Replicability and reproducibility of computational models has been somewhat understudied by “the replication movement.” In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and model reproductions in computational neuroscience. We contend that model replicability, or independent researchers' ability to obtain the same output using original code and data, and model reproducibility, or independent researchers' ability to recreate a model without original code, (...) serve different functions and fail for different reasons. This means that measures designed to improve model replicability may not enhance (and, in some cases, may actually damage) model reproducibility. We claim that although both are undesirable, low model reproducibility poses more of a threat to long-term scientific progress than low model replicability. In our opinion, low model reproducibility stems mostly from authors' omitting to provide crucial information in scientific papers and we stress that sharing all computer code and data is not a solution. Reports of computational studies should remain selective and include all and only relevant bits of code. (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 this paper, the role of the environment and physical embodiment of computational systems for explanatory purposes will be analyzed. In particular, the focus will be on cognitive computational systems, understood in terms of mechanisms that manipulate semantic information. It will be argued that the role of the environment has long been appreciated, in particular in the work of Herbert A. Simon, which has inspired the mechanistic view on explanation. From Simon’s perspective, the embodied view on cognition seems natural but (...) it is nowhere near as critical as its proponents suggest. The only point of difference between Simon and embodied cognition is the significance of body-based off-line cognition; however, it will be argued that it is notoriously over-appreciated in the current debate. The new mechanistic view on explanation suggests that even if it is critical to situate a mechanism in its environment and study its physical composition, or realization, it is also stressed that not all detail counts, and that some bodily features of cognitive systems should be left out from explanations. (shrink)

Nawet jeżeli integrację poznania rozproszonego z mechanistycznymi koncepcjami wyjaśniania można uznać za ruch interesujący, a w przypadku powodzenia prowadzący do niebanalnego rozszerzenia kognitywistycznych badań nad poznaniem, to z perspektywy teoretyka poznania rozproszonego należy uznać ten ruch za ryzykowny. W poniższej pracy, w dyskusji z propozycją Witolda Wachowskiego (2022), postaram się przedstawić ryzyko, z jakim wiąże się wspomniana integracja i zaproponuję rozwiązanie alternatywne, polegające na połączeniu rozproszenia poznania z teorią sieci. Teoria ta, w mojej opinii, pozwala na bardziej owocne badanie wzorców (...) rozproszenia poznania. ----------------------------------------- Zgłoszono: 26/09/2023. Zrecenzowano: 26/03/2024. Zaakceptowano do publikacji: 10/06/2024. (shrink)

Evidence-Based Medicine has little consideration for mechanisms and philosophers of science and medicine have recently made pleas to increase the place of mechanisms in the medical evidence hierarchy. However, in this debate the notions of mechanisms seem to be limited to 'mechanistic processes' and 'complex-systems mechanisms,' understood as 'componential causal systems'. I believe that this will not do full justice to how mechanisms are used in biological, psychological and social sciences and, consequently, in a more biopsychosocial approach to medicine. Here, (...) I propose, following (Kuorikoski, 2009), to pay more attention to 'abstract forms of interaction' mechanisms. The present work scrutinized review articles on depression and medically unexplained pain, which are considered to be of multifactorial pathogenesis, for their use of mechanisms. In review articles on these disorders there seemed to be a range of uses between more 'abstract forms of interaction' and 'componential causal system' mechanisms. I therefore propose to expand the notions of mechanisms considered in medicine to include that of more 'abstract forms of interaction' to better explain and manage biopsychosocial disorders. (shrink)

Theoreticians that defend a form of realism regarding natural kinds minimally entertain the belief that the world features divisions into kinds and that the natural kind concept is a useful tool for philosophy of science. The objective of this paper is to challenge these assumptions. First, we challenge realism toward natural kinds by showing that the main arguments for their existence, which rely on the epistemic success of natural kinds, are unsatisfactory. Second, we show that, whether they exist or not, (...) natural kinds are expendable when it comes to describing and analyzing scientific explanations accurately. (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)

In the last few decades, philosophy of science has increasingly focused on multilevel models and causal mechanistic explanations to account for complex biological phenomena. On the one hand, biological and biomedical works make extensive use of mechanistic concepts; on the other hand, philosophers have analyzed an increasing range of examples taken from different domains in the life sciences to test—support or criticize—the adequacy of mechanistic accounts. The article highlights some challenges in the elaboration of mechanistic explanations with a focus on (...) cancer research and neuropsychiatry. It jointly considers fields, which are usually dealt with separately, and keeps a close eye on scientific practice. The article has a twofold aim. First, it shows that identification of the explananda is a key issue when looking at dynamic processes and their implications in medical research and clinical practice. Second, it discusses the relevance of organizational accounts of mechanisms, and questions whether thorough self-sustaining mechanistic explanations can actually be provided when addressing cancer and psychiatric diseases. While acknowledging the merits of the wide ongoing debate on mechanistic models, the article challenges the mechanistic approach to explanation by discussing, in particular, explanatory and conceptual terms in the light of stances from medical cases. (shrink)

Completeness is an important but misunderstood norm of explanation. It has recently been argued that mechanistic accounts of scientific explanation are committed to the thesis that models are complete only if they describe everything about a mechanism and, as a corollary, that incomplete models are always improved by adding more details. If so, mechanistic accounts are at odds with the obvious and important role of abstraction in scientific modelling. We respond to this characterization of the mechanist’s views about abstraction and (...) articulate norms of completeness for mechanistic explanations that have no such unwanted implications. _1_ Introduction _2_ A Balancing Act: When Do Details Matter? _3_ The Norms of Causal Explanation _4_ The Norms of Constitutive Explanation _5_ Salmon-Completeness _6_ From More Details to More Relevant Details _7_ Non-explanatory Virtues of Abstraction _8_ From Explanatory Models to Explanatory Knowledge _9_ Mechanistic Completeness Reconsidered _10_ Conclusion. (shrink)

Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine - using the mechanistic philosophy of science as an analytic springboard - the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute of Technology. The two laboratories study gene regulatory networks, but (...) in remarkably different ways. The research strategy of the Davidson lab fits squarely into the traditional mechanist philosophy in its aim to decompose and reconstruct, in detail, gene regulatory networks of a chosen model organism. In contrast, the Elowitz lab constructs minimal models that do not attempt to represent any particular naturally evolved genetic circuits. Instead, it studies the principles of gene regulation through a template-based approach that is applicable to any kinds of networks, whether biological or not. We call for the mechanists to consider whether the latter approach can be accommodated by the mechanistic approach, and what kinds of modifications it would imply for the mechanistic paradigm of explanation, if it were to address modelling more generally. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Both clinical research and basic science rely on the epistemic practice of extrapolation from surrogate models, to the point that explanatory accounts presented in review papers and biology textbooks are in fact composite pictures reconstituted from data gathered in a variety of distinct experimental setups. This raises two new challenges to previously proposed mechanistic-similarity solutions to the problem of extrapolation: one pertaining to the absence of mechanistic knowledge in the early stages of research and the second to the large number (...) of extrapolations underpinning explanatory accounts. An analysis of the strategies deployed in experimental research supports the conclusion that while results from validated surrogate models are treated as a legitimate line of evidence supporting claims about target systems, the overall structure of research projects also demonstrates that extrapolative inferences are not considered definitive or sufficient evidence, but only partially justified hypotheses subjected to further testing. 1 Introduction2 Surrogate Models2.1 What exactly is a surrogate model?2.2 Why use surrogate models?3 Prior Validation of Surrogate Models3.1 The validation and ranking of surrogate models in the early stages of basic research3.2 The validation of surrogate models in later stages of basic research and in clinical research4 ‘Big Picture’ Accounts and the Extrapolations Underpinning Them4.1 The mosaic nature of mechanistic descriptions in basic science4.2 Challenges for mechanistic-similarity-based validation protocols5 Retrospective Testing of Extrapolated Knowledge5.1 Holistic confirmation5.2 Fallback strategies6 Conclusions. (shrink)

I argue that informational models of consciousness, including those proposed by the Integrated Information Theory, don’t presuppose or entail any particular view about the physical or metaphysical nature of consciousness. Such models only tell us how certain properties of consciousness can be mathematically described, thus providing a quantitative characterization of the phenomenon of consciousness that may contribute to the development of new methods of assessment and guide the explanatory project by supplying additional constraints on theoretical proposals. While informational models are (...) in principle compatible with multiple physical interpretations, a preliminary argument in favour of the continuity between informational approaches and the mechanistic project in neuroscience can be made based on historical precedents. (shrink)