Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...) of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

This essay examines the origin of genotype-environment interaction, or G×E. "Origin" and not "the origin" because the thesis is that there were actually two distinct concepts of G×E at this beginning: a biometric concept, or \[G \times E_B\], and a developmental concept, or \[G \times E_D \]. R. A. Fisher, one of the founders of population genetics and the creator of the statistical analysis of variance, introduced the biometric concept as he attempted to resolve one of the main problems in (...) the biometric tradition of biology - partitioning the relative contributions of nature and nurture responsible for variation in a population. Lancelot Hogben, an experimental embryologist and also a statistician, introduced the developmental concept as he attempted to resolve one of the main problems in the developmental tradition of biology - determining the role that developmental relationships between genotype and environment played in the generation of variation. To argue for this thesis, I outline Fisher and Hogben's separate routes to their respective concepts of G × E; then these separate interpretations of G × E are drawn on to explicate a debate between Fisher and Hogben over the importance of G × E, the first installment of a persistent controversy. Finally, Fisher's \[G \times E_B\] and Hogben's \[G \times E_D \] are traced beyond their own work into mid-2Oth century population and developmental genetics, and then into the infamous IQ Controversy of the 1970s. (shrink)

This article is a systematic critical survey of work done in the philosophy of biology within the logical empiricist tradition, beginning in the 1930s and until the end of the 1950s. It challenges a popular view that the logical empiricists either ignored biology altogether or produced analyses of little value. The earliest work on the philosophy of biology within the logical empiricist corpus was that of Philipp Frank, Ludwig von Bertalanffy, and Felix Mainx. Mainx, in particular, provided a detailed analysis (...) of biology in the 1930s and 1940s in his contribution to the logical empiricists’ Encyclopedia of Unified Science. However, the most important contributions to the philosophy of biology were those of Joseph Henry Woodger and Ernest Nagel. Woodger is primarily remembered for deploying the axiomatic method in biology but he also used semiformal methods for the analysis of many biological problems. While Woodger’s axiomatic work was often derided by some later philosophers of biology (e.g., David Hull and Michael Ruse), this article defends both the biological and the philosophical significance of some of that work, for instance, those aspects that led to the recognition of the conceptual complexity of mereology and temporal identity in biological systems. Woodger’s semiformal analyses were even more important, for instance, his explication of the concepts of the Bauplan and of innateness. Nagel’s importance lies in his analyses of reduction and emergence in the context of all empirical sciences and his use of these analyses in a careful exploration of biological problems. While Nagel’s model of reduction was generally rejected by philosophers of science in the 1970s and 1980s, particularly for biological contexts, it has recently been sympathetically reconstructed by many commentators; this article defends its continued relevance for the philosophy of biology. (shrink)

There are two motivations commonly ascribed to historical actors for taking up statistics: to reduce complicated data to a mean value (e.g., Quetelet), and to take account of diversity (e.g., Galton). Different motivations will, it is assumed, lead to different methodological decisions in the practice of the statistical sciences. Karl Pearson and W. F. R. Weldon are generally seen as following directly in Galton’s footsteps. I argue for two related theses in light of this standard interpretation, based on a reading (...) of several sources in which Weldon, independently of Pearson, reflects on his own motivations. First, while Pearson does approach statistics from this "Galtonian" perspective, he is, consistent with his positivist philosophy of science, utilizing statistics to simplify the highly variable data of biology. Weldon, on the other hand, is brought to statistics by a rich empiricism and a desire to preserve the diversity of biological data. Secondly, we have here a counterexample to the claim that divergence in motivation will lead to a corresponding separation in methodology. Pearson and Weldon, despite embracing biometry for different reasons, settled on precisely the same set of statistical tools for the investigation of evolution. (shrink)

This paper provides a philosophical analysis of the ongoing controversy surrounding R.A. Fisher's famous ‘fundamental theorem’ of natural selection. The difference between the ‘traditional’ and ‘modern’ interpretations of the theorem is explained. I argue that proponents of the modern interpretation have captured Fisher's intended meaning correctly and shown that the theorem is mathematically correct, pace the traditional consensus. However, whether the theorem has any real biological significance remains an unresolved issue. I argue that the answer depends on whether we accept (...) Fisher's non-standard notion of environmental change, on which the theorem rests; arguments for and against this notion are explored. I suggest that there is a close link between Fisher's fundamental theorem and the modern ‘gene's eye’ view of evolution. Introduction What Does the Fundamental Theorem Say? Key Concepts Explained Alleged Significance of the FTNS Traditional versus Modern Interpretations of the FTNS The Modern Interpretation Illustrated Fisher's Concept of ‘Environmental Change’ Causality and the Modern Interpretation The Significance of the FTNS Re-considered Appendix CiteULike Connotea Del.icio.us What's this? (shrink)

Researchers often pursue proof of concept research, but criteria for evaluating such research remain poorly specified. This article proposes a general framework for proof of concept research that k...

The relatively new field of evolutionary developmental biology continues to attract considerable attention from biologists, philosophers, and historians, in part, because work in this field demonstrates that important changes are underway within biology. Though studies of development and evolution were closely connected during the 19th century, continued work in genetics fostered a general split between the two during the first decades of the twentieth century (e.g., Allen 1978; Gilbert 1978; Mayr and Provine 1980; Gilbert, Opitz and..

The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms behave as if attempting to maximize their fitness remains widespread. Here I critically appraise the prospects for reconciliation. I first distinguish four varieties of fitness maximization. I then examine two recent developments that may appear to vindicate at least one of these varieties. The first is the ‘new’ interpretation of Fisher's fundamental theorem (...) of natural selection, on which the theorem is exactly true for any evolving population that satisfies some minimal assumptions. The second is the Formal Darwinism project, which forges links between gene frequency change and optimal strategy choice. In both cases, I argue that the results fail to establish a biologically significant maximization principle. I conclude that it may be a mistake to look for universal maximization principles justified by theory alone. A more promising approach may be to find maximization principles that apply conditionally and to show that the conditions were satisfied in the evolution of particular traits. (shrink)

According to conventional wisdom, local gauge symmetry is not a symmetry of nature, but an artifact of how our theories represent nature. But a study of the so-called theta-vacuum appears to refute this view. The ground state of a quantized non-Abelian Yang-Mills gauge theory is characterized by a real-valued, dimensionless parameter theta—a fundamental new constant of nature. The structure of this vacuum state is often said to arise from a degeneracy of the vacuum of the corresponding classical theory, which degeneracy (...) allegedly arises from the fact that “large” (but not “small”) local gauge transformations connect physically distinct states of zero field energy. If that is right, then some local gauge transformations do generate empirical symmetries. In defending conventional wisdom against this challenge I hope to clarify the meaning of empirical symmetry while deepening our understanding of gauge transformations. I distinguish empirical from theoretical symmetries. Using Galileo’s ship and Faraday’s cube as illustrations, I say when an empirical symmetry is implied by a theoretical symmetry. I explain how the theta-vacuum arises, and how “large” gauge transformations differ from “small” ones. I then present two analogies from elementary quantum mechanics. By applying my analysis of the relation between empirical and theoretical symmetries, I show which analogy faithfully portrays the character of the vacuum state of a classical non-Abelian Yang-Mills gauge theory. The upshot is that “large” as well as “small” gauge transformations are purely formal symmetries of non-Abelian Yang-Mills gauge theories, whether classical or quantized. It is still worth distinguishing between these kinds of symmetries. An analysis of gauge within the constrained-Hamiltonian formalism yields the result that “large” gauge transformations should not be classified as gauge transformations; indeed, nor should “global” gauge transformations. In a theory in which boundary conditions are modeled dynamically, “global” gauge transformations may be associated with physical symmetries, corresponding to translations of these extra dynamical variables. Such translations are symmetries if and only if charge is conserved. But it is hard to argue that these symmetries are empirical, and in any case they do not correspond to any constant phase change in a quantum state. (shrink)