Rachel Allyson Ankeny

This article examines the role of patient organizations as mediators between patients and researchers in stem cell research in Australia. We conducted semi-structured interviews with stem cell researchers and patient organization representatives as part of a broader project to deepen public understanding and foster more robust scientific practices in stem cell-based research and therapies. We used Habermas’s Theory of Communicative Action as our theoretical framework to explore the relationships between patient organizations and researchers. Using this framework allowed the identification of two different ways of conceptualizing health and illness—one based on patients’ experiences, which we call “the lifeworld,” and another grounded on researchers’, health professionals’, and policymakers’ professional perspectives, which we call “the rational system.” We found that the different conceptualizations identified influenced the interactions between patients and researchers (and other professionals involved in the healthcare system). Patient organizations, then, act as articulators of patients’ viewpoints in this scenario, which can have advantages and disadvantages. We also found that researchers need to develop less transactional forms of communication with these organizations and that policymakers and regulators could benefit from developing guidelines to encourage researchers to use diverse strategies to engage more meaningfully with patients at individual and organizational levels.

This paper considers the continued use of simpler model organisms in newer forms of toxicological research in order to inform philosophical understandings of the epistemic roles played by such organisms in the contemporary life sciences. We focus on the emerging domain of ‘precision toxicology’ and consider three uses of model organisms within it, namely as (1) models of toxic effects and other forms of environmental exposures; (2) indicator species; and (3) bioremediators. We analyze the epistemic implications of these uses, arguing that they represent hybrid forms of modelling in comparison to traditional uses of model organisms, and identify similarities and differences between these emerging research practices and the model organism repertoire being adapted for use in this domain. Model organisms are simultaneously viewed as tools for intervention and representation within precision toxicology, in ways that differ from the model organism repertoire both in terms of the extent to which the models fit applied research goals and how they foster evolutionary and developmental understanding. Hence we argue that model organisms remain highly influential models in the life sciences but are being used in research more closely associated with the concept of ‘precision,’ and characterized by an ethos of intervention particularly in response to the environmental challenges associated to climate change and attention to the evolutionary and developmental grounding of health and disease. In closing, we reflect on the ways in which using the analytic framing associated with the repertoires approach facilitates the tracking of these developments in the contemporary life sciences. We also assess how they may affect the construction and significance of model systems over coming decades particularly in relation to precision-related research.

Crop scientists often claim that gene editing will significantly increase food security and other wicked problems. However, various publics are not convinced that the potential risks are offset by the promised benefits. The crux of this disagreement is often unpacked in terms of different values, lack of scientific understanding, or a failure of crop scientists to viewed as trustworthy. This paper revisits the current stalemate between crop scientists and publics, and the resulting conceptual meta-impasse in the scholarly literature on these conflicts. It uses a policy analysis framework to challenge the traditional view that public policies are responses to problems that pre-exist outside of the policy process, waiting to be discovered and solved. Instead, if we view policies as containing implicit representations of the supposed ‘problems’ that they purport to address, along with unrecognized assumptions and silences, it becomes clear that inadequate attention has been paid to the framing of the claims made by proponents of these technologies. Articulating the underlying problem representations and scrutinizing them can lead to new problem representations and more productive scientific strategies particularly in response to climate change by allowing responsibility to be collectively pursued ‘by design.’

James R. Griesemer is an internationally renowned philosopher and historian of science whose contributions span the philosophy, history, and social studies of genetics, ecology, morphology, taxonomy, biodiversity studies, and developmental and evolutionary biology. His writings are cited and admired by scholars in all of these fields because of Griesemer’s fundamental contributions to understanding reproduction, cultural evolution, model systems, the role of theories, abstraction, visualizations and diagrams, data practices, origins of life, epigenetics, and many other topics (Fig. 1.1).

This introduction follows a different format than others in this collection in that it is an edited transcription of a lengthy facilitated interview jointly with Jim Griesemer and Bill Wimsatt performed on 27 September 2024. It includes discussion of the article that appears below and other topics likely to be of interest to readers, such as Griesemer’s intellectual and career trajectory, and Griesemer and Wimsatt’s long-standing collaboration. It has been edited due to space considerations, with references added where thought to be useful. If this introduction were to have its own title, it would be “Riffing on Thickety Problems in Philosophy of Biology, or Useful Lessons about Serendipity and Interdisciplinarity.”

In biomedicine and science more broadly, there is increasing emphasis on ‘openness’ in research practices both between those involved in research and with those who might benefit from the research. Such emphasis is often invoked because it is hoped, and often assumed, that more openness will promote greater productivity, transparency and trust in scientific research. These efforts have focussed on the availability and sharing of data and knowledge, along with more tangible resources such as biological materials. Certain types of resources are valued in particular ways, and these dynamics affect the extent to which they can be entrusted and shared with others and used in more collaborative scientific research (or not). In this chapter, we use stem cell research as a case study to examine: (1) how material resources (e.g. stem cell lines) are valued in distinct (but overlapping) ways compared to more text-based resources (e.g. data, knowledge), and (2) how the valuation of these resources informs relations of trust, sharing, communication and collaboration between researchers. We draw on empirical insights from interviews with stem cell researchers in Australia, conducted as part of a research project investigating the potential for increasing ‘openness’ in Australian stem cell research. Overall, we demonstrate how scientific resources are valued in multiple ways, which informs the possibilities for more open and collaborative scientific research.

Contemporary scientific research depends on sharing resources. Norms, cultures and infrastructures enable, incentivize or require sharing in particular ways. Commons are one type of infrastructure, and their key characteristics include the provision and governance of resources. Understanding how resources become part of a commons is critical for implementing arrangements that effectively facilitate scientific research. This article uses commons theory associated with knowledge resources to explore efforts to establish a registry for the Australian stem cell research community where registration is not a current norm. Analyzing the perspectives of stem cell researchers regarding registries, we make two contributions: (1) a conceptual contribution to the commons literature by explicating a more contingent understanding of resources, and (2) an empirical analysis of a relatively under-examined form of governance arrangement (i.e. registries). We emphasize paying close attention to the context-dependent processes through which resources are viewed as common-able and may subsequently become common-ed.

Qualitative research provides rigorous methods not only for investigating behavioral or social issues, but can also be used for exploring epistemic issues related to science and its practices. There is growing scholarly awareness that important aspects of science can be best understood through qualitative analyses and cannot be captured using more traditional textual sources such as publications or archival documents or via more quantitative or formalized methodologies such as citation analysis or bibliometrics. Reflecting on our own research on the philosophy of scientific practices, particularly on the role of model organisms in biology, we discuss some of the challenges associated with the design and conduct of qualitative research in the philosophy of science. We then explore three issues in more detail: The extent to which qualitative methods support the identification of media and spaces for the study of epistemic questions in science; the investigation of social structures particularly relevant to scientific practices and reasoning; and the conceptual and interpretative significance of analytic choices in empirical research on science. In closing, we reflect on the value of qualitative research methods for understanding scientific practices as ways to identify novel research directions, refine and augment philosophically motivated research questions, investigate the rationales and procedures through which particular scientific choices become ingrained in research, and question the implications of such habits as norms for what counts as “best practice” in particular scientific fields, all of which are topics that deserve more attention from philosophers and other scholars interested in scientific practices.

How effectively communities of scientists come together and co-operate is crucial both to the quality of research outputs and to the extent to which such outputs integrate insights, data and methods from a variety of fields, laboratories and locations around the globe. This essay focuses on the ensemble of material and social conditions that makes it possible for a short-term collaboration, set up to accomplish a specific task, to give rise to relatively stable communities of researchers. We refer to these distinctive features as repertoires, and investigate their development and implementation across three examples of collaborative research in the life sciences. We conclude that whether a particular project ends up fostering the emergence of a resilient research community is partly determined by the degree of attention and care devoted by researchers to material and social elements beyond the specific research questions under consideration.

This Element presents a philosophical exploration of the concept of the 'model organism' in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology, and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms an important type of model, and how the use of these models has shaped biological knowledge, including how model organisms represent, how they are used as tools for intervention, and how the representational commitments linked to their use as models affect the research practices associated with them. This title is available as Open Access on Cambridge Core.

Previous studies investigating attitudes to genetically modified (GM) foods suggest a correlation between negative attitudes and low levels of science education, both of which are associated with women. In a qualitative focus group study of Australian women with diverse levels of education, we found attitudes to GM foods were part of a complex process of making “good” food decisions, which included other factors such as locally produced, fresh/natural, healthy and nutritious, and convenient. Women involved in GM crop development and those with health science training differed in how they used evidence to categorize GM foods. Our findings contribute to a deeper understanding of how GM food, and the role of science and technology in food production and consumption more broadly, is understood and discussed amongst diverse “publics” and across different “sciences,” and to research related to deepening public engagement at the intersection of science and values.

Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that “for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied”. Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms “Krogh organisms.” We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as “negative models” in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights.

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.

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.

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.

Introduction: philosophy of science in practice Content Type Journal Article Category Editorial Article Pages 303-307 DOI 10.1007/s13194-011-0036-4 Authors Rachel Ankeny, School of History & Politics, University of Adelaide, Napier Building, The University of Adelaide, Adelaide, SA 5005, Australia Hasok Chang, Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH UK Marcel Boumans, Faculty of Economics and Business, University of Amsterdam, Valckenierstraat 65-67, 1018 XE Amsterdam, The Netherlands Mieke Boon, Department of Philosophy, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912 Journal Volume Volume 1 Journal Issue Volume 1, Number 3.