According to the "confrontation model," integrated history and philosophy of science operates like an empirical science. It tests philosophical accounts of science against historical case studies much like other sciences test theory against data. However, the confrontation model's critics object that historical facts can neither support generalizations nor genuinely test philosophical theories. Here I argue that most of the model's defects trace to its usual framing in terms of two problematic accounts of empirical inference: the hypothetico-deductive method and enumerative induction. (...) This framing can be taken to suggest an unprofitable one-off confrontation between particular historical facts and general philosophical theories. I outline more recent accounts of empirical inquiry, which describe an iterative back-and-forth movement between concrete empirical exemplars to their abstract descriptions. Reframed along similar lines, the confrontation model continues to offer both conceptual insight and practical guidance for a naturalized philosophy of science. (shrink)

Philosophers use historical case studies to support wide-ranging claims about science. This practice is often criticized as problematic. In this paper we suggest that the function of case studies can be understood and justified by analogy to a well-established practice in biology: the investigation of model organisms. We argue that inferences based on case studies are no more problematic than inferences from model organisms to larger classes of organisms in biology. We demonstrate our view in detail by reference to a (...) case study with a long history: Semmelweis’s discovery of the cause of childbed fever. (shrink)

Aristotle’s influence on D’Arcy Thompson was praised by Thompson himself and has been recognized by others in various respects, including the aesthetic and normative dimensions of biology, and the multicausal explanation of living forms. This article focuses on the relatedness of organic forms, one of the core problems addressed by both Aristotle’s History of Animals (HA), and the renowned chapter of Thompson’s On Growth and Form (G&F), “On the Theory of Transformations, or the Comparison of Related Forms.” We contend that, (...) far from being an incidental inspiration stemming from Thompson’s classicist background, his translation of HA played a pivotal role in developing his theory of transformations. Furthermore, we argue that Thompson’s interpretation of the Aristotelian method of comparison challenges the prevailing view of Aristotle as the founder of “typological essentialism,” and is a key episode in the revision of this narrative. Thompson understood that the method Aristotle used in HA to compare animal forms is better comprehended as a “method of transformations,” leading to a morphological arrangement of animal diversity, as opposed to a taxonomical classification. Finally, we examine how this approach to the relatedness of forms lay the foundation for a causal understanding of parts and their interconnections. Although Aristotle and Thompson emphasized distinct types of causes, we contend that they both differ in a fundamental sense from the one introduced by Darwin’s theory of natural selection, which was formulated as a solution to the species problem rather than the form problem. We conclude that Thompson’s interpretation of Aristotle’s approach to form comparison has not only impacted contemporary scholarship on Aristotle’s biology, but revitalized a perspective that has regained significance due to the resurgence of the problem of form in evo-devo. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

One foundational question in contemporarybiology is how to `rejoin evolution anddevelopment. The emerging research program(evolutionary developmental biology or`evo-devo) requires a meshing of disciplines,concepts, and explanations that have beendeveloped largely in independence over the pastcentury. In the attempt to comprehend thepresent separation between evolution anddevelopment much attention has been paid to thesplit between genetics and embryology in theearly part of the 20th century with itscodification in the exclusion of embryologyfrom the Modern Synthesis. This encourages acharacterization of evolutionary developmentalbiology as the marriage (...) of evolutionary theoryand embryology via developmental genetics. Butthere remains a largely untold story about thesignificance of morphology and comparativeanatomy (also minimized in the ModernSynthesis). Functional and evolutionarymorphology are critical for understanding thedevelopment of a concept central toevolutionary developmental biology,evolutionary innovation. Highlighting thediscipline of morphology and the concepts ofinnovation and novelty provides an alternativeway of conceptualizing the `evo and the `devoto be synthesized. (shrink)

The relationship of man himself to his environment is an inseparable part of ecology; for he also is an organism and other organisms are a part of his environment. Ecology, therefore, broadly conceived and rightly understood, instead of being an academic science merely, out of touch with humanistic interests, is really that part of every other biological science which brings it into immediate relation to human kind. The proper place of humans in ecological study has been a recurring issue for (...) ecology. Of course humans are part of Nature writ large, but are they part of the ecologist's nature? The question bothered biologists even before the discipline of ecology was firmly institutionalized.... (shrink)

The purpose of this paper is to defend, contra Fodor and Piattelli-Palmarini (F&PP), that the theory of natural selection (NS) is a perfectly bona fide empirical unified explanatory theory. F&PP claim there is nothing non-truistic, counterfactual-supporting, of an “adaptive” character and common to different explanations of trait evolution. In his debate with Fodor, and in other works, Sober defends NS but claims that, compared with classical mechanics (CM) and other standard theories, NS is peculiar in that its explanatory models are (...) a priori (a trait shared with few other theories). We argue that NS provides perfectly bona fide adaptive explanations of phenotype evolution, unified by a common natural-selection guiding principle. First, we introduce the debate and reply to F&PP’s main argument against NS. Then, by reviewing different examples and analyzing Fisher’s model in detail, we show that NS explanations of phenotypic evolution share a General Natural Selection Principle. Third, by elaborating an analogy with CM, we argue against F&PP’s claim that such a principle would be a mere truism and thus explanatorily useless, and against Sober’s thesis that NS models/explanations have a priori components that are not present in CM and other common empirical theories. Irrespective of differences in other respects, the NS guiding principle has the same epistemic status as other guiding principles in other highly unified theories such as CM. We argue that only by pointing to the guiding principle-driven nature that it shares with CM and other highly unified theories, something no-one has done yet in this debate, one can definitively show that NS is not defective in F&PP’s sense: in the respects relevant to the debate, Natural Selection is as defective and as epistemically peculiar as Classical Mechanics and other never questioned theories. (shrink)

. Philosophers and scientists often cite ontic factors when explaining the methods and success of scientific inquiry. That is, the adoption of a method or approach is explained in reference to the kind of system in which the scientist is interested: these are explanations of why scientists do what they do, that appeal to properties of their target systems. We present a framework for understanding such “Opticks to his Principia. Newton’s optical work is largely experiment-driven, while the Principia is primarily (...) mathematical, so usually, each work is taken to exemplify a different kind of science. However, Newton himself often presented them in terms of a largely consistent method. We use our framework to articulate an original and plausible position: that the differences between the Opticks and the Principia are due to the kinds of systems targeted. That is, we provide an ontic-driven explanation of methodological differences. We suspect that ontic factors should have a more prominent role in historical explanations of scientific method and development. (shrink)

The past can be a stubborn subject: it is complex, heterogeneous and opaque. To understand it, one must decide which aspects of the past to emphasise and which to minimise. Enter frameworks. Frameworks foreground certain aspects of the historical record while backgrounding others. As such, they are both necessary for, and conducive to, good history as well as good philosophy. We examine the role of frameworks in the history and philosophy of science and argue that they are necessary for both (...) forms of enquiry. We then suggest that the right attitude towards frameworks is pluralism rather than monism: there is no single correct framework to be applied to a given scientific episode. Rather, a multitude of different frameworks are more or less appropriate given various contexts and aims. From this perspective, good frameworks generate and further, rather than frustrate, historical and philosophical enquiry. Our view sheds light on historical disagreement, and on the relationship between philosophy and history of science. (shrink)

This article unpacks a particular use of ‘cases’ within developmental biology, namely as a means of describing the typical or canonical patterns of phenomena. The article explores how certain cases have come to be established within the field and argues that although they were initially selected for reasons of convenience or ease of experimental manipulation, these cases come to serve as key reference points within the field because of the epistemological structures imposed on them by the scientists using them and, (...) hence, become usable in a wider variety of circumstances including future theory development. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)