This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational target. We also examine (...) the characteristics of the communities who use these two types of models, including their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a specific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biological way of doing research using models.Keywords: Experimental organism; Genetics; Model organism; Modeling; Philosophy of biology; Representation. (shrink)

In this dissertation, I present a novel account of the components that have a peculiar epistemic role in our scientific inquiries, since they contribute to establishing a form of coordination. The issue of coordination is a classic epistemic problem concerning how we justify our use of abstract conceptual tools to represent concrete phenomena. For instance, how could we get to represent universal gravitation as a mathematical formula or temperature by means of a numerical scale? This problem is particularly pressing when (...) justification for using these abstract tools comes, in part or entirely, from knowledge which is not independent from them, thus leading to threats of circularity. Achieving coordination between some abstract conceptual tools and the concrete phenomena that they are supposed to represent is usually a complex process, which involves several epistemic components. Some of these components eventually provide stable conditions for applying those abstract representations to concrete phenomena. It is in this sense of providing certain conditions of applicability that different philosophical traditions, as well as some contemporary reappraisals, view these components as constitutive or a priori. In this work, I present a new gradualist, contextualist, and relational approach to understand these constitutive components of scientific inquiry. It is gradualist inasmuch as the degree to which some component is constitutive depends on three quantifiable features: quasi-axiomaticity, generative potential, and empirical shielding. Since the quantification of these three features impinges on the history and practice of using these components in a scientific context, my approach is a contextualist one. Finally, my approach is relational in a double sense: first, it identifies ordinal relationships among epistemic components with respect to their constitutive character; second, these relationships are relative to a scientific framework of inquiry. After introducing my account and a classic example of constitutively a priori principles, i.e., Friedman’s (2001) analysis of Newtonian mechanics, I turn to my own case studies to demonstrate the advantages of my approach. Firstly, I discuss Okasha’s (2018) view of endogenization as a pervasive theoretical strategy in evolutionary biology and suggest that the constitutive character of the core Darwinian principles progressively increases with endogenization. Secondly, I apply a conceptual distinction between two varieties or scopes of coordination – general coordination and coordination in measurement – to Ohm’s work on electrical conductivity. This distinction allows me to pinpoint to what extent components along different dimensions (e.g., instrumentation, measurement, theorising, etc.) were constitutive of the forms of coordination which Ohm relied on. Thirdly, I discuss the epistemic function of the Hardy-Weinberg principle in the history and practice of population genetics. I assess this principle in terms of my account and identify approximation and stability as two components that are highly constitutive, in that they contribute to justifying its use in population genetics. Finally, applying my account to these case studies enables me to identify at least three qualitatively different types of constitutive components: domain-specific theoretical principles, material components, and domain-independent assumptions underlying reasoning abilities. In the light of my results, I draw some general conclusions on epistemic justification and scientific knowledge. (shrink)

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project. They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced (...) and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology. (shrink)

ArgumentWe examine the criteria used to validate the use of nonhuman organisms in North-American alcohol addiction research from the 1950s to the present day. We argue that this field, where the similarities between behaviors in humans and non-humans are particularly difficult to assess, has addressed questions of model validity by transforming the situatedness of non-human organisms into an experimental tool. We demonstrate that model validity does not hinge on the standardization of one type of organism in isolation, as often the (...) case with genetic model organisms. Rather, organisms are viewed as necessarily situated: they cannot be understood as a model for human behavior in isolation from their environmental conditions. Hence the environment itself is standardized as part of the modeling process; and model validity is assessed with reference to the environmental conditions under which organisms are studied. (shrink)

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)

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the (...) curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. (shrink)

Criticism is a staple of the scientific enterprise and of the social epistemology of science. Philosophical discussions of criticism have traditionally focused on its roles in relation to objectivity, confirmation, and theory choice. However, attention to criticism and to criticizability should also inform our thinking about scientific pursuits: the allocation of resources with the aim of developing scientific tools and ideas. In this paper, we offer an account of scientific pursuitworthiness which takes criticizability as its starting point. We call this (...) the apokritic model of pursuit. Its core ideas are that pursuits are practices governed by norms for asking and answering questions, and that criticism arises from the breach of these norms. We illustrate and advertise our approach using examples from institutional grant review, neuroscience, and sociology. We show that the apokritic model can unify several indices of criticizability, that it can account for the importance of criticizing pursuits in scientific practice, and that it can offer ameliorative advice to erstwhile pursuers. (shrink)

In this paper I argue, first, that ecologists have routinely treated humans—or more specifically, anthropogenic causal factors—as disturbing conditions. I define disturbing conditions as exogenous variables, variables “outside” a model, that when present in a target system, inhibit the applicability or accuracy of the model. This treatment is surprising given that humans play a dominant role in many ecosystems and definitions of ecology contain no fundamental distinction between human and natural. Second, I argue that the treatment of humans as disturbing (...) conditions is an idealization: since it is, and has long been, known that humans are pervasive, this treatment amounts to an intentionally introduced theoretical distortion. Finally, characterizing this treatment as idealization forces us to confront the question of its justification, and so, drawing on three different kinds of idealization, I evaluate how this treatment may be justified. (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

ABSTRACT In a series of experiments at the National Institute of Mental Health, the animal ecologist John B. Calhoun offered rats everything they needed, except space. The resulting population explosion was followed by a series of “social pathologies”—violence, sexual deviance, and withdrawal. This essay examines the influence of Calhoun's experiments among psychologists and sociologists concerned with the effects of the built environment on health and behavior. Some saw evidence of the danger of the crowd in Calhoun's “rat cities” and fastened (...) on a method of analysis that could be transferred to the study of urban man. Others, however, cautioned against drawing analogies between rodents and humans. The ensuing dispute saw social scientists involved in a careful negotiation over the structure and meaning of Calhoun's experimental systems and, with it, over the significance of the crowd in the laboratory, institution, and city. (shrink)

ArgumentThis article uses four historical case studies to address epistemological issues related to the animal model of human diseases and its use in medical research on human diseases. The knowledge derived from animal models is widely assumed to be highly valid and predictive of reactions by human organisms. In this contribution, I use three significant historical cases of failure (ca. 1890, 1960, 2006), and a closer look at the emergence of the concept around 1860/70, to elucidate core assumptions related to (...) the specific practices of animal-human knowledge transfer, and to analyze the explanations provided by historical actors after each of the failures. Based on these examples, I argue that the epistemological status of the animal model changed from that of a helpful methodological tool for addressing specific questions, but with precarious validity, to an obligatory method for the production of strong knowledge on human diseases. As a result, there now exists a culture of biomedical research in human disease that, for more than a century, has taken the value of this methodological tool as self-evident, and more or less beyond question. (shrink)

From 1942 to 1952, a programme took place at Johns Hopkins to devise new methods of controlling Baltimore’s rat population. This article focuses on three individuals closely connected to this project at various stages of its development: psycho-biologist Curt Richter, animal ecologist David E. Davis, and ecologist and psychologist John B. Calhoun. For all three, the challenges of controlling rat numbers highlighted the significance of stress – a homeostatic mechanism critical to the survival of the animal. This was a process (...) that was analyzed and manipulated by (re)introducing the wild rat into the laboratory. Here the rat not only contributed to new methods of rodent control, but offered new possibilities for the control and improvement of humankind. Yet it was not just the animal, but the physical structure of the laboratory that came to model the world outside. Through examining the experimental systems of the three scientists, this article will trace a series of transgressions between laboratory and field, urban and wild, animal and human. The result was that while animals were used to model the behaviour and pathologies of human city dwellers, the laboratory spaces in which they existed came to model the urban environment. We shall also see how differing perspectives on the value and uses of animal models and environments encouraged and reinforced alternative visions as to the role of science in the service of the city. (shrink)

This paper offers an analytic perspective on epistemic dependence that is grounded in theoretical discussion and field observation at the same time. When in the course of knowledge creation epistemic labor is divided, collaborating scientists come to depend upon one another epistemically. Since instances of epistemic dependence are multifarious in scientific practice, I propose to distinguish between two different forms of epistemic dependence, opaque and translucent epistemic dependence. A scientist is opaquely dependent upon a colleague if she does not possess (...) the expertise necessary to independently carry out, and to profoundly assess, the piece of scientific labor which her colleague is contributing. If the scientist does possess the necessary expertise, I argue, her dependence is translucent. However, the distinction between opaque and translucent epistemic dependence does not exhaust dependence relations in scientific practice, because many dependence relations are neither entirely opaque nor translucent. I will discuss why this is the case, and show how we can make sense of the gray zone between opaque and translucent epistemic dependence. (shrink)

This article tracks the transformation of beagle dogs from a common breed in mid-twentieth century American laboratories to the de jure standard in global toxicological research by the turn of the twenty-first. The breed was dispersed widely due to the expanding use of dogs in pharmacology in the 1950s and a worldwide crisis around pharmaceutical safety following the thalidomide scandal of the 1960s. Nevertheless, debates continued for decades over the beagle’s value as a model of carcinogenicity, even as the dogs (...) became legislated stand-ins for human beings in multiple countries. Situating beagles as a biocommodity, the article calls for more sustained attention to the “political economy” of laboratory organism breeding, use, and production. The story of American commercial breeder Marshall Farms offers insight into the role of for-profit companies in contemporary laboratory animal provision, as the article makes a case for the value of a global perspective on transnational corporations as key sites of scientific practice and collaboration. (shrink)