This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O’Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data integration involves in more detail (...) and with a focus on the role of data-sharing tools, like online databases, in facilitating this process; and I point to the philosophical implications of focusing on data as a unit of analysis. I then analyse three cases of data integration in the field of plant science, each of which highlights a different mode of integration: inter-level integration, which involves data documenting different features of the same species, aims to acquire an interdisciplinary understanding of organisms as complex wholes and is exemplified by research on Arabidopsis thaliana; cross-species integration, which involves data acquired on different species, aims to understand plant biology in all its different manifestations and is exemplified by research on Miscanthus giganteus; and translational integration, which involves data acquired from sources within as well as outside academia, aims at the provision of interventions to improve human health and is exemplified by research on Phytophtora ramorum. Recognising the differences between these efforts sheds light on the dynamics and diverse outcomes of data dissemination and integrative research; and the relations between the social and institutional roles of science, the development of data-sharing infrastructures and the production of scientific knowledge. (shrink)

Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed (...) and applied styles, paradigms, and models simultaneously? I address these questions in general and for a specific case study: a brief history of systematics. (shrink)

This article explains Kant’s claim that sciences must take, at least as their ideal, the form of a ‘system’. I argue that Kant’s notion of systematicity can be understood against the background of de Jong & Betti’s Classical Model of Science (2010) and the writings of Georg Friedrich Meier and Johann Heinrich Lambert. According to my interpretation, Meier, Lambert, and Kant accepted an axiomatic idea of science, articulated by the Classical Model, which elucidates their conceptions of systematicity. I show that (...) Kant’s critique of the mathematical method is compatible with his adherence to this axiomatic conception of science. I further show that systematicity furthers traditionally accepted logical ideals of scientific knowledge, which explains why Meier and Kant think that sciences must be ‘systematic’. (shrink)

‘Type’ in biology is a polysemous term. In a landmark article, Paul Farber (Journal of the History of Biology 9(1): 93–119, 1976) argued that this deceptively plain term had acquired three different meanings in early nineteenth century natural history alone. ‘Type’ was used in relation to three distinct type concepts, each of them associated with a different set of practices. Important as Farber’s analysis has been for the historiography of natural history, his account conceals an important dimension of early nineteenth (...) century ‘type talk.’ Farber’s taxonomy of type concepts passes over the fact that certain uses of ‘type’ began to take on a new meaning in this period. At the closing of the eighteenth century, terms like ‘type specimen,’ ‘type species,’ and ‘type genus’ were universally recognized as referring to typical, model members of their encompassing taxa. But in the course of the nineteenth century, the same terms were co-opted for a different purpose. As part of an effort to drive out nomenclatural synonymy – the confusing state of a taxon being known to different people by different names – these terms started to signify the fixed and potentially atypical name-bearing elements of taxa. A new type concept was born: the nomenclatural type. In this article, I retrace this perplexing nineteenth century shift in meaning of ‘type.’ I uncover the nomenclatural disorder that the new nomenclatural type concept dissolved, and expose the conceptual confusion it left in its tracks. What emerges is an account of how synonymy was suppressed through the coinage of a homonym. (shrink)

Within eighteenth-century debates on animal cognition we can distinguish at least three main theoretical positions: (i) Buffon’s mechanism, (ii) Reimarus’ theory of instincts, and (iii) the sensationalism of Condillac and Leroy. In this paper, I adopt a philosophical perspective on this debate and argue that in order to fully understand the justification Buffon, Reimarus, Condillac, and Leroy gave for their respective theories, we must pay special attention to the theoretical virtues these naturalists alluded to while justifying their position. These theoretical (...) virtues have received little to no attention in the literature on eighteenth-century animal cognition, but figure prominently in the justification of the mechanist, instinctive, and sensationalist theories of animal behavior. Through my philosophical study of the role of theoretical virtues in eighteenth-century debates on animal cognition, we obtain a deeper understanding of how theoretical virtues were conceptualized in eighteenth-century science and how they influenced the justification of theories of animal cognition. (shrink)

Summary A famous debate between John Ray, Joseph Pitton de Tournefort and Augustus Quirinus Rivinus at the end of the seventeenth century has often been referred to as signalling the beginning of a rift between classificatory methods relying on logical division and classificatory methods relying on empirical grouping. Interestingly, a couple of decades later, Linnaeus showed very little excitement in reviewing this debate, and this although he was the first to introduce the terminological distinction of artificial vs. natural methods. In (...) this paper, I will explain Linnaeus's indifference by the fact that earlier debates were revolving around problems of plant diagnosis rather than classification. From Linnaeus's perspective, they were therefore concerned with what he called artificial methods alone ? diagnostic tools, that is, which were artificial no matter which characters were taken into account. The natural method Linnaeus proposed, on the other hand, was not about diagnosis, but about relations of equivalence which played a vital, although largely implicit role in the practices of specimen exchange on which naturalists relied to acquire knowledge of the natural world. (shrink)

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (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)

Scientific classification has long been recognized as involving a specific style of reasoning and doing research, and as occasionally affecting the development of scientific theories. However, the role played by classificatory activities in generating theories has not been closely investigated within the philosophy of science. I argue that classificatory systems can themselves become a form of theory, which I call classificatory theory, when they come to formalize and express the scientific significance of the elements being classified. This is particularly evident (...) in some of the classification practices used in contemporary experimental biology, such as bio-ontologies used to classify genomic data and typologies used to classify “normal” stages of development in developmental biology. In this paper, I explore some characteristics of classificatory theories and ways in which they differ from other types of scientific theories and other components of scientific epistemology, such as models and background assumptions. (shrink)

Summary This essay aims to elucidate the collaborative dimension of the knowledge-making process in eighteenth-century Linnaean botany. Due to its ever increasing and potentially infinite need for information, Linnaean botany had to rely more and more heavily on the accumulation and aggregation of contributions by many people. This, in turn, had a crucial impact on the genesis and form of botanical publications: the more comprehensive the project, the larger the effect. It was the botanist Carl Linnaeus who managed to establish (...) himself as the centre of this contributory knowledge-making process. Given the exponential growth in the number of known species and the resulting need for observation, this was the necessary condition which allowed him continuously to update and correct his systematic works, and allowed them to maintain their status as the central catalogues of a global botany for decades. (shrink)

The Swiss natural historian Johann Amman came to Russia in 1733 to take a position as professor of botany and natural history at the St. Petersburg Academy of Sciences. As part of the job, he corresponded, and exchanged plant specimens, with the English merchant collector Peter Collinson in London, and the Swedish scholar Carolus Linnaeus, among others. After briefly reviewing Amman's correspondence with these scholars and the growing commerce in exotic specimens of natural history, I explore how encyclopedias came to (...) facilitate the exchange of zoological specimens in particular. I argue that, during the seventeenth century, a new genre of zoological encyclopedias appeared on the scene whose design was particularly well-suited for the purposes of identification, a key practice in long-distance exchanges. (shrink)

This paper provides a translation of the introduction, titled ‘Account of the work’ Ratio operis, to the first edition of Genera plantarum, published in 1737 by the Swedish botanist Carl Linnaeus. The text derives its significance from the fact that it is the only published text in which Linnaeus engaged in an explicit discussion of his taxonomic method. Most importantly, it shows that Linnaeus was clearly aware that a classification of what he called ‘natural genera’ could not be achieved by (...) a top-down approach of logical division, but had to rely on inductive, bottom-up procedures. The translation is supplemented by explanatory notes. (shrink)

What is it to make an error in the identification of a named taxonomic group? In this article we argue that the conditions for being in error about the identity of taxonomic groups through their names have a history, and that the possibility of committing such errors is contingent on the regime of institutions and conventions governing taxonomy and nomenclature at any given point in time. More specifically, we claim that taxonomists today can be in error about the identity of (...) taxonomic groups in a way that Carl Linnaeus, who is routinely cited as the “founder” of modern taxonomy and nomenclature, simply could not be. Starting from a remarkable recent study into Linnaeus’s naming of Elephasmaximus that led to the discovery of a nomenclatural error by him, we reconsider what it could mean to discover that Linnaeus misidentified a biological taxon in applying his taxon names. Through a further case study in Linnaean botany, we show that his practices of applying names in taxonomic revisions reveal a take on determining “which taxon is which” that is strikingly different from that of contemporary taxonomists. Linnaeus, we argue, adopted a practice-based, hands-on concept of taxa as “nominal spaces” that could continue to represent the same taxon even if all its former members had been reallocated to other taxa. (shrink)

Are psychiatric disorders natural kinds? This question has received a lot of attention within present-day philosophy of psychiatry, where many authors debate the ontology and nature of mental disorders. Similarly, historians of psychiatry, dating back to Foucault, have debated whether psychiatric researchers conceived of mental disorders as natural kinds or not. However, historians of psychiatry have paid little to no attention to the influence of (a) theories within logic, and (b) theories within metaphysics on psychiatric accounts of proper method, and (...) on accounts of the nature and classification of mental disorders. Historically, however, logic and metaphysics have extensively shaped methods and interpretations of classifications in the natural sciences. This paper corrects this lacuna in the history of psychiatry, and demonstrates that theories within logic and metaphysics, articulated by Christian Wolff (1679-1754), have significantly shaped the conception of medical method and (psychiatric) nosology of the influential nosologist Boissier De Sauvages (1706-1767). After treating Sauvages, I discuss the method of the influential nosologist William Cullen (1710-1790), and demonstrate the continuity between the classificatory methods of Sauvages and Cullen. I show that both Sauvages and Cullen were essentialists concerning medical diseases in general and psychiatric disorders in particular, contributing to the history of conceptions of the ontology and nature of mental disorders. (shrink)

The origins of field guides and other plant identification manuals have been poorly understood until now because little attention has been paid to 18th century botanical identification guides. Identification manuals came to have the format we continue to use today when botanical instructors in post-Revolutionary France combined identification keys with the "natural method" and alphabetical indexes. Botanical works featuring multiple but linked techniques to enable plant identification became very popular in France by the first decade of the 19th century. British (...) botanists, however, continued to use Linnaeus's sexual system almost exclusively for another two decades. Their reluctance to use other methods or systems of classification Can be attributed to a culture suspicious of innovation, anti-French sentiment and the association of all things Linnaean with English national pride, fostered in particular by the President of the Linnean Society of London, Sir James Edward Smith. The British aversion to using multiple plant identification technologies in one text also helps explain why it took so long for English botanists to adopt the natural method, even after several Englishmen had tried to introduce it to their country. Historians of ornithology emphasize that the popularity of ornithological guides in the 19th and 20th centuries stems from their illustrations, illustrations made possible by printing technologies that improved illustration quality and reduced costs. Though illustrations are the most obvious features of late 19th century and 20th century guides, the organizational principles that make them functional as identification devices come from techniques developed in botanical works in the 18th century. (shrink)

Throughout the late 1840s and the early 1850s, Harvard botanist Asa Gray and his close friend George Engelmann of St. Louis engaged themselves with recruiting men who sought to make a living by natural history collecting, sending these men into the field, searching for institutions and individuals who would subscribe to incoming collections, compiling catalogs, and collecting subscription fees. Although several botanists have noted Gray and Engelmann’s bold experiment as having introduced America to a mode by which European naturalists had (...) devised to organize scientific expeditions, historians of science have not taken the “subscription mode” seriously. I argue that it was specifically by undertaking the labor of cataloging species and charging subscription fees for the cataloged species that Gray established himself as a metropolitan botanist. One crucial consequence of Gray’s rising profile was that he acquired sufficient “cataloging power” to secure his status as an authoritative cataloger of species, and as a kind of “mint” or “storehouse” :1–28, 2001a) who produced well-pruned lists of American species to enable transactions between American and European botanists. But this essay is not focused on the Europeanization of American taxonomy. Drawing on work by scholars who place emphasis on how new forms of knowledge get produced when knowledge travels, my focus here is the evolution of the subscription mode when Gray and Engelmann adapted it to American natural history. My conclusion examines what historian of science Vanessa Heggie :318–334, 2014) identifies as the “danger of category dominance” in today’s historiography of science and shows how a kind of “assemblage thinking” may help historians cope with this danger. (shrink)

The invisible object, in the eighteenth century, is not an evidence. It is the result of textual and semantic learning. Which concrete strategies are used to construct and depict objects out of sight? How do we make them a cognitive reality acceptable to a scientific community? This paper first highlights the conditions for the emergence of a field of microscopic knowledge and its epistemological consequences. Then we consider the microscopic gaze in terms of learning, situated between the act of observation (...) as such and discursive practices. We conclude by studying a concrete case of “negotiation of the invisible” in a correspondence between Carl Linnaeus and John Ellis concerning corpuscles observed in mushroom infusions. (shrink)

Nehemiah Grew is rightly lauded as one of the first and most sophisticated promoters of the discipline of plant anatomy—the observation and representation of the insides of plants. Overlooked so far, though, are his activities as a plant collector. In this paper, I reconstruct Grew's plant-collection practices from his first medical garden, through his incorporation of specimens from the Royal Society's repository, and to its expansion through his support of intercontinental plant-gathering missions. These activities gave Grew access both to fresh, (...) local plant samples, which he could observe again and again, as well as to foreign specimens that exhibited some of the more curious variations of nature. I argue that these different plant-collecting strategies reflected his overarching ambitions with his plant anatomy, which was to construct an idealised model of plant formation, generation, and growth. In order to do this, Grew pieced together his observations of individual specimens into one generalised model through the method of collation. While not offering concrete advice on how to grow plants more efficiently, I argue that Grew's idealised representation of the processes of plant life was offered as a framework for further botanical experimentation. (shrink)

The dichotomy between ‘typological thinking’ and ‘population thinking’ features in a range of debates in contemporary and historical biology. The origins of this dichotomy are often traced to Ernst Mayr, who is said to have coined it in the 1950s as a rhetorical device that could be used to shield the Modern Synthesis from attacks by the opponents of population biology. In this two-part essay, I argue that the origins of the typology/population dichotomy are considerably more complicated and more interesting (...) than is commonly thought. In the first part, I argued that Mayr's dichotomy was based on two distinct type/population contrasts that had been articulated much earlier by George Gaylord Simpson and Theodosius Dobzhansky. Their distinctions made eminent sense in their own, isolated contexts. In this second part, I will show how Mayr conflated these type/population distinctions and blended in some of his own, unrelated concerns with ‘types’ of a rather different sort. Although Mayr told his early critics that he was merely making “a temporary oversimplification,” he ended up burdening the history and philosophy of biology with a troubled dichotomy. (shrink)

The dichotomy between ‘typological thinking’ and ‘population thinking’ features in a range of debates in contemporary and historical biology. The origins of this dichotomy are often traced to Ernst Mayr, who is said to have coined it in the 1950s as a rhetorical device that could be used to shield the Modern Synthesis from attacks by the opponents of population biology. In this two-part essay I argue that the origins of the typology/population dichotomy are considerably more complicated and more interesting (...) than is commonly thought. In this first part, I will argue that Mayr's dichotomy was based on two distinct type/population contrasts that had been articulated much earlier by George Gaylord Simpson and Theodosius Dobzhansky. Their distinctions made eminent sense in their own, isolated contexts. In the second part, I will show how Mayr conflated these type/population distinctions and blended in some of his own, unrelated concerns with ‘types’ of a rather different sort. Although Mayr told his early critics that he was merely making “a temporary oversimplification,” he ended up burdening the history and philosophy of biology with a troubled dichotomy. (shrink)

ArgumentHere I analyze the anatomical thought of the French physician and naturalist Félix Vicq d'Azyr (1748–1794) in order to bring to light its importance in the development of comparative anatomy at the end of the eighteenth century. I argue that his work and career can be understood as an ambitious program for a radical reform of all biomedical sciences and a reorganization of this whole field around comparative anatomy, on the conceptual as well as the institutional level. In particular, he (...) recommended a close connection between anatomical and physiological studies, and a generalization of the comparative approach towards organs and functions in man and animals. This conception led him not only to reform the scope, the methods, the style of description, and the vocabulary in anatomy, but also to construct a new classification of living beings and to pursue a quest for laws of organization. This strategy was successful, since Vicq d'Azyr was able to promote his thought as well as his institutional position efficiently. The Revolution and his untimely death prevented him from achieving his program, but his attempt would serve as an example for younger scientists like Cuvier. (shrink)

Travelling is an activity closely associated with Carolus Linnaeus and his circle of students. This article discusses the transformative role of studying nature outdoors in eighteenth-century Sweden, using the little-known journeys of Carl Bäck , Sven Anders Hedin and Johan Lindwall as examples. On these journeys, through different parts of Sweden in the 1770s, the outdoors was used, simultaneously, as both a classroom and a space for exploration. The article argues that this multifunctional use of the landscape encouraged a democratization (...) of the consumption of scientific knowledge and also, to some degree, of its production. More generally, the study also addresses issues of how and why science and scientists travel by discussing how botanical knowledge was reproduced and extended ‘on the move’, and what got senior and junior students moving. (shrink)

193 and 246 of Linnaeus's Philosophia botanica have recently been invoked to suggest that Linnaeus used, or even introduced, the "Method of Type", which implies that a genus is centred around a "typical" species. However, there is no support for this conclusion in either of the two paragraphs, rather the opposite. A recapitulation of the last twenty years' reassessment of Linnaeus's taxonomic philosophy is given.

In Philosophia Botanica, Carolus Linnaeus presented a calculation of the number of plant genera that may be distinguished based on his taxonomic concepts. In order to derive that number, he relied upon the organs of fructification, which represent the flower and the fruit, by selecting over 30 elements from them, and then assuming that each could vary by four dimensions. However, while Linnaeus was good in counting stamens and pistils, he and many of his followers who edited or translated Philosophia (...) Botanica were less careful, basing their calculations of the number of possible genera on flawed assumptions, or even introducing basic arithmetic errors. Furthermore, although mathematics was quite advanced in the eighteenth century, the gap between combinatorial and botanical thinking was too deep, preventing Linnaeus to seek a reasonable solution to the problem he raised. The authors demonstrate this by a historical analysis of 15 editions of Philosophia Botanica, plus many references to it, and conclude that the desired number almost always appeared in error during the past 265 years. The German botanist J. G. Gleditsch was the most successful with respect to Linnaeus’ original intention. Elementary mathematics demonstrates that if Linnaeus’ assumptions were taken seriously, then the possible number of genera would be astronomical. The practice he followed in Genera Plantarum shows, however, that the fructification dimensions served as a universal set for Linnaeus from which he chose only the relevant ones for describing a particular genus empirically. Based on the corrections and modifications implemented in reworked editions, we suggest an evolutionary network for the historical and modern versions or translations of Philosophia Botanica. (shrink)