In this paper I sketch William Whewell’s attempts to impose order on classificatory mineralogy, which was in Whewell’s day (1794e1866) a confused science of uncertain prospects. Whewell argued that progress was impeded by the crude reductionist assumption that all macroproperties of crystals could be straightforwardly explained by reference to the crystals’ chemical constituents. By comparison with biological classification, Whewell proposed methodological reforms that he claimed would lead to a natural classification of minerals, which in turn would support advances in causal (...) understanding of the properties of minerals. Whewell’s comparison to successful biological classification is particularly striking given that classificatory biologists did not share an understanding of the causal structure underlying the natural classification of life (the common descent with modification of all organisms). Whewell’s key proposed methodological reform is consideration of multiple, distinct principles of classification. The most powerful evidence in support of a natural classificatory claim is the consilience of claims arrived at through distinct lines of reasoning, rooted in distinct conceptual approaches to the target objects. Mineralogists must consider not only elemental composition and chemical affinities, but also symmetry and polarity. Geometrical properties are central to what makes an individual mineral the type of mineral that it is. In Whewell’s view, function and organization jointly define life, and so are the keys to understanding what makes an organism the type of organism that it is. I explain the relationship between Whewell’s teleological account of life and his natural theology. I conclude with brief comments about the importance of Whewell’s classificatory theory for the further development of his philosophy of science and in particular his account of consilience. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

William Whewell’s work on historical science has received some attention from historians and philosophers of science. Whewell’s own work on the history of German Gothic church architecture has been touched on within the context of the history of architecture. To a large extent these discussions have been conducted separately. I argue that Whewell intended his work on Gothic architecture as an attempt to (help) found a science of historical architecture, as an exemplar of historical science. I proceed by analyzing the (...) key features of Whewell’s philosophy of historical science. I then show how his architectural history exemplifies this philosophy. Finally, I show how Whewell’s philosophy of historical science matches some developments in a science (biological systematics) that, in the mid-to latenineteenth century, came to be reinterpreted as a historical science. I comment briefly on Whewell as a potential influence on nineteenth century biology and in particular on Darwin. (shrink)

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the (...) term. (shrink)

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator (...) with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams. (shrink)

Sterner and Lidgard urge that philosophers of phylogenetics move beyond the “systematics wars”, referring to the 1960s–80s debates between numerical taxonomists, evolutionary taxonomists, and phylogenetic systematists. Indeed, philosophers would do well to move beyond those wars, and to focus even more recently than the parsimony versus likelihood debates of the 1980s–90s. In this paper I use integrated historical-philosophical analysis of those debates to clarify a contemporary dispute between proponents of coalescence-based methods and proponents of concatenation. My intent is to illuminate (...) the present state of the field of phylogenetics by tracing the use of one particular philosophical argument, “total evidence”, through several distinct scientific debates. (shrink)

Business models for biomedical research prescribe decentralization due to market selection pressures. I argue that decentralized biomedical research does not match four normative philosophical models of the role of values in science. Non-epistemic values affect the internal stages of for-profit biomedical science. Publication planning, effected by Contract Research Organizations, inhibits mechanisms for transformative criticism. The structure of contracted research precludes attribution of responsibility for foreseeable harm resulting from methodological choices. The effectiveness of business strategies leads to overrepresentation of profit values (...) versus the values of the general public. These disconnects in respect to the proper role of values in science results from structural issues ultimately linked to the distinct goals of business versus applied science, and so it seems likely that disconnects will also be found in other dimensions of attempts to combine business and science. The volume and integration in the publishing community of decentralized biomedical research imply that the entire community of biomedical research science cannot match the normative criteria of community-focused models of values in science. Several proposals for changing research funding structure might successfully relieve market pressures that drive decentralization. (shrink)

We analyze the relationship between evolutionary theory and classification of higher taxa in the work of three ichthyologists: Albert C.L.G. Günther (1830–1914), Edward Drinker Cope (1840–1897), and Theodore Gill (1837–1914). The progress of ichthyology in the early years following the Origin has received little attention from historians, and offers an opportunity to further evaluate the extent to which evolutionary theorizing influenced published views on systematic methodology. These three ichthyologists held radically different theoretical views. The apparent commensurability of claims about relationships (...) among groups of fishes belies differences in what the relationships actually were supposed to be. As well, interpreting classification as genealogical did not lead to agreement about taxonomic methodology; instead, applying evolutionary theory raised new axes of disagreement. (shrink)

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with (...) eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes. (shrink)