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 dissertation focuses on teleology and functions in biology. More precisely, it focuses on the scientific legitimacy of teleofunctional attributions and explanations in biology. It belongs to a multi-faceted debate that can be traced back to at least the 1970s. One aspect of the debate concerns the naturalization of functions. Most authors try to reduce, translate or explain functions and teleology in terms of efficient causes so that they find their place in the framework of the natural sciences. Our approach (...) here is radically different, as we question the premise that teleological explanations are disguised causal explanations. On the contrary, we defend that they are acceptable in natural sciences and in biology in particular. We challenge the idea that teleological explanations are immature causal explanations, as well as the idea that teleology and functions are some sort of intentional explanations. We therefore reject the accusations of anthropomorphism, vitalism and finalism. On the contrary, we defend that teleology, causality and intentionality correspond to different, autonomous and complementary modes of representation of the outside world. -/- ———[FRANÇAIS]——— -/- Ce travail de thèse porte sur la téléologie et les fonctions en biologie. Plus précisément, il porte sur la légitimité scientifique des attributions et des explications téléofonctionnelles en biologie. Il s’inscrit dans le cadre d’un débat à plusieurs facettes que l’on peut faire remonter au moins jusqu’aux années 1970 et qui est encore très actif aujourd’hui. L’un des aspects du débat porte sur la naturalisation des fonctions, c’est-à-dire sur la manière de les réduire, de les traduire ou de les expliciter en termes de causes efficientes de sorte qu’elles trouvent leur place dans le cadre des sciences de la nature. Notre approche ici est radicalement différente, car nous remettons en question la prémisse selon laquelle les explications téléologiques seraient des explications causales déguisées. Nous défendons au contraire qu’elles sont acceptables en tant que telles aussi bien de façon générale que dans le domaine scientifique et en particulier en biologie. De façon générale, nous remettons en question l’idée selon laquelle la pensée téléologique serait une pensée causale immature, ainsi que sa dépendance présumée vis-à-vis de la psychologie, c’est-à-dire de l’intentionnalité. Nous rejetons donc les accusations d’anthropomorphisme, de vitalisme et de finalisme formulées contre elle. Nous défendons au contraire que la téléologie, la causalité et l’intentionnalité correspondent à des modes différents, autonomes et complémentaires de représentation du monde extérieur. (shrink)

This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...) that it exemplifies a weak of form of explanatory unification. (shrink)

Resumen -/- El objetivo de este trabajo consiste en analizar las relaciones entre los modelos de optimalidad y la selección natural. Defenderemos que esas relaciones pueden dividirse en dos tipos, en tanto hay dos tipos de explicaciones seleccionistas, que llamaremos “históricas” y “ahistóricas”. Las explicaciones históricas revelan como una población dada adquiere un rasgo que es adaptativo en ese ambiente e involucran muchas generaciones, variación, etc. Las explicaciones ahistóricas, explican por qué, en determinado momento, ciertos tipos de organismos tienen un (...) mayor éxito reproductivo que otros. Mostraremos que los modelos de optimalidad pueden jugar un rol en la determinación del explanandum de las explicaciones histórica seleccionistas, esto es, que ayudan a reconocer qué rasgos son adaptativos. Por otra parte, mostramos que los modelos de optimalidad nos permiten determinar a veces la parte del explanans de las explicaciones ahistóricas (particularmente, el concepto de fitness). -/- Abstract -/- The goal of this paper is to analyze the relations between optimality models and natural selection. We contend that these relationships can be divided into two kinds, as there are two kinds of natural selection explanations, which we call “historical” and “ahistorical”. Historical explanations reveal how a given population acquires a trait which is adaptive in its environment, and involves many generations, variations, etc. Ahistorical ones, explain why, at a given moment, certain kinds of organisms have a greater reproductive success than others. We show that optimality models can play a role in determining the explanandum of historical selectionist explanations, that is, they help us to recognize which traits are adaptive. And, on the other hand, that optimality models sometimes allow us to determine part of the explanans of ahistorical explanations (particularly, the concept of fitness). (shrink)

It has commonly been argued that certain types of mental descriptions, specifically those characterized in terms of propositional attitudes, are part of a folk psychological understanding of the mind. Recently, however, it has also been argued that this is the case even when such descriptions are employed as part of scientific theories in domains like social psychology and comparative psychology. In this paper, I argue that there is no plausible way to understand the distinction between folk and scientific psychology that (...) can support such claims. Moreover, these sorts of claims can have adverse consequences for the neuroscientific study of the brain by downplaying the value of many psychological theories that provide information neuroscientists need in order to build and test neurological models. (shrink)

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

Recent philosophy of science has witnessed a shift in focus, in that significantly more consideration is given to how scientists employ models. Attending to the role of models in scientific practice leads to new questions about the representational roles of models, the purpose of idealizations, why multiple models are used for the same phenomenon, and many more besides. In this paper, I suggest that these themes resonate with central topics in feminist epistemology, in particular prominent versions of feminist empiricism, and (...) that model-based science and feminist epistemology each has crucial resources to offer the other's project. (shrink)

In evolutionary biology, a trait is said to be optimal if it maximizes the fitness of the organism, that is, if the trait allows the organism to survive and reproduce better than any other competing trait would. In engineering, a design is said to be optimal if it complies with its functional requirements as well as possible. Cognitive science is both a biological and engineering discipline and hence it uses both notions of optimality. Unfortunately, the lack of a clear methodological (...) stance on this tissue has made it common for researchers to conflate these two kinds of optimality. In this paper, I argue that a strict distinction must kept in order to avoid inaccurate assumptions. (shrink)

In this paper I distinguish various ways in which empirical claims about evolutionary and ecological models can be supported by data. I describe three basic factors bearing on confirmation of empirical claims: fit of the model to data; independent testing of various aspects of the model, and variety of evident. A brief description of the kinds of confirmation is followed by examples of each kind, drawn from a range of evolutionary and ecological theories. I conclude that the greater complexity and (...) precision of my approach, as compared to, for instance, a Popperian approach, can facilitate detailed analysis and comparison of empirical claims. (shrink)

Accounts of the relation between theories and models in biology concentrate on mathematical models. In this paper I consider the dual role of models as representations of natural systems and as a material basis for theorizing. In order to explicate the dual role, I develop the concept of a remnant model, a material entity made from parts of the natural system(s) under study. I present a case study of an important but neglected naturalist, Joseph Grinnell, to illustrate the extent to (...) which mundane practices in a museum setting constitute theorizing. I speculate that historical and sociological analyses of institutions can play a specific role in the philosophical analysis of model-building strategies. (shrink)

Within evolutionary biology a distinction is frequently made between proximate and ultimate causes. One apparently plausible interpretation of this dichotomy is that proximate causes concern processes occurring during the life of an organism while ultimate causes refer to those processes (particularly natural selection) that shaped its genome. But ultimate causes are not sought through historical investigations of an organisms lineage. Rather, explanations referring to ultimate causes typically emerge from functional analyses. But these functional analyses do not identify causes of any (...) kind, much less ultimate ones. So-called ultimate explanations are not about causes in any sense resembling those of proximate explanations. The attitude, implicit in the term ultimate cause, that these functional analyses are somehow superordinate to those involving proximate causes is unfounded. Ultimate causes are neither ultimate nor causes. (shrink)

Paul Thompson, John Beatty, and Elisabeth Lloyd argue that attempts to resolve certain conceptual issues within evolutionary biology have failed because of a general adherence to the received view of scientific theories. They maintain that such issues can be clarified and resolved when one adopts a semantic approach to theories. In this paper, I argue that such conceptual issues are just as problematic on a semantic approach. Such issues arise from the complexity involved in providing formal accounts of theoretical laws (...) and scientific explanations. That complexity is due to empirical and pragmatic considerations, not one's adherence to a particular formal approach to theories. This analysis raises a broader question. How can any formal account properly represent the complex nature of empirical phenomena? (shrink)

A precise formulation of the structure of modern evolutionary theory has proved elusive. In this paper, I introduce and develop a formal approach to the structure of population genetics, evolutionary theory's most developed sub-theory. Under the semantic approach, used as a framework in this paper, presenting a theory consists in presenting a related family of models. I offer general guidelines and examples for the classification of population genetics models; the defining features of the models are taken to be their state (...) spaces, parameters, and laws. The suggestions regarding the various aspects of the characterization of population genetics models provide an outline for further detailed research. (shrink)

The conflation of two fundamentally distinct issues has generated serious confusion in the philosophical and biological literature concerning the units of selection. The question of how a unit of selection of defined, theoretically, is rarely distinguished from the question of how to determine the empirical accuracy of claims--either specific or general--concerning which unit(s) is undergoing selection processes. In this paper, I begin by refining a definition of the unit of selection, first presented in the philosophical literature by William Wimsatt, which (...) is grounded in the structure of natural selection models. I then explore the implications of this structural definition for empirical evaluation of claims about units of selection. I consider criticisms of this view presented by Elliott Sober--criticisms taken by some (for example, Mayo and Gilinsky 1987) to provide definitive damage to the structuralist account. I shall show that Sober has misinterpreted the structuralist views; he knocks down a straw man in order to motivate his own causal account. Furthermore, I shall argue, Sober's causal account is dependent on the structuralist account that he rejects. I conclude by indicating how the refined structural definition can clarify which sorts of empirical evidence could be brought to bear on a controversial case involving units of selection. (shrink)

Ethologists and others studying animal behavior in a spirit are in need of a descriptive language and method that are neither anachronistically bound by behaviorist scruples nor prematurely committed to particular Just such an interim descriptive method can be found in intentional system theory. The use of intentional system theory is illustrated with the case of the apparently communicative behavior of vervet monkeys. A way of using the theory to generate data - including usable, testable data - is sketched. The (...) underlying assumptions of this approach can be seen to ally it directly with theorizing in evolutionary biology, which has recently come under attack from Stephen Gould and Richard Lewontin, who castigate it as the Their arguments, which are strongly analogous to B. F, Skinner's arguments against point to certain pitfalls that attend the careless exercise of such thinking (and rival varieties of thinking as well), but do not constitute a fundamental objection to either adaptationist theorizing or its cousin, intentional system theory. (shrink)

Stuart Kauffman’s forthcoming book, The Origins of Order: Self Organization and Selection in Evolution (1991), is a large and ambitious attempt to bring about a major reorientation in theoretical biology and to provide a fundamental reinterpretation of the place of selection in evolutionary theory. Kauffman offers a formal framework which allows one to pose precise and well-defined questions about the constraints that self-organization imposes on the evolution of complex systems, and the relation of self-organization and selection. He says at the (...) outset that he wants to “delineate the spontaneous sources of order, the self organized properties of simple and complex systems” and to understand how they “permit, enable and limit the efficacy of natural selection” (Introduction, p. 2).2 As he says somewhat later, the central theme running through his book is that “the order in organisms may largely reflect spontaneous order in complex systems” (ch. 6, p. 224). (shrink)

The semantic view of theories is normally considered to be an ac-count of theories congenial to Scientific Realism. Recently, it has been argued that Ontic Structural Realism could be fruitfully applied, in combination with the semantic view, to some of the philosophical issues peculiarly related to bi-ology. Given the central role that models have in the semantic view, and the relevance that mathematics has in the definition of the concept of model, the fo-cus will be on population genetics, which is (...) one of the most mathematized areas in biology. We will analyse some of the difficulties which arise when trying to use Ontic Structural Realism to account for evolutionary biology. (shrink)

In what follows, I argue that the semantic approach to scientific theories fails as a means to present the Wright—Fisher formalism (WFF) of population genetics. I offer an account of what population geneticist understand insofar as they understand the WFF, a variation on Lloyd's view that population genetics can be understood as a family of models of mid-level generality.

The supervenience and multiple realizability of biological properties have been invoked to support a disunified picture of the biological sciences. I argue that supervenience does not capture the relation between fitness and an organism's physical properties. The actual relation is one of causal dependence and is, therefore, amenable to causal explanation. A case from optimality theory is presented and interpreted as a microreductive explanation of fitness difference. Such microreductions can have considerable scope. Implications are discussed for reductive physicalism in evolutionary (...) biology and for the unity of science. (shrink)

No response that was not as long and intricate as the two commentaries combined could do justice to their details, so what follows will satisfy nobody, myself included. I will concentrate on one issue discussed by both commentators: the relationship between evolution and teleological (or intentional) explanation. My response, in its brevity, may have just one virtue: it will confirm some of the hunches (or should I say suspicions) that these and other writers have entertained about my views. For more (...) closely argued defenses of my points, see Dennett 1990a,b,c; 1991a,b. (shrink)

The conflation of two fundamentally distinct issues has generated serious confusion in the philosophical and biological literature concerning the units of selection. The questions of how a unit of selection is defined, theoretically, is rarely distinguished from the question of how to determine the empirical accuracy of claims--either specific or general--concerning which unit(s) are undergoing selection processes. In this paper, I begin by refining a definition of the unit of selection, first presented by William Wimsatt, that is grounded in the (...) structure of natural selection models. I then explore the implications of this definition for empirical evaluation of group selection models. I examine an objection to Wimsatt’s definition raised by Elliott Sober, and I conclude by indicating how the proposed refined definition can clarify which sorts of empirical evidence could be brought to bear on group selection controversies. (shrink)

The aim of this article is to discuss and develop the diagnose of the Hardy-Weinberg law made by van Fraassen (1987, p. 110), according to which: 1) that law cannot be considered a law used as an axiom for the classical population genetics as a whole, since it is an equilibrium-law that holds only under certain special conditions; 2) it just determines a subclass of models; 3) its generalization shades off into logical vacuity; and 4) more complex variants of the (...) law can be deduced for more realistic assumptions. The discussion and development of such a diagnose will be carried out with the notions of another semantic conceptions of theories, related to that of van Fraassen, namely, the structuralist view of theories, and a rational reconstruction of classical population genetics made within the framework of such a metatheory, also presented in this paper. (shrink)

In a recent paper, Potochnik (Biol Philos 24(2):183–197, 2009) analyses some uses of optimality modelling in light of the anti-adaptationism criticism. She distinguishes two broad classes of such uses (weak and strong) on the basis of assumptions held by biologists about the role and the importance of natural selection. This is an interesting proposal that could help in the epistemological characterisation of some biological practices. However, Potochnik’s distinction also rests on the assumption that all optimality modelling represent the selection dynamic (...) involved in the system of phenomena being considered. Since this assumption does not hold for models belonging to optimal foraging theory (OFT)—one of behavioural ecology’s important modelling traditions—Potochnik’s proposal has to be critically reappraised. In this paper, we briefly discuss what is optimality modelling and what it means for a model to represent a dynamic of selection or of evolution. Then, we demonstrate that OFT modelling is unable to represent either past or contemporary selection dynamics. In order to make this point, we carefully delineate the theory’s rationale. This allows us to identify and analyse the assumptions on which the theory is built, and to circumscribe precisely the role that natural selection plays in it. Next, we show that the distinction of weak and strong uses of optimality modelling is seriously weakened when OFT modelling is taken into account. More precisely, the distinction is either irrelevant (if the assumption that selection dynamics are represented in all optimality modelling is held) or of a modest utility (if the assumption is dropped). However, we suggest that Potochnik’s original proposal could be saved, and that it even constitutes a tool to appraise the marks left in the literature by the evolution of optimality modelling practices in the last four decades, provided that it is made into a tripartite distinction. (shrink)

In these notes, unadorned page numbers under 350 refer to Dennett (1987) - The Intentional Stance, hereafter referred to as Stance - and ones over 495 refer to Dennett (1988) - mostly to material by him but occasionally to remarks of his critics. Since the notes will focus on disagreements, I should say now that I am in Dennett’s camp and am deeply in debt to his work in the philosophy of mind, which I think is wider, deeper, more various (...) and more fruitful than mine or anyone else’s. Still, I have some ideas and emphases that I think he could profit from. In the final chapter of Stance Dennett compares his work with that of several others, including me. He sees me as having a position like his, the main difference being that I think (as he doesn’t) that our attributions of mental content can always be highly determinate (pp. 347f). In fact, there are differences between us but this isn’t one of them. I want to get this straight, so as to clear the decks for the positive points I am going to make. There is some indeterminacy and there could be lots of it; Dennett’s case for that is unanswerable. As for how much there actually is: I don’t know and don’t even suspect; there is simply no declared issue between Dennett and myself on that. Nor do we disagree on a related matter. If there is no evidence that settles whether the animal believes that P or believes that Q, should we say that nevertheless one of these is right, and it’s just that we can’t know which it is? Dennett says No. I perfectly agree. (shrink)

The rights and wrongs of adaptationism areoften discussed by appeal to what I call theartefact model. Anti-adaptationistscomplain that the use of optimality modelling,reverse engineering and other techniques areindicative of a mistaken and outmoded beliefthat organisms are like well-designedartefacts. Adaptationists (e.g. Dennett 1995)respond with the assertion that viewingorganisms as though they were well designed isa fruitful, perhaps necessary research strategyin evolutionary biology. Anti-adaptationistsare right when they say that techniques likereverse engineering are liable to mislead. This fact does not undermine the artefact (...) modelprecisely because the same techniques misleadus for the same reasons when they are appliedunreflectively to artefacts. Thoseadaptationists who hold only that it isworthwhile to investigate organisms as thoughthey were artefacts and thoseanti-adaptationists who criticise simplisticdesign models have far more in common than thelabels attached to their positions mightsuggest. (shrink)

This paper argues against the view that the standard explanation of phase transitions in statistical mechanics may be considered a causal explanation, a distortion that can nevertheless successfully represent causal relations.

This work consists of two parts. Part I will be a contribution to a philo- sophical discussion of the nature of causal explanation. It will present my contrastive counterfactual theory of causal explanation and show how it can be used to deal with a number of problems facing theories of causal explanation. Part II is a contribution to a discussion of the na- ture of interest explanation in social studies of science. The aim is to help to resolve some controversies (...) concerning interest explanation by explicating the concept of interest and its explanatory uses by using the account of explanation developed in Part I. (shrink)

Darwin’s claim about natural selection is reconstructed as an empirical claim about a causal connection leading from the match of the physiology of an individual and its environment to leaving surviving progeny. Variations in this match, Darwin claims, cause differences in the survival of the progeny. Modern concepts of fitness focus the survival side of this chain. Therefore, the assumption that evolutionary theory wants to explain reproductive success in terms of a modern concept of fitness has given rise to the (...) so-called tautology problem. It is shown that the tautology problem reappears in the treatment of fitness proxies in today’s experimental evolutionary biology when these proxies are considered to indicate fitness only. Taking Darwin’s empirical claim seriously suggests, by contrast, that fitness proxies are first of all measures of the match between organism and environment, which I call the organism’s ‘fittedness’. At the same time, they are indeed related to reproductive success. Thus looking in both directions, at fitness and at fittedness, they are janiform. Acknowledging this situation not only allows for rejection of the tautology objection, but also for integration of Darwin’s argument into current evolutionary biology. It is suggested that this helps reframe and alleviate the dispute between the Modern Synthesis and the Extended Evolutionary Synthesis. (shrink)

In this essay, I first consider a popular view of models and modeling, the similarity view. Second, I contend that arguments for it fail and it suffers from what I call “Hughes’ worry.” Third, I offer a deflationary approach to models and modeling that avoids Hughes’ worry and shows how scientific representations are of apiece with other types of representations. Finally, I consider an objection that the similarity view can deal with approximations better than the deflationary view and show that (...) this is not so. (shrink)