Scientists and laypeople alike use the sense of understanding that an explanation conveys as a cue to good or correct explanation. Although the occurrence of this sense or feeling of understanding is neither necessary nor sufficient for good explanation, it does drive judgments of the plausibility and, ultimately, the acceptability, of an explanation. This paper presents evidence that the sense of understanding is in part the routine consequence of two well-documented biases in cognitive psychology: overconfidence and hindsight. In light of (...) the prevalence of counterfeit understanding in the history of science, I argue that many forms of cognitive achievement do not involve a sense of understanding, and that only the truth or accuracy of an explanation make the sense of understanding a valid cue to genuine understanding. (shrink)

A biochemical pathway is a sequence of chemical reactions in a biological organism. Such pathways specify mechanisms that explain how cells carry out their major functions by means of molecules and reactions that produce regular changes. Many diseases can be explained by defects in pathways, and new treatments often involve finding drugs that correct those defects. This paper presents explanation schemas and treatment strategies that characterize how thinking about pathways contributes to biomedical discovery. It discusses the significance of pathways for (...) understanding the nature of diseases, explanations, and theories. (shrink)

Naturalism implies unity of method--an application of the methods of science to the methodology of science itself and to value theory. Epistemological naturalists have tried to find a privileged discipline to be the methodological model of philosophy of science and epistemology. However, since science itself is not unitary, the use of one science as a model amounts to a reduction and distorts the philosophy of science just as badly as traditional philosophy of science distorted science, despite the fact that the (...) central theme of naturalized philosophy of science is that methodology should be true to science as practiced. I argue that naturalized philosophy of science must apply a plurality of methods to epistemological issues. (shrink)

This paper examines the nature of model-based reasoning in the interplay between theory and experiment in the context of biomedical engineering research laboratories, where problem solving involves using physical models. These "model systems" are sites of experimentation where in vitro models are used to screen, control, and simulate specific aspects of in vivo phenomena. As with all models, simulation devices are idealized representations, but they are also systems themselves, possessing engineering constraints. Drawing on research in contemporary cognitive science that construes (...) cognition as occurring in a complex distributed system comprising people and artifacts, I argue that reasoning with model systems is a constraint satisfaction process involving co-construction, manipulation, and revision of mental and physical models. (shrink)

In this paper, a criticism of the traditional theories of approximation and idealization is given as a summary of previous works. After identifying the real purpose and measure of idealization in the practice of science, it is argued that the best way to characterize idealization is not to formulate a logical model – something analogous to Hempel's D-N model for explanation – but to study its different guises in the praxis of science. A case study of it is then made (...) in thermostatistical physics. After a brief sketch of the theories for phase transitions and critical phenomena, I examine the various idealizations that go into the making of models at three difference levels. The intended result is to induce a deeper appreciation of the complexity and fruitfulness of idealization in the praxis of model-building, not to give an abstract theory of it. (shrink)

How is scientific knowledge used, adapted, and extended in deriving phenomena and real-world systems? This paper aims at developing a general account of 'applying science' within the exemplar-based framework of Data-Oriented Processing (DOP), which is also known as Exemplar-Based Explanation (EBE). According to the exemplar-based paradigm, phenomena are explained not by deriving them all the way down from theoretical laws and boundary conditions but by modelling them on previously derived phenomena that function as exemplars. To accomplish this, DOP proposes to (...) maintain a corpus of derivation trees of previous phenomena together with a matching algorithm that combines subtrees from the corpus to derive new phenomena. By using a notion of derivational similarity, a new phenomenon can be modelled as closely as possible on previously explained phenomena. I will propose an instantiation of DOP which integrates theoretical and phenomenological modelling and which generalises over various disciplines, from fluid mechanics to language technology. I argue that DOP provides a solution for what I call Kuhn's problem and that it redresses Kitcher's account of explanation. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

The practice of model-building is very common in analytic philosophical theology. Yet many other theologians worry that any attempt to model God must be hubristic and idolatrous. A better understanding of scientific modeling can set the stage for a more fruitful engagement between analytic theologians and their critics. I first present an account of scientific modeling that draws on recent work in the philosophy of science. I then apply that account to a prominent analytic model of the trinity, Michael Rea (...) and Jeffrey Brower’s “material constitution model.” I argue that modeling – whether scientific or theological – need not be understood as a hubristic enterprise. A model does not always try to grasp its target at all, let alone grasp it fully and completely. Even theologians who are committed to a strong doctrine of divine mystery can therefore find value in analytic modeling. (shrink)

In this essay, I attempt to assess Henk de Regt and Dennis Dieks recent pragmatic and contextual account of scientific understanding on the basis of an important historical case-study: understanding in Newton’s theory of universal gravitation and Huygens’ reception of universal gravitation. It will be shown that de Regt and Dieks’ Criterion for the Intelligibility of a Theory (CIT), which stipulates that the appropriate combination of scientists’ skills and intelligibility-enhancing theoretical virtues is a condition for scientific understanding, is too strong. (...) On the basis of this case-study, it will be shown that scientists can understand each others’ positions qualitatively and quantitatively, despite their endorsement of different worldviews and despite their convictions as what counts as a proper explanation. (shrink)

Richard Cytowic has done considerable service to the scientific study of synesthesia, conducting important research and publishing two recent books on the subject. The study of synesthesia raises interesting questions about scientific method, both because of the negative reception it received initially--often being viewed as tainted by a reliance upon introspective reports--and because of the connections Cytowic has found between synesthetic perception and the limbic system, thereby possibly undermining some of the claims to objectivity in perception and scientific method. I (...) dispute some of the more extreme methodological conclusions Cytowic draws from his work and reinforce others by reference to different arguments current within the philosophy of science. (shrink)

The ontological status of theories themselves has recently re-emerged as a live topic in the philosophy of science. We consider whether a recent approach within the philosophy of art can shed some light on this issue. For many years philosophers of aesthetics have debated a paradox in the (meta)ontology of musical works (e.g. Levinson [1980]). Taken individually, there are good reasons to accept each of the following three propositions: (i) musical works are created; (ii) musical works are abstract objects; (iii) (...) abstract objects cannot be created. However it seems clear that, if one wants to avoid inconsistency, one cannot commit to all three. Following up recent developments courtesy of Cameron ([2008a]), we consider how one might respond to the corresponding set of propositions in the (meta)ontology of scientific theories. 1 Introduction2 Setting up the Problem3 What to Reject? 3.1 Scientific theories are not created? 3.2 Scientific theories are not abstract objects? 3.3 Abstract objects can be created?4 A Fourth Way: Truth-maker Theory5 Objections and Replies 5.1 What are the truth-makers? 5.2 Objections from World 3 5.3 Fictionalism 5.4 Concrete/abstract6 Conclusion. (shrink)

This article deals with the problematic concepts of the rational and the social, which have been typically seen as dichotomous in the history and philosophy of science literature. I argue that this view is mistaken and that the social can be seen as something that enables rationality in science, and further, that a scientific community as well as an individual can be taken as an epistemic subject. Furthermore, I consider how scientific communities could be seen as freely acting and choosing (...) agents. Fundamentally, this boils down to the question whether we accept the voluntarist conception of human beings, one consequence of which is that scientists possess, in principle, the capacity for deliberative reflection and choice. If this is accepted, we can talk about the degrees of autonomy that communities possess. I also examine what kinds of decisions an autonomous community should make in order to produce objective knowledge. My suggestion is that objectivity be understood as intersubjectivity: a view is objective when it has been exposed to critical reflection from various points of view, and due to this, transcends subjective idiosyncrasies. (shrink)

Formidable difficulties face anyone trying to model social phenomena using a formal system, such as a computer program. The differences between formal systems and complex, multi-facetted and meaning-laden social systems are so fundamental that many will criticise any attempt to bridge this gap. Despite this, there are those who are so bullish about the project of social simulation that they appear to believe that simple computer models, that are also useful and reliable indicators of how aspects of society works, are (...) not only possible but within our grasp. This paper seeks to pour water on such optimism but, on the other hand, show that useful computational models might be ‘evolved’ In this way it is disagreeing with both naive positivist and relativistic post-modernist positions. However this will require a greater ‘selective pressure’ against models that are not grounded in evidence, ‘floating models’, and will result in a plethora of complex and context-specific models. (shrink)

The paper investigates what is meant by "good science" and "bad science" and how these differ as between the natural (physical and biological) sciences on the one hand and social sciences on the other. We conclude on the basis of historical evidence that the natural science are much more heavily constrained by evidence and observation than by theory while the social sciences are constrained by prior theory and hardly at all by direct evidence. Current examples of the latter proposition are (...) taken from recent issues of leading social science journals. We argue that agent based social simulations can be used as a tool to constrain the development of a new social science by direct (what economists dismiss as anecdotal) evidence and that to do so would make social science relevant to the understanding and influencing of social processes. We argue that such a development is both possible and desirable. We do not argue that it is likely. (shrink)

The classical model of the molecule assumes that it has a definite shape and structure like a mechanical object in the world of possible experience. This study deals with this assumption so as to shed some light on the foundations of the model. Arguments based on Kant’s theory of transcendental idealism suggest that neither shape nor structure are attributes of the molecule, but are rather contributions of the subject. This claim has great relevance to the questions of whether or not (...) a quantum treatment of the molecule can derive structure without recourse to any approximation, and the possible existence of emergence and downward causation. The answer to the first question is in the negative, and to the second is that agnosticism is the only possible attitude to have toward this problem. We are creatures who can only imagine what is going on by observing phenomena. All that is accessible to us is the modal structure of the model. The causal structure of the real system is not. From the same point of view and taking the concept of the affordance into account, the adequacy of the concept of molecular structure will be argued. The point is to specify what objects the concept can legitimately be applied to. Also briefly discussed in relation to shape and structure is the idea that molecular chirality might be a probe to reveal the nature of space. (shrink)

In this paper, I briefly present the regularity and necessity views and assess their difficulties. I construe scientific laws as universal propositions satisfied by empirically successful scientific models and made — approximately — true by the real systems represented, albeit partially, by these models. I also conceive a scientific theory as a set of models together with a set of propositions, some of which are laws. A scientific law is a universal proposition or statement that belongs to a scientific theory. (...) Scientific laws also are laws of nature since we can provide arguments in favour of natural causal powers that ground the truth of laws. I argue that the truth of counterfactual conditional statements and the occurrence of regularities in nature provide good reasons to believe that real causal powers exist in nature and that the truth of scientific laws is based on a metaphysics of nature. (shrink)

While agreeing that cognition in the sciences is usefully thought of as involving processes encompassing both humans and artifacts, I object to attributing cognitive states to extended systems. I argue that cognitive states, such as ?knowing?, should be confined to the human components of cognitive systems. My argument appeals to the large dimensions, both spatial and temporal, of many scientific cognitive systems, the existence of epistemic norms, and the need for agents in science.

This paper's purpose is to set forth the conditions of explanation in the domain of formal modelling of social action. Explanation is defined as an adequate account of the underlying factors bringing about a phenomenon. The modelling of a social phenomenon can claim explanatory value in this sense if the following two conditions are fulfilled. (1) The generative mechanisms involved translate the effects of real factors abstracted from their phenomenal context, not those of purely ideal ones. (2) The explanatory hypotheses, (...) which account for the effects of explanatory factors, and the purely descriptive hypotheses, which introduce conceptual simplifications and summarise complex secondary mechanisms, are relatively independent from each other with regard to the phenomenon represented. This condition subjects the model to testing by alternatives through the development of purely descriptive hypotheses in the sense of explanatory or analytical realism. (shrink)

Trygve Haavelmo's 1944 article ‘The Probability Approach in Econometrics’ is considered by most to have provided the foundations for present day econometrics (Morgan, 1990, Chapters 8 and 9). Since Haavelmo (1944), extraordinary advances have been made in econometrics. However, over the last two decades the efficacy and scientific status of econometrics has become questionable. Not surprisingly, the growing discontent with econometrics has been accompanied by a growing interest in econometric methodology.

I erect a framework within the semantic view of theories for explaining the empirical success of internally inconsistent models and theories, with scientific realism in mind. The framework is an instance of the ‘content-driven’ approach to inconsistency, advocated by both Norton (Philos Sci 54:327–350, 1987) and Smith (Stud Hist Philos Sci 19:429–445, 1988a, In: Fine A, Leplin J (eds) PSA1988, 1988b), whose ideas my analysis aims to clarify and substantiate.

I explore a type of computational social simulation known as artificial societies. Artificial society simulations are dynamic models of real-world social phenomena. I explore the role that these simulations play in social explanation, by situating these simulations within contemporary philosophical work on explanation and on models. Many contemporary philosophers have argued that models provide causal explanations in science, and that models are necessary mediators between theory and data. I argue that artificial society simulations provide causal mechanistic explanations. I conclude that (...) in their current form, these simulations are based on methodologically individualist assumptions that could limit their potential scope of social explanation. (shrink)

The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, particularly where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in (...) causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be "expressed," but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the "genetic code," mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. This includes: 1 (i) The description of whole-organism phenotypic traits (including complex behavioral traits) as specified or coded for by information contained in the genes, (ii) The treatment of many causal processes within cells, and perhaps of the wholeorganism developmental sequence, in terms of the execution of a program stored in the genes, (iii) The idea that genes themselves, for the purpose of evolutionary theorizing, should be seen as, in some sense, "made" of information.. (shrink)

http://dx.doi.org/10.5007/1808-1711.2008v12n1p97 This paper defends the idea that there are three determinant elements in the identity of theories in accordance with the semantic approach of theories: the kind of theoretic models, the data models and the empirical claims, but with some exceptions in each case. I uphold this thesis in an analysis the Structuralist view and van Fraassen’s one about this respect.

This paper argues that truth is by nature context-dependent – that no truth can be applied regardless of context. I call this “strong contextualism”. Some objections to this are considered and rejected, principally: that there are universal truths given to us by physics, logic and mathematics; and that claiming “no truths are universal” is self-defeating. Two “models” of truth are suggested to indicate that strong contextualism is coherent. It is suggested that some of the utility of the “universal framework” can (...) be recovered via a more limited “third person viewpoint”. Keywords: philosophy, universality, context, truth, knowledge. (shrink)