no longer to develop the ultimate individualistic approach ordefending the holist approach, but rather how to be combine individualism and holism; howcan they co-exist, interact, be integrated or develop some division of labour, while making thebest out of the strengths and limitations of the respective explanatory strategies of holists andindividualists? Thus, the debate shifts to how exactly pluralism should be understood as thenext leading question, going beyond the current individualism/holism debate. The paper endswith a discussion and evaluation of different understandings of explanatory pluralismdefended in the literature. (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)

This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O’Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data (...) class='Hi'>integration involves in more detail and with a focus on the role of data-sharing tools, like online databases, in facilitating this process; and I point to the philosophical implications of focusing on data as a unit of analysis. I then analyse three cases of data integration in the field of plant science, each of which highlights a different mode of integration: inter-level integration, which involves data documenting different features of the same species, aims to acquire an interdisciplinary understanding of organisms as complex wholes and is exemplified by research on Arabidopsis thaliana; cross-species integration, which involves data acquired on different species, aims to understand plant biology in all its different manifestations and is exemplified by research on Miscanthus giganteus; and translational integration, which involves data acquired from sources within as well as outside academia, aims at the provision of interventions to improve human health and is exemplified by research on Phytophtora ramorum. Recognising the differences between these efforts sheds light on the dynamics and diverse outcomes of data dissemination and integrative research; and the relations between the social and institutional roles of science, the development of data-sharing infrastructures and the production of scientific knowledge. (shrink)

The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, (...) I argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

The explanatory role of natural selection is one of the long-term debates in evolutionary biology. Nevertheless, the consensus has been slippery because conceptual confusions and the absence of a unified, formal causal model that integrates different explanatory scopes of natural selection. In this study we attempt to examine two questions: (i) What can the theory of natural selection explain? and (ii) Is there a causal or explanatory model that integrates all natural selection explananda? For the first question, (...) we argue that five explananda have been assigned to the theory of natural selection and that four of them may be actually considered explananda of natural selection. For the second question, we claim that a probabilistic conception of causality and the statistical relevance concept of explanation are both good models for understanding the explanatory role of natural selection. We review the biological and philosophical disputes about the explanatory role of natural selection and formalize some explananda in probabilistic terms using classical results from population genetics. Most of these explananda have been discussed in philosophical terms but some of them have been mixed up and confused. We analyze and set the limits of these problems. (shrink)

Nearly two decades of debate have not settled the definition of research misconduct. The literature provides four explanatory frameworks for misconduct. The paper examines these frameworks and maps them onto efforts by the U.S. Public Health Service to define research misconduct and subsequent responses to these efforts by the scientific community. The changing frameworks suggest that closure will not be achieved without an authoritative effort, which may occur through the Research Integrity Panel’s recent attempt to create a government-wide definition.

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)

We present a multiscale integrationist interpretation of the boundaries of cognitive systems, using the Markov blanket formalism of the variational free energy principle. This interpretation is intended as a corrective for the philosophical debate over internalist and externalist interpretations of cognitive boundaries; we stake out a compromise position. We first survey key principles of new radical views of cognition. We then describe an internalist interpretation premised on the Markov blanket formalism. Having reviewed these accounts, we develop our positive multiscale account. (...) We argue that the statistical seclusion of internal from external states of the system—entailed by the existence of a Markov boundary—can coexist happily with the multiscale integration of the system through its dynamics. Our approach does not privilege any given boundary, nor does it argue that all boundaries are equally prescient. We argue that the relevant boundaries of cognition depend on the level being characterised and the explanatory interests that guide investigation. We approach the issue of how and where to draw the boundaries of cognitive systems through a multiscale ontology of cognitive systems, which offers a multidisciplinary research heuristic for cognitive science. (shrink)

The paper investigates measures of explanatory power and how to define the inference schema “Inference to the Best Explanation”. It argues that these measures can also be used to quantify the systematic power of a hypothesis and the inference schema “Inference to the Best Systematization” is defined. It demonstrates that systematic power is a fruitful criterion for theory choice and IBS is truth-conducive. It also shows that even radical Bayesians must admit that systemic power is an integral component of (...) Bayesian reasoning. Finally, the paper puts the achieved results in perspective with van Fraassen’s famous criticism of IBE. (shrink)

Philosophical and scientific investigations of the proprietary aspects of self—mineness or mental ownership—often presuppose that searching for unique constituents is a productive strategy. But there seem not to be any unique constituents. Here, it is argued that the “self-specificity” paradigm, which emphasizes subjective perspective, fails. Previously, it was argued that mode of access also fails to explain mineness. Fortunately, these failures, when leavened by other findings (those that exhibit varieties and vagaries of mineness), intimate an approach better suited to searching (...) for an explanation. Having an alternative in hand, one that shows promise of achieving explanatory adequacy, provides an additional reason to suspend the search for unique constituents. In short, a negative and a positive thesis are developed: we should cease looking for unique constituents and should seek to explain mineness in accord with the model developed here. This model rejects attempts to explain the phenomenon in terms of either a narrative or a minimal sense of self; it seeks to explain at a “molecular” level, one that appeals to multiple, interacting dimensions. The molecular-level model allows for the possibility that subjective perspective is distinct from a stark perspective (one that does not imply mineness). It proposes that the confounding of tacit expectations plays an important role in explaining mental ownership and its complement, disownership. But the confounding of tacit expectations is not sufficient. Because we are able to be aware of the existence of mental states that do not belong to self, we require a mechanism for determining degree of self-relatedness. One such mechanism is proposed here, and it is shown how this mechanism can be integrated into a general model of mental ownership. In the spirit of suggesting how this model might be able to help resolve outstanding problems, the question as to whether inserted thoughts belong to the patient who reports them is also considered. (shrink)

A recent article by Herzog provides a much-needed integration of ethical and epistemological arguments in favor of explicable AI in medicine. In this short piece, I suggest a way in which its epistemological intuition of XAI as “explanatory interface” can be further developed to delineate the relation between AI tools and scientific research.

Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty—a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an (...) apt locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines . These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration—data and standards—have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks. (shrink)

Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic (...) and environmental explanations that can be embedded in an evolutionary framework. The third line of research focuses on the role of gut microbes in the production of obesity, and how microbial activities interact with host genetics, development and metabolism. These interwoven explanatory strategies are driven by an orientation to intervention, both for experimental and therapeutic outcomes. We connect the integrative and intervention-oriented aspects of obesity research through a discussion of translation, broadening the concept to capture the dynamic, iterative processes of scientific practice and therapy development. This system-oriented analysis of obesity research expands the philosophical scrutiny of contemporary developments in the biosciences and biomedicine, and has the potential to enrich philosophy of science and medicine. (shrink)

The paper presents a research programme for the neuroscience of consciousness called 'neurophenomenology' and illustrates it with a recent pilot study . At a theoretical level, neurophenomenology pursues an embodied and large-scale dynamical approach to the neurophysiology of consciousness . At a methodological level, the neurophenomenological strategy is to make rigorous and extensive use of first-person data about subjective experience as a heuristic to describe and quantify the large-scale neurodynamics of consciousness . The paper focuses on neurophenomenology in relation to (...) three challenging methodological issues about incorporating first-person data into cognitive neuroscience: first-person reports can be biased or inaccurate; the process of generating first-person reports about an experience can modify that experience; and there is an 'explanatory gap' in our understanding of how to relate first-person, phenomenological data to third-person, biobehavioural data. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that (...) appeal to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

In this essay, I argue that Ted Poston's theory of explanatory coherentism is well-suited as a tool for causal explanation in the health sciences, particularly in epidemiology. Coherence has not only played a role in epidemiology for more than half a century as one of Hill's viewpoints, it can also provide background theory for the development of explanatory systems by integrating epidemiologic evidence with a diversity of other error-independent data. I propose that computational formalization of Hill's viewpoints in (...) an explanatory coherentist framework would provide an excellent starting point for a formal epistemological (knowledge-theoretical) project designed to improve causal explanation in the health sciences. As an example, I briefly introduce Paul Thagard's ECHO system and offer my responses to possible objections to my proposal. (shrink)

We explore the integrated structure of consciousness by examining the “phenomenological axioms” of the “integrated information theory of consciousness ” from the perspective of Husserlian phenomenology. After clarifying the notion of phenomenological axioms by drawing on resources from Edmund Husserl and Maurice Merleau-Ponty, we develop a critique of the integration axiom by drawing on phenomenological analyses developed by Aron Gurwitsch and Merleau-Ponty. This axiom is ambiguous. It can be read either atomistically as claiming that the phenomenal content of conscious (...) experience is an integrated complex and holistically as claiming that it is an integrated Gestalt. We argue that the latter reading provides a better characterization of the internal structure of the phenomenal content. Furthermore, the integrated structure of consciousness is not confined to the phenomenal content, but it also extends into the subjective attitude. Subjective attitudes and phenomenal contents are interdependent constituents that jointly make up conscious experiences. This implies a novel theoretical challenge to the scientific component of IIT, which is to explain how to accommodate the subjective dimension of consciousness into its explanatory scope. IIT can respond in a few different ways, but most importantly, it cannot just ignore it once and for all. As one possible way to address the challenge, we propose introducing a novel construct, noetic complex, to develop a fine-grained model of the neural underpinning of consciousness. (shrink)

The prominence of Bayesian modeling of cognition has increased recently largely because of mathematical advances in specifying and deriving predictions from complex probabilistic models. Much of this research aims to demonstrate that cognitive behavior can be explained from rational principles alone, without recourse to psychological or neurological processes and representations. We note commonalities between this rational approach and other movements in psychology – namely, Behaviorism and evolutionary psychology – that set aside mechanistic explanations or make use of optimality assumptions. Through (...) these comparisons, we identify a number of challenges that limit the rational program's potential contribution to psychological theory. Specifically, rational Bayesian models are significantly unconstrained, both because they are uninformed by a wide range of process-level data and because their assumptions about the environment are generally not grounded in empirical measurement. The psychological implications of most Bayesian models are also unclear. Bayesian inference itself is conceptually trivial, but strong assumptions are often embedded in the hypothesis sets and the approximation algorithms used to derive model predictions, without a clear delineation between psychological commitments and implementational details. Comparing multiple Bayesian models of the same task is rare, as is the realization that many Bayesian models recapitulate existing (mechanistic level) theories. Despite the expressive power of current Bayesian models, we argue they must be developed in conjunction with mechanistic considerations to offer substantive explanations of cognition. We lay out several means for such an integration, which take into account the representations on which Bayesian inference operates, as well as the algorithms and heuristics that carry it out. We argue this unification will better facilitate lasting contributions to psychological theory, avoiding the pitfalls that have plagued previous theoretical movements. (shrink)

Integrated Information Theory (IIT) is currently one of the most influential scientific theories of consciousness. Here, we focus specifically on a metaphysical aspect of the theory’s most recent version (IIT 4.0), what we may call its idealistic ontology, and its tension with a kind of realism about the external world that IIT also endorses. IIT 4.0 openly rejects the mainstream view that consciousness is generated by the brain, positing instead that consciousness is ontologically primary while the physical domain is just (...) “operational”. However, this philosophical position is presently underdeveloped and is not rigorously formulated in IIT, potentially leading to many misinterpretations and undermining its overall explanatory power. In the present paper we aim to address this issue. We argue that IIT’s idealistic ontology should be understood as a specific combination of phenomenal primitivism, reductionism regarding Φ-structures and complexes, and eliminativism about non-conscious physical entities. Having clarified this, we then focus on the problematic tension between IIT’s idealistic ontology and its simultaneous endorsement of realism, according to which there is some kind of external reality independent of our minds. After refuting three potential solutions to this theoretical tension, we propose the most plausible alternative: understanding IIT’s realism as an assertion of the existence of other experiences beyond one’s own, what we call a non-solipsistic idealist realism. We end with concluding remarks and future research avenues. (shrink)

Some scholars see interdisciplinarity as a special case of a broader unificationist program. They accept the unification of the sciences as a regulative ideal, and derive from this the normative justification of interdisciplinary research practices. The crucial link for this position is the notion of integration: integration increases the cohesion of concepts and practices, and more specifically of explanations, ontologies, methods and data. Interdisciplinary success then consists in the integration of fields or disciplines, and this constitutes success (...) in the sense that unification is epistemically desirable. In contrast to this account, I defend the thesis that successful interdisciplinary interaction does not necessarily imply the integration of these disciplines. I show this at the hand of two cases. In both the case of evolutionary game theory and the case of hyperbolic discounting, genuine interdisciplinary exchange took place. From both exchanges, the respective economic fields emerged substantially altered – it wasn’t just a juxtaposition of disciplines in which disciplinary identities remained unchanged. Yet in neither case did the disciplines integrate. Rather, they developed their own concepts and methods, their own explanations, own ontologies, and their own views of what proper data standards were. Furthermore, the fields that emerged from these exchanges were very successful, if measured at the hand of properties like explanatory success, increase of control, bibliometrics and grant yields. Thus, I argue, there are cases of interdisciplinary success without integration. (shrink)

Defining disease and delineating its boundaries is a contested area in contemporary philosophy of medicine. The leading naturalistic theory faces a new round of difficulties related to defining a normal environment alongside normal organismic functioning and to delineating a discrete boundary between risk factors and disease. Normative theories face ongoing and seemingly intractable difficulties related to value pluralism and the problematic relation between theory and practice. In this article, I argue for an integral—as opposed to a hybrid—philosophy of health based (...) on Bernard Lonergan’s notion of generalized empirical method that provides a way to settle these difficulties dynamically and comprehensively, both in theory, by orienting functional and statistical investigation toward an explanatory ecological viewpoint, and in practice, by framing critiques in relation to the normativity intrinsic to all human inquiry. (shrink)

The paper examines the concept of "implicit philosophy" as used in the integrated psychotherapy, making clear its content as a "potential philosophy". The author sees its meaning as opposite to the meaning of "explicit philosophy". To use the relationship between implicit and explicit philosophy in an explanation involves a binary conception of philosophy in its narrow and broader senses. The author shows, how the philosophy critically explains certain primal sponatneous genera_lizations in order to offer "secondary reimplications" of new philosophical attitudes. (...) The philosophical work is thus the middle stage of the whole process of proceeding from primary to secondary implicit philosophy. The concept of "implicit philosophy" can be applied also beyond the psychotherapy - e. g. in social philosophy or in the philosophy of science. (shrink)

Research in evolutionary biology and philosophy of biology and cognition strongly suggests that human organisms modify their environment through active processes of niche construction. Recently, proponents of the free-energy principle and variational active inference have argued that their approach can deepen our understanding of the reciprocal causal relationship between organisms and their niche on various scales. This paper examines the feasibility and scope of variational formalisations and conceptualisations of the organism-niche nexus with a particular focus on the extended active inference (...) account. I will draw a conceptual distinction between selective niche construction, developmental niche construction, and organism-niche coordination dynamics and argue that these notions capture different causal patterns, each of which with a distinct scope. Against this background, I will analyse and discuss the extended active inference account and its strategy to integrate variational active inference with work on extended cognition. The proponents of extended active inference assume that their account can provide an explanation of selective niche construction, developmental niche construction, and organism-niche coordination dynamics. However, my key claim will be that this account has the potential to elucidate the workings of organism-niche coordination dynamics, but does not adequately capture the causal patterns of selective niche construction and developmental niche construction. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism (...) – different understandings of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

Debate about cognitive science explanations has been formulated in terms of identifying the proper level(s) of explanation. Views range from reductionist, favoring only neuroscience explanations, to mechanist, favoring the integration of multiple levels, to pluralist, favoring the preservation of even the most general, high-level explanations, such as those provided by embodied or dynamical approaches. In this paper, we challenge this framing. We suggest that these are not different levels of explanation at all but, rather, different styles of explanation that (...) capture different, cross-cutting patterns in cognitive phenomena. Which pattern is explanatory depends on both the cognitive phenomenon under investigation and the research interests occasioning the explanation. This reframing changes how we should answer the basic questions of which cognitive science approaches explain and how these explanations relate to one another. On this view, we should expect different approaches to offer independent explanations in terms of their different focal patterns and the value of those explanations to partly derive from the broad patterns they feature. (shrink)

This book develops a new approach to naturalizing phenomenology. The author proposes to integrate phenomenology with the mechanistic framework that offers new methodological perspectives for studying complex mental phenomena such as consciousness. While mechanistic explanatory models are widely applied in cognitive science, their approach to describing subjective phenomena is limited. The author argues that phenomenology can fill this gap. He proposes two novel ways of integrating phenomenology and mechanism. First, he presents a new reading of phenomenological analyses as functional (...) analyses. Such functional phenomenology delivers a functional sketch of a target system and provides constraints on the space of possible mechanisms. Second, he develops the neurophenomenological approach in the direction of dynamic modeling of experience. He shows that neurophenomenology can deliver dynamical constraints on mechanistic models and thus inform the search for an underlying mechanism. (shrink)

Integrated Information Theory (IIT) of Consciousness is becoming an increasingly popular neuroscientific account of phenomenal experience. IIT claims that consciousness is integrated information in a system. I set this theory against the hard problem of consciousness (Chalmers, 1996, 1995) as the goal for a theory of consciousness to meet. In this essay I look to examine and ultimately critique IIT’s use of the notion of information to base a theory of consciousness. I argue that the notion of information in IIT (...) is a purely structural-dynamical notion, and so falls afoul of the structure and dynamics argument (Chalmers, 2003). I bolster these claims by appeal to the explanatory gap argument and show how IIT succumbs to this argument as well. For these reasons, I call into doubt IIT’s ability to answer the hard problem of consciousness. Although this paper argues against the notion of information in IIT, in a broader context the criticisms which I raise here can be brought against any theory that attempts to explain consciousness as an information-theoretic phenomenon. (shrink)

There is a plurality of theoretical approaches, methodological tools, and explanatory strategies in the social sciences. Different fields rely on different methods and explanatory tools even when they study the very same phenomena. We illustrate this plurality of the social sciences with the studies of crowds. We show how three different takes on crowd phenomena—psychology, rational choice theory, and network theory—can complement one another. We conclude that social scientists are better described as researchers endowed with explanatory toolkits (...) than specialists of some specific social domain. Social scientists’ toolkits are adapted for identifying and specifying the role of specific causal factors among the multiple factors that produce social phenomena. These factors can be, in a nonexclusive way, economic incentives, psychological processes, the ecology, or aspects of the social and cultural environment. The plurality of methods and theories in the social sciences flies in the face of the project to unify the sciences associated with the positivists of the nineteenth and twentieth centuries. Yet, the compatibility and consilience of theories and practices still have epistemic value: they enable the development of more powerful and robust theories and they allow the advent of interdisciplinary studies. We present the integrative stance as the will to improve compatibility and consilience across fields, yet recognize that the plurality of causes of social phenomena invite a diversity of methodological and theoretical tools. We conclude by characterizing naturalism as an integrative stance applied to fields that belong to the social science and to the natural sciences. (shrink)

In this essay, I revisit and extend my arguments for a view of science that is pluralistic, perspectival and pragmatist. I attempt to resolve mismatches between metaphysical assumptions, epistemological desiderata, and scientific practice. I consider long-held views about unity of science and reductionism, emergent properties and physicalism, exceptionless necessity in explanatory laws, and in the justification for realism. My solutions appeal to the partiality of representation, the perspectivism of theories and data, and the interactive co-construction of warranted claims for (...) realism. (shrink)

Effective and specifically targeted social and therapeutic responses for antisocial personality disorders and psychopathy are scarce. Some authors maintain that this scarcity should be overcome by revising current syndrome - based classifications of these conditions and devising better biocognitive classifications of antisocial individuals. The inspiration for the latter classifications has been embedded in the Research domain criteria approach (RDoC). RDoC - type approaches to psychiatric research aim at transforming diagnosis, provide valid measures of disorders, aid clinical practice, and improve health (...) outcomes by integrating the data on the genetic, neural, cognitive, and affective systems underlying psychiatric conditions. In the first part of the paper, we discuss the benefits of such approaches in comparison to the dominant syndrome-based ones and review recent attempts at building biocognitive classifications of antisocial individuals. Other researchers, how ever, have objected that biocognitive approaches in psychiatry are committed to an untenable form of explanatory. (shrink)

In a pluralistic society, consensus in spirituality must rest on a common human basis. The relevant social sciences as currently conceived cannot provide one. Bernard Lonergan's analysis of the human spirit – or intentional consciousness – elaborates the overlooked element in a psychological account of the human mind and, thus, grounds a psychology of spirituality as the natural expression of ongoing human integration, an account that is fully open to and, indeed, begs for theological elaboration. Initially unpacking the complexities (...) of this matter and sketching a Lonerganian response, this paper focuses on the key complexity – the misidentification of the spiritual with the divine and the pervasive insistence, inherited from a pre-scientific age and perpetuated by Western piety, that first and foremost spirituality entails an explicit relationship with God. Treatment of a specifically Lonerganian topic – the suggestion that, because of the transformation effected by sanctifying grace in the human soul, consciousness includes a supposed fifth level characterized by the love of God – occasions an in-depth argument for the practical adequacy of a psychological treatment of spirituality apart from theological considerations. The ultimate goal of this argument is to establish, within a coherent interdisciplinary framework, an explanatory and normative treatment of spiritual issues, a science of spirituality. (shrink)

Questions surrounding the evolution of cooperation, especially human cooperation, have driven research in many disciplines. Two key methodologies used to research and explain the evolution of cooperation are modeling and narrative construction. A number of scientists and philosophers have suggested that advancing research on the evolution of cooperation will require integrating models and narratives. But, relatively little has been said about what challenges exist to integrating models and narratives, how to go about integrating models and narratives, and what particular benefits (...) might be gained by accomplishing such integration. In this dissertation project, I address these questions in order to show how models and narratives can be integrated to produce better research on and explanations of the evolution of cooperation. The major challenge to integrating models and narratives concerning the evolution of cooperation that I address in this dissertation stems from the criticisms that such models and narratives lack empirical support. I answer this challenge by defending models and narratives from these criticisms. In the case of models, I argue both that at least some models of the evolution of cooperation have stronger empirical support than supposed by critics and that evolutionary robotics modeling approaches can be used to create even better models. In the case of narratives, I argue that several means of defending narratives from evidential challenges already developed by philosophers can be used to defend narratives about the evolution of cooperation as well. To show how narratives and models can be integrated to better research and explain the evolution of cooperation, I first establish an account of integration by drawing on the work of other philosophers. I then argue that models and narratives can provide certain benefits to each other via integration. Models can benefit from integration with narratives by using the narratives as sources of information as well as hypotheses to test. Indeed, as models are used to test such hypotheses, they also gain explanatory power. Narratives can benefit from integration with models by using the models as sources of support and constraint. Moreover, models can help deepen the understanding of historical contingency provided by narratives. (shrink)

An intuitive and appealing way to characterize problem solving is as the application of constraints which reduce the problem-solution space. Any advantage offered by interdisciplinary problem solving would then plausi- bly derive from the integration of constraints from the fields involved. We propose an account of interdisciplinary problem solving which treats the integration of constraints as an iterative process. Appealing to a general- ization of entity-activity dualism from mechanical explanation, we extend the accounts of Bechtel and of Craver (...) to non-hierarchical, non-life-science, interdisciplinary problem-solving. Integration of disciplines occurs at the level of fields and their explanatory frameworks. (shrink)