This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing characteristic (...) of protein taxonomy. (shrink)

This paper evaluates a general argument for the conclusion that visual representations in science must play the role of truth bearers if they are to figure as legitimate contributors to scientific arguments and explanations. The argument is found to be unsound. An alternative approach to assessing the role of visual representations in science is exemplified by an examination of the role of structural formulas in organic chemistry. Structural formulas are found not to play the role of truth bearers; nonetheless, they (...) contribute to the arguments and explanations of organic chemistry. An early success of conformational analysis is presented in order to illustrate the role of structural formulas in the discourse of organic chemistry. *Received January 2007; revised July 2009. †To contact the author, please write to: Department of Philosophy and Religious Studies, Rowan University, 201 Mullica Hill Road, Glassboro, NJ 08028; e‐mail: [email protected]. (shrink)

This paper characterizes the increase in ‘scientific understanding’ that resulted from the Ingold Revolution in organic chemistry. By describing both the sorts of explanations facilitated by Ingold’s Revolution and the sense in which organic chemistry was ‘unified’ by adopting these approaches to explanation, one can appreciate how this revolution led to a dramatic qualitative improvement in organic chemists’ understanding of the phenomena that they study. The explanatory unification responsible for this transformation in organic chemistry is contrasted with contemporary philosophical accounts (...) of unification and its relationship to both scientific understanding and explanation. (shrink)

Organic chemistry provides fertile ground for scholars interested in understanding the role of non-linguistic representations in scientific thinking. In this discipline, it is not plausible to regard diagrams as simply heuristic aids for expressing or applying what is essentially a linguistic theory. Instead, it is more plausible to think of linguistic representation as supplementing theories whose principal expression is diagrammatic. Among the many sorts of diagrams employed by organic chemists, structural formulas are the most important. In this paper, by examining (...) two central episodes in the development of structural formulas—Kekulé’s proposal of a structure for benzene and Ingold’s explanation of dipole moments in terms of ‘mesomerism’—I investigate how the norms for the production and interpretation of structural formulas evolve in response to experimental results and theoretical developments. I conclude that one principal way in which structural formulas embody the theory of organic chemistry is through these evolving norms. (shrink)

Next SectionOne of the indisputable signs of the progress made in organic chemistry over the last two hundred years is the increased ability of chemists to manipulate, control, and design chemical reactions. The technological expertise manifest in contemporary synthetic organic chemistry is, at least in part, due to developments in the theory of organic chemistry. By appealing to a notable chemist's attempts to articulate and codify the heuristics of synthetic design, this paper investigates how understanding theoretical organic chemistry facilitates progress (...) in synthetic organic chemistry. The picture that emerges of how the applications of organic chemistry are grounded in its theory is contrasted with both standard and some more contemporary philosophical accounts of the applications of science. IntroductionTotal Synthesis as Applied ScienceUnderstanding Organic ChemistryThe Heuristics of Synthetic DesignAn Example: LongifoleneConclusion. (shrink)

Roman Frigg and others have developed a general epistemological argument designed to cast doubt on the capacity of a broad range of mathematical models to generate “decision relevant predictions.” In this article, we lay out the structure of their argument—an argument by analogy—with an eye to identifying points at which certain epistemically significant distinctions might limit the force of the analogy. Finally, some of these epistemically significant distinctions are introduced and defended as relevant to a great many of the predictive (...) mathematical modeling projects employed in contemporary climate science. (shrink)

This article examines a scientific controversy that raged for twenty years in physical organic chemistry during the second half of the twentieth century. After explaining what was at stake in the non-classical ion debate, I attempt—by examining the methodological reflections of some of the participants—a partial explanation of what sustained this controversy, particularly during its early stages. Instead of suggesting a breakdown of scientific method or the unavoidable historical contingency of scientific development, the endurance of this controversy instead reveals the (...) heuristic and pragmatic character of many of the explanations and predictions generated by theoretical organic chemistry. The results in this case are used to suggest a new role for the study of scientific controversies in revealing the economics of scientific inquiry. 1 Introduction2 The Non-classical Ion Debate3 Models for the 2-Norbornyl System4 Soft Theories and Reasoning by Analogy5 Scientific Controversy and the Non-classical Ion Debate6 Conclusion. (shrink)

In this paper I examine the sorts of arguments that motivate skepticism about the predictive powers of global climate models. I contend that these arguments work by contrasting the development and testing of global climate models with an idealized image of science drawn largely from a theologized model of fundamental physics. A richer appreciation of the methodology of a full range of successful empirical predictions—particularly in practical fields that study complex systems––can dispel some of these skeptical worries about climate science. (...) If this is right, the good company into which climate science will have been drawn may help to save it from contemptuous ill-treatment at the hands of a theologized image of physics. (shrink)

In this paper I argue that the appropriate analogy for “understanding what makes simulation results reliable” in global climate modeling is not with scientific experimentation or measurement, but—at least in the case of the use of global climate models for policy development—with the applications of science in applied design problems. The prospects for using this analogy to argue for the quantitative reliability of GCMs are assessed and compared with other potential strategies.

In this paper I argue that the appropriate analogy for “understanding what makes simulation results reliable” in Global Climate Modeling is not with scientific experimentation or measurement, but—at least in the case of the use of global climate models for policy development—with the applications of science in engineering design problems. The prospects for using this analogy to argue for the quantitative reliability of GCMs are assessed and compared with other potential strategies.

This paper adapts Kuhn’s conceptual framework to developmental episodes in the theory and practice of medicine. Previous attempts to understand the reception of Ignaz Semmelweis’s work on puerperal fever in Kuhnian terms are used as a starting point. The author identifies some limitations of these attempts and proposes a new way of understanding the core Kuhnian notions of “paradigm,” “progress,” and “revolution” in the context of a socially embedded technoscience such as medicine.

This article investigates how understanding the theory of organic chemistry facilitates the total synthesis of organic compounds. After locating the philosophical significance of this question within the methodology or epistemology of applied science, I summarize the results of previous work on this issue—roughly that theoretical organic chemistry underwrites a sequence of heuristic policies that help to isolate plausible synthetic routes from the array of possibilities provided by structural or descriptive organic chemistry. While this prior account makes a solid start, it (...) does not capture all of the ways that the theory of organic chemistry contributes to total synthesis. This article aspires to enrich this account by exploring some additional ways that theory contributes. More specifically, I investigate how understanding the theory of organic chemistry can facilitate both the development of novel synthetic reactions and the implementation of a synthetic plan. The role of theory in these aspects of total synthesis will be explored by considering a particular, novel synthesis of longifolene. (shrink)

In this paper, I highlight the importance of models and social structure to Kuhn’s conception of science, and then use these elements to sketch a Kuhnian classification of scientific controversies. I show that several important sorts of non-revolutionary scientific disagreements were both identified and analyzed in Structure. Ultimately, I contend that Kuhn’s conception of science supports an approach to scientific controversies that has the potential to both reveal the importantly different sources of scientific disagreements and to provide useful resources for (...) understanding their endurance and eventual termination. Several brief examples are used to suggest the power of a Kuhnian analysis and this analysis is contrasted with several more contemporary alternatives. (shrink)

In this paper, I highlight the importance of models and social structure to Kuhn’s conception of science, and then use these elements to sketch a Kuhnian classification of scientific controversies. I show that several important sorts of non-revolutionary scientific disagreements were both identified and analyzed in Structure. Ultimately, I contend that Kuhn’s conception of science supports an approach to scientific controversies that has the potential to both reveal the importantly different sources of scientific disagreements and to provide useful resources for (...) understanding their endurance and eventual termination. Several brief examples are used to suggest the power of a Kuhnian analysis and this analysis is contrasted with several more contemporary alternatives. (shrink)

The notion of the "construction" or "exhibition" of a concept in intuition is central to Kant's philosophical account of geometry. Kant invokes this notion in all of his major Critical Era discussions of mathematics. The most extended discussion of mathematics, and geometry more specifically, occurs in "The Discipline of Pure Reason in its Dogmatic Employment." In this later section of the Critique, Kant makes it clear that construction-in-intuition is central to his philosophy of mathematics by presenting it as the defining (...) characteristic of mathematical knowledge. He claims: [M]athematical knowledge is the knowledge gained by reason from the construction of concepts. To construct a concept means to exhibit a... (shrink)

In this essay I consider, by way of the reflections of accomplished synthetic chemists, how the experimental work of the synthetic organic chemist supports the testing, refinement, and creation of theories of organic chemistry. The role of experiments in modern Baconian sciences like organic chemistry is contrasted with their role in fields of more traditional philosophical concern, such as experimental physics.

Understanding what is distinctive about the role of models in science requires characterizing broad patterns in how these models evolve in the face of experimental results. That is, we must examine not just model statics—how the model relates to theory, or represents the world, at some point in time—but also model dynamics—how the model both generates new experimental results and is modified in response to them. Visual representations of structure play a central role in the theoretical reasoning of organic chemists. (...) Not surprisingly, these representations have changed in important ways–in response to experimental and theoretical developments– throughout the history of organic chemistry. In many cases it is appropriate to understand the visual representations used by organic chemists as models. The evolution of the structural representations of organic chemists therefore provides a clear example of the dynamics of scientific modeling. In this paper I use a conception of scientific modeling drawn from the work of Mary Hesse to examine how the concept of a molecular conformation was incorporated into the visual representations of structure used by organic chemists. (shrink)

In this essay I consider whether the theory of organic chemistry is reducible to the theory of quantum chemistry. Using philosophical machinery developed by James Woodward, I characterize the understanding provided by both theories. Then I argue that there are systematic reasons to suspect that quantum chemistry is incapable of supporting some of the significant explanations, predictions, and applications underwritten by an understanding of theoretical organic chemistry. Consequently, even should quantum chemistry be ‘reducible to’ quantum physics in some suitable sense, (...) there are good reasons to doubt that many of the significant results of organic chemistry could be reproduced by quantum chemistry alone. (shrink)

According to Alberto Coffa in The Semantic Tradition from Kant to Carnap, Kant’s account of mathematical judgment is built on a ‘semantic swamp’. Kant’s primitive semantics led him to appeal to pure intuition in an attempt to explain mathematical necessity. The appeal to pure intuition was, on Coffa’s line, a blunder from which philosophy was forced to spend the next 150 years trying to recover. This dismal assessment of Kant’s contributions to the evolution of accounts of mathematical necessity is fundamentally (...) backward-looking. Coffa’s account of how semantic theories of the a priori evolved out of Kant’s doctrine of pure intuition rightly emphasizes those developments, both scientific and philosophical, that collectively served to undermine the plausibility of Kant’s account. What is missing from Coffa’s story, apart from any recognition of Kant’s semantic innovations, is an attempt to appreciate Kant’s philosophical context and the distinctive perspective from which Kant viewed issues in the philosophy of mathematics. When Kant’s perspective and context are brought out, he can not only be seen to have made a genuinely progressive contribution to the development of accounts of mathematical necessity, but also to be relevant to contemporary issues in the philosophy of mathematics in underappreciated ways. (shrink)

According to Alberto Coffa in The Semantic Tradition from Kant to Carnap, Kant’s account of mathematical judgment is built on a ‘semantic swamp’. Kant’s primitive semantics led him to appeal to pure intuition in an attempt to explain mathematical necessity. The appeal to pure intuition was, on Coffa’s line, a blunder from which philosophy was forced to spend the next 150 years trying to recover. This dismal assessment of Kant’s contributions to the evolution of accounts of mathematical necessity is fundamentally (...) backward-looking. Coffa’s account of how semantic theories of the a priori evolved out of Kant’s doctrine of pure intuition rightly emphasizes those developments, both scientific and philosophical, that collectively served to undermine the plausibility of Kant’s account. What is missing from Coffa’s story, apart from any recognition of Kant’s semantic innovations, is an attempt to appreciate Kant’s philosophical context and the distinctive perspective from which Kant viewed issues in the philosophy of mathematics. When Kant’s perspective and context are brought out, he can not only be seen to have made a genuinely progressive contribution to the development of accounts of mathematical necessity, but also to be relevant to contemporary issues in the philosophy of mathematics in underappreciated ways. (shrink)

This paper describes an approach to teaching the philosophy of science to science students that was developed in a context where the course is a lower-level requirement for all natural science majors. This audience made it appropriate to reconsider standard approaches to the field and resulted in an innovative pedagogical strategy subsequently used, in modified form, in more traditional philosophical contexts. This paper describes the pedagogical approach, explains reasons for it, motivates more specific ways of enacting it, and assess its (...) value, not only for science students, but for philosophy majors as well. (shrink)

Organic chemists have been able to develop a robust, theoretical understanding of the phenomena they study; however, the primary theoretical devices employed in this field are not mathematical equations or laws, as is the case in most other physical sciences. Instead it is the diagram, and in particular the structural formula, that carries the explanatory weight in the discipline. To understand how this is so, it is necessary to investigate both the nature of the diagrams employed in organic chemistry and (...) how these diagrams are used in the explanations of the discipline. I will begin this paper by describing and characterizing the roles of the most important sort of diagram used in organic chemistry. Next I will present a model of explanations in organic chemistry and describe how diagrams contribute to these explanations. This will be followed by two examples that will support my abstract account of the role of diagrams in the explanations of organic chemistry. (shrink)

This paper investigates the emergence of conformational analysis in organic chemistry as a case of conceptual change in science. In this case, the mechanism of conceptual change is identified as the emergence of a new exemplar. This new exemplar was made possible because of the identification of a distinctive chemical structure to which ‘foothold’ concepts were applicable. These concepts facilitated both clear explanation in the particular case, and the analogical extension of the conceptual innovation throughout the discipline. The case suggests (...) a cognitive explanation for the importance of exemplars to scientific content. (shrink)

In my dissertation, I argue that contemporary interpretive work on Kant's philosophy of geometry has failed to understand properly the diagrammatic aspects of Euclidean reasoning. Attention to these aspects is amply repaid, not only because it provides substantial insight into the role of intuition in Kant's philosophy of mathematics, but also because it brings out both the force and the limitations of Kant's philosophical account of geometry. ;Kant characterizes the predecessors with which he was engaged as agreeing that mathematical judgments (...) are analytic a priori. This is an inadequate account of geometrical judgments for Kant, because it cannot be reconciled with the evident success of the Euclidean practice in producing a priori knowledge of the nature of space. The ubiquitous presence of diagrams in Euclidean proofs suggests that, at least in Kant's time, any plausible account of the establishment of geometrical judgments must provide for the role of quasi-perceptual representations of individuals. Kant's claim that mathematical judgments are synthetic a priori reflects, in its positive aspect, his recognition of the importance of these 'intuitive' representations to Euclidean reasoning. Furthermore, Kant's doctrine that geometrical knowledge is established by the construction of concepts in intuition can be usefully understood as an attempt to accommodate the role of diagrams in the establishment of synthetic a priori geometrical judgments. ;Both Kant's rejection of the analytic a priori account of mathematics and his positive account of geometry depend on the plausibility of his appeals to Euclidean practice. Attention to the role of diagrams in Euclidean proof supports Kant's contention that intuitive representations are an essential component of Euclidean reasoning; however, the role of diagrams in both reductio proofs and in proofs by cases brings out tensions in Kant's positive account. The use of diagrams to represent impossible geometrical situations in reductio proofs indicates that Kant's notion of 'construction in intuition' can have a broader application than the construction of instances of geometrical concepts . Similarly, proofs by cases undermine Kant's attempts to explain the generality of judgments established through the consideration of individuals by appeal to the rules for the construction of those individuals. ;Contemporary interpretive debates about Kant's philosophy of geometry have centered on the philosophical role played by his appeal to intuition. This appeal cannot be primarily understood as an attempt to establish that the fundamental assumptions of Euclidean geometry are necessary truths about space. Nor can the role for intuition be regarded as merely licensing moves in geometrical proofs like an inference rule in modern logic. Instead, by understanding Kant's appeal to intuition as, at least in part, an attempt to accommodate the diagrammatic features of Euclidean reasoning, a much richer role for intuition is revealed. Intuition is required to play a logical role by expressing spatial relationships and establishing the existence of geometrical entities. In addition, it plays a quasi-perceptual role by supporting the truth of certain claims appealed to during the course of Euclidean proof. (shrink)

In this paper, I characterize Susan Haack’s so called passes-for fallacy, analyze both what makes this inference compelling and why it is illegitimate, and finally explain why reflecting on the passes-for fallacy—and others like it—should become part of critical thinking pedagogy for humanities students. The analysis proceeds by examining a case of the passes-for fallacy identified by Haack in the work of Ruth Bleier. A charitable reconstruction of Bleier’s reasoning shows that it is enlightening to regard the passes-for fallacy as (...) an abuse of the application conditions of the concept of bias, rather than as an egregious case of Hasty Generalization. (shrink)