Scientific Models

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it (...) is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account of (...) Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

Empiricist modal epistemologies can be attractive, but are often limited in the range of modal knowledge they manage to secure. In this paper, I argue that one such account – similarity-based modal empiricism – can be extended to also cover justification of many scientifically interesting possibility claims. Drawing on recent work on modelling in the philosophy of science, I suggest that scientific modelling is usefully seen as the creation and investigation of relevantly similar epistemic counterparts of real target systems. On (...) the basis of experiential knowledge of what is actually the case with the models, one can draw justified conclusions about what is de re possible for the target systems. (shrink)

Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Critiques of the framework have focused on its lack of empirical support and a failure to generate concrete, falsifiable predictions. I take both positive and negative evaluations of the FEP thus far to have been largely in error, and appeal to a robust literature on scientific modelling to rectify the situation. A (...) prominent account of scientific modelling distinguishes between model structure and model construal. I propose that the FEP be reserved to designate a model structure, to which philosophers and scientists add various construals, leading to a plethora of models based on the formal structure of the FEP. An entailment of this position is that demands placed on the FEP that it be falsifiable or that it conform to some degree of biological realism rest on a category error. To this end, I deliver first an account of the phenomenon of model transfer and the breakdown between model structure and model construal. In the second section, I offer an overview of the formal elements of the framework, tracing their history of model transfer and illustrating how the formalism comes apart from any interpretation thereof. Next, I evaluate existing comprehensive critical assessments of the FEP, and hypothesise as to potential sources of existing confusions in the literature. In the final section, I distinguish between what I hold to be the FEP—taken to be a modelling language or modelling framework—and what I term “FEP models.”. (shrink)

The second edition of the work of the Brazilian physicist Paulo C. Abrantes (2016), entitled Images of nature, images of science, is a good alternative for students of history and philosophy of science. The reason is Abrantes' thesis in this work: to defend that the development of scientific knowledge is dependent on the influence of different images of "nature" and "science" existing during the history of Western scientific-philosophical thought; and an advocate for the historian of science Studying as reasons that (...) allow the adoption of such images at a given time. Through the analysis of historical cases of scientific thought, Abrantes argues that the consolidation of research programs in different subareas of natural science - such as biology, physics and chemistry - was only possible due to the influence, in particular time, of images of nature and science. (shrink)

ABSTRACT This article distinguishes nine senses of polarization and provides formal measures for each one to refine the methodology used to describe polarization in distributions of attitudes. Each distinct concept is explained through a definition, formal measures, examples, and references. We then apply these measures to GSS data regarding political views, opinions on abortion, and religiosity—topics described as revealing social polarization. Previous breakdowns of polarization include domain-specific assumptions and focus on a subset of the distribution’s features. This has conflated multiple, (...) independent features of attitude distributions. The current work aims to extract the distinct senses of polarization and demonstrate that by becoming clearer on these distinctions we can better focus our efforts on substantive issues in social phenomena. (shrink)

A first take, matured in later work, in modeling belief polarization.

Para el constructivismo, la ciencia y la cognición comparten intereses similares. Ambos dominios pueden describirse como dos sistemas entrelazados que se activan mutuamente y se modulan entre sí a través de un lazo interno de retroalimentación, lazo que opera mediante la dinámica interna representativa en el caso de la cognición y mediante la dinámica del desarrollo teórico en el caso de la ciencia. Cada uno de estos dominios —ciencia y cognición— busca generar un marco de interacción adecuado que garantice, por (...) parte de la ciencia, el éxito predictivo a partir de los modelos utilizados en la investigación y, por parte de la cognición, una amplia gama de estrategias funcionalmente exitosas con las que salvaguardar una imagen viable del mundo. Al pensar la ciencia como una extensión de nuestra apertura cognitiva al mundo, el constructivismo adopta la noción de viabilidad, es decir, de ajuste funcional, con el entorno como fundamental en la correcta aproximación al estudio tanto de la cognición como de la modelización, ya que, al igual que ocurre con las estructuras y procesos que conforman la arquitectura cognitiva de cualquier sistema de observación, más o menos evolucionado, los modelos en ciencia se encuentran limitados por su propia estructura teórica, así como por su dinámica operativa. Adoptando el constructivismo como una factible filosofía de la ciencia, este trabajo tiene como objetivo estudiar el fenómeno de la modelización, así como examinar el papel que asumen algunas estrategias tropológicas inherentes a la actividad científica, como la analogía y la metáfora, a la hora de configurar modelos y formular hipótesis y conjeturas que sirven de aproximación para la indagación y el estudio del mundo empírico. (shrink)

Tony Lawson, founder of The Social Ontology Group and The Realist Workshop of Cambridge, has proposed critical realism to reorient economics. The transformation of the social world that Lawson tries, emerges from the adherence to critical realism, this is, from taking the transcendental realism of Roy Bhaskar to the social realm. With the purpose of deepening the criticisms to this movement, we will specify what is critical realism, and which are the philosophical assumptions of the mainstream according to this author. (...) We will set out the criticisms on: a) the notion of mainstream economics, b) the possibilities of economics based on social ontology, c) the realism of economic models, and d) the notions of isolation and abstraction. (shrink)

La presente obra ofrece un análisis crítico de la filosofía de la economía de Uskali Mäki; en particular de la consideración realista científica de la economía. Se intenta a lo largo del texto responder, de algún modo, a las preguntas que plantea Lehtinen en la introducción: “¿Están los economistas aspirando en absoluto a la verdad, o están solamente jugando un juego intelectual en que tales supuestos son aceptables por alguna razón misteriosa? ¿Están estudiando la economía en serio? ¿Están simplemente desinteresados (...) en la verdad?, o ¿hay tal vez alguna otra forma de considerar sus prácticas de modelar?” p. 1. (shrink)

In the debate on realism of models in economics, the Austrian School and Hayekin particular, seem to have, in a certain way, remained outside. Assuming neoclassical models asunrealistic, the theory of the market as a process looks like a more realistic proposal. However, oneof the fundamental issue s in Hayek’s dissent is not so much the unrealism of the assumptions, but that the market equilibrium theory was not correctly raised, especially with regards to the perfectknowledge assumption. Despite this, in this (...) setting and in line with a previous paper (Zanotti & Borella, 2015), we will argue that Hayek’s spontaneous order may be understood as the Austrian School’s “model”, assuming Mäki’s MISS version of models (Models as Isolations and Surrogate Systems) and emphasizing the place of the ontological foundation of Hayek’s proposal when assessing his model. (shrink)

There has recently been an explosion of formal models of signalling, which have been developed to learn about different aspects of meaning. This paper discusses whether that success can also be used to provide an original naturalistic theory of meaning in terms of information or some related notion. In particular, it argues that, although these models can teach us a lot about different aspects of content, at the moment they fail to support the idea that meaning just is some kind (...) of information. As an alternative, I suggest a more modest approach to the relationship between informational notions used in models and semantic properties in the natural world. (shrink)

In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in order to demonstrate their own (...) hypotheses. Using as an example the controversy over the use of null hypotheses and null models in species co-occurrence studies, I argue that null-model-based hypothesis testing fails to work as a proper analog to traditional statistical null-hypothesis testing as used in well-controlled experimental research, and that the random process hypothesis should not be privileged as a null hypothesis. Instead, the possible use of the null model resides in its role of providing a way to challenge scientists’ commonsense judgments about how a seemingly unusual pattern could have come to be. Despite this possible use, null-model-based hypothesis testing still carries certain limitations, and it should not be regarded as an obligation for biologists who are interested in explaining patterns in nature to first conduct such a test before pursuing their own hypotheses. (shrink)

South Korean high school students are being taught Einstein’s Special Theory of Relativity. In this article, I examine the portrayal of this theory in South Korean high school physics textbooks and discuss an alternative method used to solve the analyzed problems. This examination of how these South Korean textbooks present this theory has revealed two main flaws: First, the textbooks’ contents present historically fallacious backgrounds regarding the origin of this theory because of a blind dependence on popular undergraduate textbooks, which (...) ignore the revolutionary aspects of the theory in physics. And second, the current ingredients of teaching this theory are so simply enumerated and conceptually confused that students are not provided with good opportunities to develop critical capacities for evaluating scientific theories. Reviewing textbooks used in South Korea, I will, first, claim that the history of science contributes to understand not merely the origins but also two principles of this theory. Second, in addition to this claim, I argue that we should distinguish not only hypotheses from principles but also phenomena from theoretical consequences and evidence. Finally, I suggest an alternative way in which theory testing occurs in the process of evaluation among competitive theories on the basis of data, not in the simple relation between a hypothesis and evidence. (shrink)

Experimental activity is traditionally identified with testing the empirical implications or numerical simulations of models against data. In critical reaction to the ‘tribunal view’ on experiments, this essay will show the constructive contribution of experimental activity to the processes of modeling and simulating. Based on the analysis of a case in fluid mechanics, it will focus specifically on two aspects. The first is the controversial specification of the conditions in which the data are to be obtained. The second is conceptual (...) clarification, with a redefinition of concepts central to the understanding of the phenomenon and the conditions of its occurrence. (shrink)

The received view about emergence and reduction is that they are incompatible categories. I argue in this paper that, contrary to the received view, emergence and reduction can hold together. To support this thesis, I focus attention on dynamical systems and, on the basis of a general representation theorem, I argue that, as far as these systems are concerned, the emulation relationship is sufficient for reduction (intuitively, a dynamical system DS1 emulates a second dynamical system DS2 when DS1 exactly reproduces (...) the whole dynamics of DS2). This representational view of reduction, contrary to the standard deductivist one, is compatible with the existence of structural properties of the reduced system that are not also properties of the reducing one. Therefore, under this view, by no means are reduction and emergence incompatible categories but, rather, complementary ones. (shrink)

Contemporary action theory is generally concerned with giving theories of action ontology. In this paper, we make the novel proposal that the standard view in action theory—the Causal Theory of Action—should be recast as a “model”, akin to the models constructed and investigated by scientists. Such models often consist in fictional, hypothetical, or idealized structures, which are used to represent a target system indirectly via some resemblance relation. We argue that recasting the Causal Theory as a model can not only (...) accomplish the goals of causal theorists, but also give the theory greater flexibility in responding to common objections. (shrink)

In the Western tradition, at least since the 14th century, the philosophy of knowledge has been built around the idea of knowledge as a representation [Boulnois 1999]. The question of the evaluation of knowledge refers at the same time (1) to the object represented (which one does one represent?), (2) to the process of knowledge formation, in particular with the role of the knowing subject (which one does one represent and how does one represent it?), and finally (3) to the (...) relationship between the representation and the represented object. Criteria of evaluation such as “validity”, “adequacy” or “truth”, as mentioned in chapter 4, make sense only with respect to these three dimensions. An evaluation can thus (1) depend on the ontological nature of the object of knowledge, (2) relate to the relationship between subject and object—including the structures (cognitive, social) which organize this relationship, or (3) relate to the relation of similarity between the object and its representation as well. The relevant criteria of evaluation thus depend on the points of view adopted on these questions. As there are indeed a plurality of points of view in this field, the goal of this appendix is to summarize, as briefly as possible, the various positions adopted by the philosophers and to refer to the relevant texts of reference for more information. The first section introduces useful discussions about the philosophy of theoretical knowledge and general epistemology, from a quasi-historical perspective. Section two discusses the intermediary but central notion of models. Section three, more exploratory, intro-duces an approach to simulation as “concrete experiment”. It suggests that such a frequent claim in the literature, when precisely evaluated, can, to some extent, renew both the representational and the linguistic views on simulation. (shrink)

The practice of scientific modelling often resorts to hypothetical, false, idealised, targetless, partial, generalised, and other types of modelling that appear to have at least partially non-actual targets. In this paper, I will argue that we can avoid a commitment to non-actual targets by sketching a framework where models are understood as having networks of possibilities as their targets. This raises a further question: what are the truthmakers for the modal claims that we can derive from models? I propose that (...) we can find truthmakers for the modal claims derived from models in actuality, even in the case of supposedly non-actual targets. I then put this framework to use by examining a case study concerning the modelling of superheavy elements. (shrink)

Many philosophers have drawn parallels between scientific models and fictions. In this paper I will be concerned with a recent version of the analogy, which compares models to the imagined characters of fictional literature. Though versions of the position differ, the shared idea is that modeling essentially involves imagining concrete systems analogously to the way that we imagine characters and events in response to works of fiction. Advocates of this view argue that imagining concrete systems plays an ineliminable role in (...) the practice of modeling that cannot be captured by other accounts. The approach thus leaves open what we should say about the ontological status of model-systems, and here advocates differ among themselves, defending a variety of realist or anti-realist positions. I argue that this debate over the ontological status of model-systems is misguided. If model-systems are the kinds of objects fictional realists posit, they can play no role in explaining the epistemology of modeling for an advocate of this approach. So they are at best superfluous. Defenders of the approach should focus on developing an account of the epistemological role of imagining model-systems. (shrink)

A well known conception of axiomatization has it that an axiomatized theory must be interpreted, or otherwise coordinated with reality, in order to acquire empirical content. An early version of this account is often ascribed to key figures in the logical empiricist movement, and to central figures in the early “formalist” tradition in mathematics as well. In this context, Reichenbach’s “coordinative definitions” are regarded as investing abstract propositions with empirical significance. We argue that over-emphasis on the abstract elements of this (...) approach fails to appreciate a rich tradition of empirical axiomatization in the late nineteenth and early twentieth centuries, evident in particular in the work of Moritz Pasch, Heinrich Hertz, David Hilbert, and Reichenbach himself. We claim that such over-emphasis leads to a misunderstanding of the role of empirical facts in Reichenbach’s approach to the axiomatization of a physical theory, and of the role of Reichenbach’s coordinative definitions in particular. (shrink)

Maps and mapping raise questions about models and modeling and in science. This chapter archives map discourse in the founding generation of philosophers of science (e.g., Rudolf Carnap, Nelson Goodman, Thomas Kuhn, and Stephen Toulmin) and in the subsequent generation (e.g., Philip Kitcher, Helen Longino, and Bas van Fraassen). In focusing on these two original framing generations of philosophy of science, I intend to remove us from the heat of contemporary discussions of abstraction, representation, and practice of science and thereby (...) see in a more distant and neutral light the many productive ways in which maps can stand in analytically for scientific theories and models. The chapter concludes by complementing the map analogy – i.e., a scientific theory is a map of the world – with a model analogy, viz., a scientific model is a vehicle for understanding. (shrink)

Disagreement about how best to think of the relation between theories and the realities they represent has a longstanding and venerable history. We take up this debate in relation to the free energy principle (FEP) - a contemporary framework in computational neuroscience, theoretical biology and the philosophy of cognitive science. The FEP is very ambitious, extending from the brain sciences to the biology of self-organisation. In this context, some find apparent discrepancies between the map (the FEP) and the territory (target (...) systems) a compelling reason to defend instrumentalism about the FEP. We take this to be misguided. We identify an important fallacy made by those defending instrumentalism about the FEP. We call it the literalist fallacy: this is the fallacy of inferring the truth of instrumentalism based on the claim that the properties of FEP models do not literally map onto real-world, target systems. We conclude that scientific realism about the FEP is a live and tenable option. (shrink)

Theoretical models are widely held as sources of knowledge of reality. Imagination is vital to their development and to the generation of plausible hypotheses about reality. But how can imagination, which is typically held to be completely free, effectively instruct us about reality? In this paper I argue that the key to answering this question is in constrained uses of imagination. More specifically, I identify make-believe as the right notion of imagination at work in modelling. I propose the first overarching (...) taxonomy of types of constraints on scientific imagination that enables knowledge of reality. And I identify two main kinds of knowledge enabled by models, knowledge of the imaginary scenario specified by models and knowledge of reality. (shrink)

Several philosophers of science claim that scientific toy models afford knowledge of possibility, but answers to the question of why toy models can be expected to competently play this role are scarce. The main line of reply is that toy models support possibility claims insofar as they are credible. I raise a challenge for this credibility-thesis, drawing on a familiar problem for imagination-based modal epistemologies, and argue that it remains unanswered in the current literature. The credibility-thesis has a long way (...) to go if it is to account for the epistemic merits of toy models. (shrink)

The epistemic value of models has traditionally been approached from a representational perspective. This paper argues that the artifactual approach evades the problem of accounting for representation and better accommodates the modal dimension of modeling. From an artifactual perspective, models are viewed as erotetic vehicles constrained by their construction and available representational tools. The modal dimension of modeling is approached through two case studies. The first portrays mathematical modeling in economics, while the other discusses the modeling practice of synthetic biology, (...) which exploits and combines models in various modes and media. Neither model intends to represent any actual target system. Rather, they are constructed to study possible mechanisms through the construction of a model system with built-in dependencies. (shrink)

This paper discusses modeling from the artifactual perspective. The artifactual approach conceives models as erotetic devices. They are purpose-built systems of dependencies that are constrained in view of answering a pending scientific question, motivated by theoretical or empirical considerations. In treating models as artifacts, the artifactual approach is able to address the various languages of sciences that are overlooked by the traditional accounts that concentrate on the relationship of representation in an abstract and general manner. In contrast, the artifactual approach (...) focuses on epistemic affordances of different kinds of external representational and other tools employed in model construction. In doing so, the artifactual account gives a unified treatment of different model types as it circumvents the tendency of the fictional and other representational approaches to separate model systems from their “model descriptions”. (shrink)

This chapter elaborates and develops the thesis originally put forward by Mary Morgan (2005) that some mathematical models may surprise us, but that none of them can completely confound us, i.e. let us unable to produce an ex post theoretical understanding of the outcome of the model calculations. This chapter intends to object and demonstrate that what is certainly true of classical mathematical models is however not true of pluri-formalized simulations with multiple axiomatic bases. This chapter thus proposes to show (...) that - and why - some of these computational simulations that are now booming in the sciences not only surprise us but also confound us. To do so, it shows too that it is needed to elaborate and articulate with some new precision the concept of weak emergence initially due, for its part, to Mark A. Bedau (1997). (shrink)

Ecological-enactive approaches to cognition aim to explain cognition in terms of the dynamic coupling between agent and environment. Accordingly, cognition of one’s immediate environment (which is sometimes labeled “basic” cognition) depends on enaction and the picking up of affordances. However, ecological-enactive views supposedly fail to account for what is sometimes called “higher” cognition, i.e., cognition about potentially absent targets, which therefore can only be explained by postulating representational content. This challenge levelled against ecological-enactive approaches highlights a putative explanatory gap between (...) basic and higher cognition. In this paper, we examine scientific cognition—a paradigmatic case of higher cognition—and argue that it shares fundamental features with basic cognition, for enaction and affordance selection are central to the scientific enterprise. Our argument focuses on modeling, and on how models promote scientific understanding. We base our argument on a non-representational account of scientific understanding and on the material engagement theory, for models are hereby conceived as material objects designed for scientific engagements. Having done so, we conclude that the explanatory gap is significantly less threatening to the ecological-enactive approach than it might appear. (shrink)

Three metascientific concepts that have been object of philosophical analysis are the concepts oflaw, model and theory. The aim ofthis article is to present the explication of these concepts, and of their relationships, made within the framework of Sneedean or Metatheoretical Structuralism (Balzer et al. 1987), and of their application to a case from the realm of biology: Population Dynamics. The analysis carried out will make it possible to support, contrary to what some philosophers of science in general and of (...) biology in particular hold, the following claims: a) there are "laws" in biological sciences, b) many of the heterogeneous and different "models" of biology can be accommodated under some "theory", and c) this is exactly what confers great unifying power to biological theories. (shrink)

Preface to the Thematic Volume: Models and Theories in Biology.

Two metascientific concepts that have been ― and still are ― object of philosophical analysis are the concepts of model and theory. But while the concept of scientific theory was one of the concepts to which philosophers of science devoted most attention during the 20th century, it is only in recent decades that the concept of scientific model has come to occupy a central position in philosophical reflection. However, it has done so in such a way that, at present, as (...) Jim Bogen states in the back cover of the book Scientific Models in the Philosophy of Science, by Daniela Bailer-Jones, “[t]he standard philosophical literature on the role of models in scientific reasoning is voluminous, disorganized, and confusing”. In spite of this, one of the axes that would allow us to organize at least part of this literature, and with which Bailer-Jones’ book closes, is that which is identified as one of the “contemporary philosophical issues: how theories and models relate to each other” (Bailer-Jones 2009, p. 208).That is why, in this introduction to the special issues of Metatheoria devoted to the topic of “Models and Theories in Biology”, we will present the main advances that have been made in the philosophical analysis of the concepts of model and theory in general and in biology in particular, and we will also do the same with the answers that have been given to the problem of "how theories and models relate to each other”. (shrink)

This paper constitutes a radical departure from the existing philosophical literature on models, modeling-practices, and model-based science. I argue that the various entities and practices called 'models' and 'modeling-practices' are too diverse, too context-sensitive, and serve too many scientific purposes and roles, as to allow for a general philosophical analysis. From this recognition an alternative view emerges that I shall dub model anarchism.

The book suggests a "phenomological" philosophy of science, in the sense of Husserl and Heidegger. Reality is consideried as continuity. The scientific model is entangled into reality by many links in a single context rather than to redlect a certain separate part of reality studied by a scientific discipline as an "image of reality", A coherent, rather than correspondent, concept of truth is relevant to that kind of philosophy of science.

I discuss Mary Hess’s interaction-view of scientific metaphor, outline an alternative view and show how it may prove fruitful when applied to chapters of the history of science. I start with a reconstruction of the discussion on the nature of scientific models and on their relationship to metaphors that has taken place in the Anglo-Saxon philosophy of Science starting from the Fifties; the discovery started with Stephen Pepper and Kenneth Burke, reaching Thomas Kuhn, Marx Wartofsky, and George Lakoff via Max (...) Black's and Mary Hesse's interaction view. I argue that Hesse's view has a number of weak points: uncritically accepting Black's idea of "interaction", for keeping too much of a logical empiricist view of observation language, and for keeping too much of a Scholastic distinction between formal and material analogy. I argue that a few insights from Kuhn and Wartofsky seem to go in the same direction as Granger's view of metaphor as opposed to metonymy, thus severing the link between metaphor and the "qualitative". I argue that the Cartesian legacy and its implicit ideal of a "mirroring" relationship between the world and the mind is the main obstacle to be eventually overcome if we are to work out a satisfactory account of the language of science and that suggestions from pragmatism as well as from French epistemology may be used in order to work out a post-Cartesian view of science. (shrink)

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation (...) and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies. (shrink)

Discussion of modeling within philosophy of science has focused in how models, understood as finished products, represent the world. This approach has some issues accounting for the value of modeling in situations where there are controversies as to which should be the object of representation. In this work I show that a historical analysis of modeling complements the aforementioned representational program, since it allows us to examine processes of integration of analogies that play a role in the generation of criteria (...) of relevance, which are important for the configuration of the object of research. This, in turn, shows that there are norms in modeling practices whose historical reconstruction is relevant for their philosophical analysis. (shrink)

In recent decades, philosophers of science have devoted considerable efforts to understand what models represent. One popular position is that models represent fictional situations. Another position states that, though models often involve fictional elements, they represent real objects or scenarios. Though these two positions may seem to be incompatible, I believe it is possible to reconcile them. Using a threefold distinction between different signs proposed by Peirce, I develop an argument based on a proposal recently made by Kralemann and Lattman (...) (in Synthese 190:3397–3420, 2013) that shows that the two aforementioned positions can be reconciled by distinguishing different ways in which a model representation can be used. In particular, on the basis of Peirce’s distinction between icons, indices and symbols, I argue that models can sometimes function as icons, sometimes as indexes and sometimes as symbols, depending on the context in which they are considered and the use that they are developed for because they all have iconic, indexical and symbolic features. In addition, I show that conceiving models as signs enables us to develop an account of scientific representation that meets the main desiderata that Shech (in Synthese 192:3463–3485, 2015) presents. (shrink)

Recent contributions by Kuhn, Wartofsky, and Granger, converge in the direction of an extended view of models, one that acknowledges a metaphorical dimension in the language of science. Such a view is in some respects the opposite of the views of both Bachelard and the Logical Empiricists. A number of familiar puzzles of the philosophy of science, such as the problem of reference, the opposition of realism and instrumentalism, that between explanation and understanding, and the status of scientific objectivity, may (...) receive a new solution in the light of the Kuhn/Wartofsky/Granger view of scientific metaphors. (shrink)

This is the introduction to the special issue of the Spanish journal Ágora-Papeles de Filosofía (31/2, 2012) devoted to new Ibero-American contributions to metatheoretical structuralism.

There is a long tradition in formal epistemology and in the psychology of reasoning to investigate indicative conditionals. In psychology, the propositional calculus was taken for granted to be the normative standard of reference. Experimental tasks, evaluation of the participants’ responses and psychological model building, were inspired by the semantics of the material conditional. Recent empirical work on indicative conditionals focuses on uncertainty. Consequently, the normative standard of reference has changed. I argue why neither logic nor standard probability theory provide (...) appropriate rationality norms for uncertain conditionals. I advocate coherence based probability logic as an appropriate framework for investigating uncertain conditionals. Detailed proofs of the probabilistic non-informativeness of a paradox of the material conditional illustrate the approach from a formal point of view. I survey selected data on human reasoning about uncertain conditionals which additionally support the plausibility of the approach from an empirical point of view. (shrink)

The aim of this dissertation is to comprehensively study various robustness arguments proposed in the literature from Levins to Lloyd as well as the opposition offered to them and pose enquiry into the degree of epistemic virtue that they provide to the model prediction results with respect to climate science and modeling. Another critical issue that this dissertation strives to examine is that of the actual epistemic notion that is operational when scientists and philosophers appeal to robustness. In attempting to (...) explicate this idea, the discussion turns to arguments provided by Schupbach who completely rejects probabilistic independence in favour of explanatory reasoning, Stegenga and Menon who still see some value in probabilistic independence, and Winsberg who takes applies Schupbach’s to climate science, going beyond models to involve multi-modal evidence. After an exhaustive discussion on these arguments, this dissertation attempts to provide a thorough and updated notion of robustness in climate modeling and climate science. (shrink)

I argue that verbal models should be included in a philosophical account of the scientific practice of modelling. Weisberg (2013) has directly opposed this thesis on the grounds that verbal structures, if they are used in science, only merely describe models. I look at examples from Darwin's On the Origin of Species (1859) of verbally constructed narratives that I claim model the general phenomenon of evolution by natural selection. In each of the cases I look at, a particular scenario is (...) described that involves at least some fictitious elements but represents the salient causal components of natural selection. I pronounce the importance of prioritising observation of scientific practice for the philosophy of modelling and I suggest that there are other likely model types that are excluded from philosophical accounts. (shrink)

This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s. -/- Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how (...) and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations. -/- . (shrink)

The general aim of this article is to carry out a reconstruction of the theory of Population Dynamics (DP) in Ecology, according to Castle’s (2001) general stance with regard to the semantic view of theories, but doing it within the framework of metatheoretical structuralism. Thus, we will first identify Population Dynamics’ basic theory-element: its core K(DP) – with the class of potential models, the class of models (through the identification of its fundamental law) and the class of partial potential models (...) (though leaving aside the identification of its constraints and its intertheoretical links) –, and its domain of intended applications I(DP). Then, we will establish the general guiding lines of its theory-net, developing in some detail one of its main lines of specialization – namely, that related to the so-called “continuous growing” of the considered populations –, with DP’s principal “models”, and leave developing of the other of its main lines of specialization – namely, that related to the so-called “discrete growing” of the considered populations – for a further publication. (shrink)

In this paper, I characterize visual epistemic representations as concrete two- or three-dimensional tools for conveying information about aspects of their target systems or phenomena of interest. I outline two features of successful visual epistemic representation: that the vehicle of representation contain sufficiently accurate information about the phenomenon of interest for the user’s purpose, and that it convey this information to the user in a manner that makes it readily available to her. I argue that actual epistemic representation may involve (...) tradeoffs between these and is successful to the extent that they are present. (shrink)

It is plausible to think that, in order to actively employ models in their inquiries, scientists should be aware of their existence. The question is especially puzzling for realists in the case of abstract models, since it is not obvious how this is possible. Interestingly, though, this question has drawn little attention in the relevant literature. Perhaps the most obvious choice for a realist is appealing to intuition. In this paper, I argue that if scientific models were abstract entities, one (...) could not be aware of them intuitively. I deploy my argumentation by building on Chudnoff’s elaboration on intuitive awareness. Furthermore, I shortly discuss some other options to which realists could turn in order to address the question of awareness. (shrink)

The work done in the philosophy of modeling by Vaihinger (1876), Craik (1943), Rosenblueth and Wiener (1945), Apostel (1960), Minsky (1965), Klaus (1966) and Stachowiak (1973) is still almost completely neglected in the mainstream literature. However, this work seems to contain original ideas worth to be discussed. For example, the idea that diverse functions of models can be better structured as follows: in fact, models perform only a single function – they are replacing their target systems, but for different purposes. (...) Another example: the idea that all of cognition is cognition in models or by means of models. Even perception, reflexes and instincts (animal and human) can be best analyzed as modeling. The paper presents an analysis of the above-mentioned work. (shrink)