ABSTRACT In our current moment, there is considerable interest in networks, in how people and things are connected. This essay outlines one approach that brings together insights from actor-network theory, social network analysis, and digital history to interpret past scientific activity. Multispecies network analysis (MNA) is a means of understanding the historical interactions among scientists, institutions, and preferred experimental animals. A reexamination of studies of sexual behavior funded by the Committee for Research in Problems of Sex between the 1920s and (...) the 1940s demonstrates the applicability of MNA to clarifying the relations that sustained this area of psychology. The measures of weighted degree and betweenness can highlight which nodes (whether organisms or institutions) were particularly “central” to this network. Rats featured as the animals most widely studied during this period, but the analysis also reveals distinct institutional and disciplinary cultures where different species were favored as either surrogates for humans or representatives of more general biological groups. (shrink)

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)

Model organismism—the over-reliance on model organisms without sufficient attention to the adequacy of the models—continues to hobble our understanding of human brains and behaviors. I outline the problem of model organismism in contemporary biology and biomedicine, and discuss the virtues of a genuinely comparative biology for understanding ourselves, our evolutionary history, and our place in nature.

Multiscale modeling techniques have attracted increasing attention by philosophers of science, but the resulting discussions have almost exclusively focused on issues surrounding explanation (e.g., reduction and emergence). In this paper, I argue that besides explanation, multiscale techniques can serve important exploratory functions when scientists model systems whose organization at different scales is ill-understood. My account distinguishes explanatory and descriptive multiscale modeling based on which epistemic goal scientists aim to achieve when using multiscale techniques. In explanatory multiscale modeling, scientists use multiscale (...) techniques to select information that is relevant to explain a particular type of behavior of the target system. In descriptive multiscale modeling scientists use multiscale techniques to explore lower-scale features which could be explanatorily relevant to many different types of behavior, and to determine which features of a target system an upper-scale data pattern could refer to. Using multiscale models from data-driven neuroscience as a case study, I argue that descriptive multiscale models have an exploratory function because they are a sources of potential explanations and serve as tools to reassess our conception of the target system. (shrink)

Berichte zur Wissenschaftsgeschichte, Volume 45, Issue 3, Page 344-354, September 2022.

The discovery of RNA interference in 1998 has made a lasting impact on biological research. Identifying the regulatory role of small RNAs changed the modes of molecular biological inquiry as well as biologists' understanding of genetic regulation. This article examines the early years of small RNA biology's success story. I query which factors had to come together so that small RNA research came into life in the blink of an eye. I primarily look at scientific repertoires as facilitators of rapid (...) scientific change. I show that for a short period of time, between the years 1998 and 2002, different model organism communities, investigative strategies, technological innovations, and research interests could be successfully aligned to take small RNA research off the ground. I discuss how the keystone discoveries were situated in specific experimental traditions and what strategies were employed to establish these discoveries as more general phenomena. Providing thus a practice-based approach of rapid scientific change, I ask how to relate the change in propositional bits of scientific knowledge with changes in scientific practice. (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)

Emphatic claims of a “microbiome revolution” aside, the study of the gut microbiota and its role in organismal development and evolution is a central feature of so-called postgenomics; namely, a conceptual and/or practical turn in contemporary life sciences, which departs from genetic determinism and reductionism to explore holism, emergentism and complexity in biological knowledge-production. This paper analyses the making of postgenomic knowledge about developmental symbiosis in Drosophila melanogaster by a specific group of microbiome scientists. Drawing from both practical philosophy of (...) science and Science and Technology Studies, the paper documents epistemological questions of artefactuality and representativeness of model organisms as they emerge in the day-to-day labour producing and being produced by the “microbiome revolution." Specifically, the paper builds on all the written and editorial exchanges involved in the troubled publication of a research paper studying the symbiotic role of the microbiota in the flies’ development. These written materials permit us to delimit the network of justifications, evidence, standards of knowledge-production, trust in the tools and research designs that make up the conditions of possibility of a postgenomic fact. More than reframing the organism as a radically novel multiplicity of reactive genomes, we conclude, doing postgenomic research on the microbiota and symbiosis means producing a story that deviates from the scripts embedded into the sociotechnical experimental systems of post-Human Genome Project life sciences. (shrink)

Model organisms are a living form of scientific models. Despite the widespread use of model organisms in scientific research, the actual representational relationship between model organisms and their target species is often poorly characterized in the context of cross-species research. Many model organisms do not represent the target species adequately, let alone accurately. This is partly due to the complex and emergent life phenomena in the organism, and partly due to the fact that a model organism is always taken to (...) represent a broad range of diverse organisms. More often than not, model organisms are taken as a reference point for an extrapolation to be made to the unknown characteristics of other species. I propose to view model organisms as analogue simulators which represent the emergent phenomenon in the context of cross-species research. A model organism represents a wide range of species by simulating their molecular microstates which underlie various emergent phenomena. I show that although model organisms represent the target species inadequately at many levels of complexity, they have epistemic values as a simulator in virtue of which the emergent phenomenon can be modeled dynamically, a virtue that is hardly attainable by non-dynamic models. (shrink)

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

This article unpacks a particular use of ‘cases’ within developmental biology, namely as a means of describing the typical or canonical patterns of phenomena. The article explores how certain cases have come to be established within the field and argues that although they were initially selected for reasons of convenience or ease of experimental manipulation, these cases come to serve as key reference points within the field because of the epistemological structures imposed on them by the scientists using them and, (...) hence, become usable in a wider variety of circumstances including future theory development. (shrink)

Berichte zur Wissenschaftsgeschichte, Volume 45, Issue 3, Page 344-354, September 2022.