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)

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)

After 1900, the selective breeding of a few standard animals for research in the life sciences changed the way science was done. Among the pervasive changes was a transformation in scientists' assumptions about relationship between diversity and generality. Examination of the contents of two prominent physiology journals between 1885 and 1900, reveals that scientists used a diverse array of organisms in empirical research. Experimental physiologists gave many reasons for the choice of test animals, some practical and others truly comparative. But, (...) despite strong philosophical differences in the approaches they represented, the view that it was best to incorporate as many species as possible into research on physiological processes was widespread in both periodicals. Authors aimed for generality, but they treated it as a conclusion that would or would not follow from the examination of many species. After 1900, an increasing emphasis on standardization, the growth of the experimental method and the growing industrialization of the life sciences led to a decline in the number of species used in research. In this context, the selective breeding of animals for science facilitated a change in assumptions about the relationship between generality and diversity. As animals were increasingly viewed as things that were assumed to be fundamentally similar, scientific generality became an a priori assumption rather than an empirical conclusion. (shrink)

Sewall Wright first encountered the complex systems characteristic of gene combinations while a graduate student at Harvard's Bussey Institute from 1912 to 1915. In Mendelian breeding experiments, Wright observed a hierarchical dependence of the organism's phenotype on dynamic networks of genetic interaction and organization. An animal's physical traits, and thus its autonomy from surrounding environmental constraints, depended greatly on how genes behaved in certain combinations. Wright recognized that while genes are the material determinants of the animal phenotype, operating with great (...) regularity, the special nature of genetic systems contributes to the animal phenotype a degree of spontaneity and novelty, creating unpredictable trait variations by virtue of gene interactions. As a result of his experimentation, as well as his keen interest in the philosophical literature of his day, Wright was inspired to see genetic systems as conscious, living organisms in their own right. Moreover, he decided that since genetic systems maintain ordered stability and cause unpredictable novelty in their organic wholes, it would be necessary for biologists to integrate techniques for studying causally ordered phenomena and chance phenomena. From 1914 to 1921 Wright developed his "method of path coefficient", a new procedure drawing from both laboratory experimentation and statistical correlation in order to analyze the relative influence of specific genetic interactions on phenotype variation. In this paper I aim to show how Wright's philosophy for understanding complex genetic systems logically motivated his 1914-1921 design of path analysis. (shrink)

This paper explores the many meanings attached to the designation,"the rodent in the laboratory". Generations of selective breeding have created these rodents. They now differ markedly from their wild progenitors, nonhuman animals associated with carrying all kinds of diseases.Through selective breeding, they have moved from the rats of the sewers to become standardized laboratory tools and saviors of humans in the fight against disease. This paper sketches two intertwined strands of metaphors associated with laboratory rodents.The first focuses on the idea (...) of medical/scientific progress; in this context, the paper looks at laboratory rodents often depicted as epitomizing medical triumph or serving as helpers or saviors. The second strand concerns the ambiguous status of the laboratory rodent who is both an animal and not an animal.The paper argues that, partly because of these ambiguous and multiple meanings, the rodent in the laboratory is doubly "othered"—first in the way that animals so often are made other to ourselves and then other in the relationship of the animal in the laboratory to other animals. (shrink)

The article reevaluates the reception of Mendelism in France, and more generally considers the complex relationship between Mendelism and plant breeding in the first half on the 20th century. It shows on the one side that agricultural research and higher education institutions have played a key role in the development and institutionalization of genetics in France, whereas university biologists remained reluctant to accept this approach on heredity. But on the other side, plant breeders, and agricultural researchers, despite an interest in (...) Mendelism, never came to see it as the breeders' panacea, and regarded it instead as of only limited value for plant breeding. I account for this judgment in showing that the plant breeders and Mendelism designed two contrasting kinds of experimental systems and inhabited distinct experimental cultures. While Mendelian geneticists designed experimental systems that allowed the production of definite ratios of different forms that varied in relation to a few characters, plant breeders' experimental systems produced a wide range of variation, featuring combinations between hundreds of traits. Rather than breaking this multiple variation down into simple elements, breeders designed and monitored a genetic lottery. The gene was a unit in a Mendelian experimental culture, an "epistemic thing" as Rheinberger put it, that could be grasped by means of statistical regularities, but it remained of secondary importance for French plant breeders, for whom the strain or the variety -- not the gene -- was the fundamental unit of analysis and manipulation. (shrink)

In the postgenomic era, interactions between organism and environment are central in disciplines such as epigenetics, medical physiology, and immunology. Particularly in the more "applied" medical fields, an emphasis lies on interactions of the organism with other organisms, that is, other living things. There is, however, a growing amount of research investigating the impact of abiotic triggers on the immune system. While the distinction between biota and abiota features heavily in other contexts, its status is not explicit within immunology. Do (...) immunologists distinguish living from nonliving triggers? In this article, I will carve out whether and in which ways the biotic/abiotic distinction operates in immunology. I will look into responses to biotic and abiotic stressors in plant and invertebrate model species and ask how and why they are conceptually separated. I will trace the reasons by investigating the disciplinary situatedness of immune phenomena and the import of vertebrate immunology when conceptualizing immune responses in other model organisms. I will then investigate how the convergence of biotic and abiotic stress responses in plants and invertebrates adds to the recent philosophical programs advocating an ecological perspective on immune systems. (shrink)

Through an examination of the actual research strategies and assumptions underlying the Human Genome Project, it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models. In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help to reveal forms of (...) reasoning that are explicit, or more often implicit, in the practice of a particular field of scientific study. It is suggested that a more valid characterization of the reasoning structure at work here is a form of case-based reasoning. This conceptualization of the role of model organisms can guide our understanding and assessment of these research programs, their knowledge claims and progress, and their limitations, as well as how we educate the public about this type of biomedical research. (shrink)

In Making Sense of Life , Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive (...) science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (shrink)

Taking up the body turn in sociology, this paper discusses scientific practices as embodied action from the perspective of Husserl’s phenomenological theory of the “Body”. Based on ethnographic data on a biology laboratory it will discuss the importance of the scientist’s Body for the performance of scientific activities. Successful researchers have to be skilled workers using their embodied knowledge for the process of tinkering towards the material transformation of their objects for data production. The researcher’s body then is an instrument (...) of measuring as well as a kind of archive of knowing. Their body becomes a disciplined instrument which has its own place and function inside the laboratory. Furthermore, the appresentational apperception of Bodies (Husserl) is being discussed as a basis for the emotional and ethical concerns towards laboratory-animals. Attitudes towards animals in the laboratory setting (as well as elsewhere) are highly emotional. Nevertheless, following the literature of the sociology of the body, those emotional reactions still follow certain cultural patterns which themselves can be understood as embodied ways of knowing “right” or “wrong”. Besides as an instrument, the scientist’s body can also be understood as a resource of emotional attachment towards animals. It is an instrument for performing transformation as well as one for caring. (shrink)