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)

The niche has been central to ecology for most of the discipline’s history, yet there have been few attempts by philosophers to work out the ontology of the niche. A challenge is that there is a plurality of seemingly inconsistent definitions of the niche in ecology. This paper characterizes the population-level ecological niche by distinguishing among niche concepts, niche models, and the niche as a phenomenon. I argue that 'niche concepts' should be interpreted as theoretical frameworks or modelling strategies. I (...) also argue that there is a unified niche phenomenon underlying the seemingly heterogeneous models and definitions. The plurality of niche concepts in ecology should be seen as an expected consequence of the nature of modelling complex systems. (shrink)

Susan Mills and John Beatty proposed a propensity interpretation of fitness (1979) to show that Darwinian explanations are not circular, but they did not address the critics' chief complaint that the principle of the survival of the fittest is either tautological or untestable. I show that the propensity interpretation cannot rescue the principle from the critics' charges. The critics, however, incorrectly assume that there is nothing more to Darwin's theory than the survival of the fittest. While Darwinians all scoff at (...) this assumption, they do not agree about what role, if any, this principle plays in Darwin's theory of natural selection. I argue that the principle has no place in Darwin's theory. His theory does include the idea that some organisms are fitter than others. But greater reproductive success is simply inferred from higher fitness. There is no reason to embody this inference in the form of a special principle of the survival of the fittest. (shrink)

In this paper I propose to examine, and in part revive, a time-honoured perspective to inquiry in general and scientific explanation in particular. The perspective is to view inquiry as a search for answers to questions. If there is anything that deserves to be called a working scientist's view of his or her daily work, it surely is that he or she phrases questions and attempts to find satisfactory answers to them.

Cancer is not one, but many diseases, and each is a product of a variety of causes acting (and interacting) at distinct temporal and spatial scales, or “levels” in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the (...) history of the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with “integrative” research. (shrink)

Cancer is not one, but many diseases, and each is a product of a variety of causes acting at distinct temporal and spatial scales, or ‘‘levels’’ in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of (...) the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with ‘‘integrative’’ research. (shrink)

According to standard accounts of mathematical representations of physical phenomena, positing structure-preserving mappings between a physical target system and the structure picked out by a mathematical theory is essential to such representations. In this paper, I argue that these accounts fail to give a satisfactory explanation of scientific representations that make use of inconsistent mathematical theories and present an alternative, robustly inferential account of mathematical representation that provides not just a better explanation of applications of inconsistent mathematics, but also a (...) compelling explanation of mathematical representations of physical phenomena in general. 1Inconsistent Mathematics and the Problem of Representation2The Early Calculus3Mapping Accounts and the Early Calculus3.1Partial structures3.2Inconsistent structures3.3Related total consistent structures4A Robustly Inferential Account of the Early Calculus in Applications 4.1The robustly inferential conception of mathematical representation4.2The robustly inferential conception and inconsistent mathematics4.3The robustly inferential conception and mapping accounts5Beyond Inconsistent Mathematics. (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)

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)

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)

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)

We develop an account of laboratory models, which have been central to the group selection controversy. We compare arguments for group selection in nature with Darwin's arguments for natural selection to argue that laboratory models provide important grounds for causal claims about selection. Biologists get information about causes and cause-effect relationships in the laboratory because of the special role their own causal agency plays there. They can also get information about patterns of effects and antecedent conditions in nature. But to (...) argue that some cause is actually responsible in nature, they require an inference from knowledge of causes in the laboratory context and of effects in the natural context. This process, cause detection, forms the core of an analogical argument for group selection. We discuss the differing roles of mathematical and laboratory models in constructing selective explanations at the group level and apply our discussion to the units of selection controversy to distinguish between the related problems of cause determination and evaluation of evidence. Because laboratory models are at the intersection of the two problems, their study is crucial for framing a coherent theory of explanation 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.

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)

Selection type theories solve adaptation problems. Natural selection, clonal selection for antibody production, and selective theories of higher brain function are examples. An abstract characterization of typical selection processes is generated by analyzing and extending previous work on the nature of natural selection. Once constructed, this abstraction provides a useful tool for analyzing the nature of other selection theories and may be of use in new instances of theory construction. This suggests the potential fruitfulness of research to find other theory (...) types and construct their abstractions. (shrink)

Sustained controversy over a philosophical issue is often times symptomatic of differing commitments at a more fundamental philosophical level. I will argue that two current debates over the foundations of the theory of natural selection are cases in point. Alexander Rosenberg, at times together with Mary Williams, challenges what is becoming received orthodoxy about the foundations of this theory. He argues that the currently popular propensity interpretation of fitness does not legitimize explanations in terms of natural selection, and that furthermore, (...) the biological fields which typically study the ways in which selection pressures originate in the organism/environment complex are not in fact part of the theory of natural selection at all. His foils in the first case are Robert Brandon, John Beatty and Susan Mills;2 on the second issue he is engaged in debate with Elliott Sober.3 We will see that, although the controversies are ostensibly about the interpretation of fitness, the issues, at bottom, involve the nature of scientific explanation. (shrink)

This paper argues for the theoretical and practical validity of similarity as a useful epistemological tool in scientific knowledge generation, specifically in chemistry. Classical analyses of similarity in philosophy of science do not account for the concept’s practical significance in scientific activities. We recur to examples from chemistry to counter the claim of authors like Quine or Goodman to the effect that similarity must be excluded from scientific practices . In conclusion we argue that more recent conceptualizations of the notion (...) of similarity, particularly Giere’s one, are appropriate for a philosophical analysis that considers scientific practices on equal terms with scientific theory. (shrink)

Science provides us with representations of atoms, elementary particles, polymers, populations, genetic trees, economies, rational decisions, aeroplanes, earthquakes, forest fires, irrigation systems, and the world’s climate. It's through these representations that we learn about the world. This entry explores various different accounts of scientific representation, with a particular focus on how scientific models represent their target systems. As philosophers of science are increasingly acknowledging the importance, if not the primacy, of scientific models as representational units of science, it's important to (...) stress that how they represent plays a fundamental role in how we are to answer other questions in the philosophy of science. This entry begins by disentangling ‘the’ problem of scientific representation, before critically evaluating the current options available in the literature. (shrink)

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)

The concept of natural kind is center stage in the debates about scientific realism. Champions of scientific realism such as Richard Boyd hold that our most developed scientific theories allow us to “cut the world at its joints” (Boyd, 1981, 1984, 1991). In the long run we can disclose natural kinds as nature made them, though as science progresses improvements in theory allow us to revise the extension of natural kind terms.

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)

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)