This is not an article: Model organism newsletters and the question of ‘open science’

Who We Test For: Aligning Relational and Public Health Responsibilities in COVID-19 Testing in Scotland

COVID-19 testing programs in the UK often called on people to test to "protect others." In this article we explore motivations to test and the relationships to "others" involved in an asymptomatic testing program at a Scottish university. We show that participants engaged with testing as a relational technology, through which they navigated multiple overlapping responsibilities to kin, colleagues, flatmates, strangers, and to more diffuse publics. We argue that the success of testing as a technique of governance depends not only on the production of disciplined selves, but also on the program's capacity to align interpersonal and public scales of responsibility.

An economy of details: standards and data reusability

Reusability has been a key issue since the origins of the parts-based approach to synthetic biology. Starting with the BioBrick™ standard part, multiple efforts have aimed to make biology more exchangeable. The reusability of parts and other deoxyribonucleic acid-based data has proven over time to be challenging, however. Drawing on a series of qualitative interviews and an international workshop, this article explores the challenges of reusability in real laboratory practice. It shows particular ways that standards are experienced as presenting shortcomings for capturing the kinds of contextual information crucial for scientists to be able to reuse biological parts and data. I argue that researchers in specific laboratories develop a sense of how much circumstantial detail they need to share for others to be able to make sense of their data and possibly reuse it. When choosing particular reporting formats, recharacterizing data to gain closer knowledge or requesting additional information, researchers enact an 'economy of details'. The farther apart two laboratories are in disciplinary, epistemological, technical and geographical terms, the more detailed information needs to be captured for data to be reusable across contexts. In synthetic biology, disciplinary distance between computing science and engineering researchers and experimentalist biologists is reflected in diverging views on standards: what kind of information should be included to enable reusability, what kind of information can be captured by standards at all and how they may serve to produce and circulate knowledge. I argue that such interdisciplinary tensions lie at the core of difficulties in setting standards in synthetic biology.

Taking hobbyists seriously: The reef tank hobby and knowledge production in serious leisure

Studies of communities that produce knowledge about the natural world have largely focused on groups working with or for academic scientists and conforming to the epistemic values of academic knowledge production. This paper details a community that produces natural knowledge outside of those parameters. The reef hobbyist community, a group that works with aquariums as a form of non-professional leisure, has developed historical narratives, publishing standards, and recognized forms of expertise that are not shared by academic scientists. However, their goal is to produce knowledge about coral systems and their hobby has resulted in a wealth of knowledge about coral husbandry. In this paper, I identify the structure of this community, highlight several prominent groups that make up the network of reef hobbyists, and trace the ways that they produce knowledge about the marine environment through their actions. This paper contributes to discussions about diverse ways of knowing and differing forms of knowledge production in the history and philosophy of science. By examining the history and practices of a well-developed knowledge community outside of academic science, I hope to call attention to the ways that philosophers and historians have centered academic science and its structure and use of knowledge, even in conversations about non-professional knowledge producers. This paper pushes scholars to think more deeply about the way knowledge is developed in non-academic groups.

Animal research nexus: a new approach to the connections between science, health and animal welfare

Animals used in biological research and testing have become integrated into the trajectories of modern biomedicine, generating increased expectations for and connections between human and animal health. Animal research also remains controversial and its acceptability is contingent on a complex network of relations and assurances across science and society, which are both formally constituted through law and informal or assumed. In this paper, we propose these entanglements can be studied through an approach that understands animal research as a nexus spanning the domains of science, health and animal welfare. We introduce this argument through, first, outlining some key challenges in UK debates around animal research, and second, reviewing the way nexus concepts have been used to connect issues in environmental research. Third, we explore how existing social sciences and humanities scholarship on animal research tends to focus on different aspects of the connections between scientific research, human health and animal welfare, which we suggest can be combined in a nexus approach. In the fourth section, we introduce our collaborative research on the animal research nexus, indicating how this approach can be used to study the history, governance and changing sensibilities around UK laboratory animal research. We suggest the attention to complex connections in nexus approaches can be enriched through conversations with the social sciences and medical humanities in ways that deepen appreciation of the importance of path-dependency and contingency, inclusion and exclusion in governance and the affective dimension to research. In conclusion, we reflect on the value of nexus thinking for developing research that is interdisciplinary, interactive and reflexive in understanding how accounts of the histories and current relations of animal research have significant implications for how scientific practices, policy debates and broad social contracts around animal research are being remade today.

How to choose your research organism

Despite August Krogh's famous admonition that a 'convenient' organism exists for every biological problem, we argue that appeals to 'convenience' are not sufficient to capture reasoning about organism choice. Instead, we offer a detailed analysis based on empirical data and philosophical arguments for a working set of twenty criteria that interact with each other in the highly contextualized judgements that biologists make about organism choice. We propose to think of these decisions as a form of 'differential analysis' where researchers weigh multiple criteria for organismal choice against each other, and often utilize multidimensional refinement processes to finalize their choices. The specific details of any one case make it difficult to draw generalizations or to abstract away from specific research situations. However, this analysis of criteria for organismal choice and how these are related in practice allows us to reflect more generally on what makes a particular organism useful or 'good.'

Living collections: care and curation at Drosophila stock centres

Biological stock centres collect, care for and distribute living organisms for scientific research. In the 1990s, several of the world's largest Drosophila (fruit fly) stock centres were closed or threatened with closure. This paper reflects on why this happened, and uses the visibility of these endings to examine how stock centre collections are managed, who maintains them and how they are kept valuable and accessible to biologists. One stock centre came under threat because of challenges in caring for flies and monitoring the integrity of stocks. Another was criticized for keeping too many 'archival' stocks, an episode that reveals what it can mean for a living scientific collection to remain 'relevant' to a research community. That centre also struggled with the administrative and documentary practices that have proved crucial for sustaining a collection's meaning, value and availability. All of the stock centres in this story faced challenges of how to pay for care and curation, engaging with a problem that has been discussed by biologists and their funders since the 1940s: what are the best models for stock provision, and how could these models be changed?

From bean collection to seed bank: transformations in heirloom vegetable conservation, 1970-1985

In 1975, the Missouri homesteaders Kent and Diane Ott Whealy launched True Seed Exchange (later Seed Savers Exchange), a network of 'serious gardeners' interested in growing and conserving heirloom and other hard-to-find plant varieties, especially vegetables. In its earliest years, the organization pursued its conservation mission through member-led exchange and cultivation, seeing members' gardens and seed collections as the best means of ensuring that heirloom varieties remained both extant and available to growers. Beginning in 1981, however, Kent Whealy began to develop a central seed repository. As I discuss in this paper, the development of this central collection was motivated in part by concerns about the precariousness of very large individual collections, the maintenance of which was too demanding to entrust to most growers. Although state-run institutions were better positioned to take on large collections, they were nonetheless unsuitable stewards because they placed limits on access. For seed savers, loss of access to varieties via their accession into a state collection could be as much an ending for treasured collections as total physical loss, as it did not necessarily enable continued cultivation. As I show here, these imagined endings inspired the adoption of a new set of conservation practices that replicated those seen in the formal genetic conservation sector, including seed banking, cold storage and safety duplication.

The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). 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 (NIH) 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 (LMB) 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.

Science communication in the field of fundamental biomedical research (editorial)

The aim of this special issue on science communication is to inspire and help scientists who are taking part or want to take part in science communication and engage with the wider public, clinicians, other scientists or policy makers. For this, some articles provide concise and accessible advice to individual scientists, science networks, or learned societies on how to communicate effectively; others share rationales, objectives and aims, experiences, implementation strategies and resources derived from existing long-term science communication initiatives. Although this issue is primarily addressing scientists working in the field of biomedical research, much of it similarly applies to scientists from other disciplines. Furthermore, we hope that this issue will also be used as a helpful resource by academic science communicators and social scientists, as a collection that highlights some of the major communication challenges that the biomedical sciences face, and which provides interesting case studies of initiatives that use a breadth of strategies to address these challenges. In this editorial, we first discuss why we should communicate our science and contemplate some of the different approaches, aspirations and definitions of science communication. We then address the specific challenges that researchers in the biomedical sciences are faced with when engaging with wider audiences. Finally, we explain the rationales and contents of the different articles in this issue and the various science communication initiatives and strategies discussed in each of them, whilst also providing some information on the wide range of further science communication activities in the biomedical sciences that could not all be covered here.

How lives became lists and scientific papers became data: cataloguing authorship during the nineteenth century

The Catalogue of Scientific Papers, published by the Royal Society of London beginning in 1867, projected back to the beginning of the nineteenth century a novel vision of the history of science in which knowledge was built up out of discrete papers each connected to an author. Its construction was an act of canon formation that helped naturalize the idea that scientific publishing consisted of special kinds of texts and authors that were set apart from the wider landscape of publishing. By recovering the decisions and struggles through which the Catalogue was assembled, this essay aims to contribute to current efforts to denaturalize the scientific paper as the dominant genre of scientific life. By privileging a specific representation of the course of a scientific life as a list of papers, the Catalogue helped shape underlying assumptions about the most valuable fruits of a scientific career. Its enumerated lists of authors' periodical publications were quickly put to use as a means of measuring scientific productivity and reputation, as well as by writers of biography and history. Although it was first conceived as a search technology, this essay locates the Catalogue's most consequential legacy in its uses as a technology of valuation.

How Does One "Open" Science? Questions of Value in Biological Research

Open Science policies encourage researchers to disclose a wide range of outputs from their work, thus codifying openness as a specific set of research practices and guidelines that can be interpreted and applied consistently across disciplines and geographical settings. In this paper, we argue that this "one-size-fits-all" view of openness sidesteps key questions about the forms, implications, and goals of openness for research practice. We propose instead to interpret openness as a dynamic and highly situated mode of valuing the research process and its outputs, which encompasses economic as well as scientific, cultural, political, ethical, and social considerations. This interpretation creates a critical space for moving beyond the economic definitions of value embedded in the contemporary biosciences landscape and Open Science policies, and examining the diversity of interests and commitments that affect research practices in the life sciences. To illustrate these claims, we use three case studies that highlight the challenges surrounding decisions about how--and how best--to make things open. These cases, drawn from ethnographic engagement with Open Science debates and semistructured interviews carried out with UK-based biologists and bioinformaticians between 2013 and 2014, show how the enactment of openness reveals judgments about what constitutes a legitimate intellectual contribution, for whom, and with what implications.

Bermuda 2.0: reflections from Santa Cruz

In February 1996, the genome community met in Bermuda to formulate principles for circulating genomic data. Although it is now 20 years since the Bermuda Principles were formulated, they continue to play a central role in shaping genomic and data-sharing practices. However, since 1996, "openness" has become an increasingly complex issue. This commentary seeks to articulate three core challenges data-sharing faces today.

Beams of particles and papers: How digital preprint archives shape authorship and credit

In high energy physics, scholarly papers circulate primarily through online preprint archives based on a centralized repository, arXiv, that physicists simply refer to as 'the archive'. The archive is not just a tool for preservation and memory but also a space of flows where written objects are detected and their authors made available for scrutiny. In this article, I analyze the reading and publishing practices of two subsets of high energy physicists: theorists and experimentalists. In order to be recognized as legitimate and productive members of their community, they need to abide by the temporalities and authorial practices structured by the archive. Theorists live in a state of accelerated time that shapes their reading and publishing practices around precise cycles. Experimentalists turn to tactics that allow them to circumvent the slowed-down time and invisibility they experience as members of large collaborations. As digital platforms for the exchange of scholarly articles emerge in other fields, high energy physics could help shed light on general transformations of contemporary scholarly communication systems.

It is what it eats: Chemically defined media and the history of surrounds

The cultivation of living organs, cells, animals, and embryos in the laboratory has been central to the production of biological knowledge. Over the twentieth century, the drive to variance control in the experimental setting led to systematic efforts to generate synthetic, chemically defined substitutes for complex natural foods, housing, and other substrates of life. This article takes up the history of chemically defined media with three aims in mind. First, to characterize patterns of decontextualization, tinkering, and negotiation between life and experimenter that occur across disparate histories of cultivation. Second, to highlight the paradoxical historicity of cultivated organisms generated to be freed from context, as they incorporate and embody the purified amino acids, vitamins, plastics, and other artificial supports developed in the name of experimental control. Third, to highlight the figure-ground reversal that occurs as these cells and organisms are reconsidered as accidentally good models of life in industrialized conditions of pollution and nutrient excess, due to the man-made nature of their surrounds. Methodologically, the history of surrounds is described as an epigenetic approach that focuses on the material relations between different objects and organisms previously considered quite separately, from explanted organs to bacteria to plant cells to rats to human embryos.

What Difference Does Quantity Make? On the Epistemology of Big Data in Biology

Is big data science a whole new way of doing research? And what difference does data quantity make to knowledge production strategies and their outputs? I argue that the novelty of big data science does not lie in the sheer quantity of data involved, but rather in (1) the prominence and status acquired by data as commodity and recognised output, both within and outside of the scientific community; and (2) the methods, infrastructures, technologies, skills and knowledge developed to handle data. These developments generate the impression that data-intensive research is a new mode of doing science, with its own epistemology and norms. To assess this claim, one needs to consider the ways in which data are actually disseminated and used to generate knowledge. Accordingly, this paper reviews the development of sophisticated ways to disseminate, integrate and re-use data acquired on model organisms over the last three decades of work in experimental biology. I focus on online databases as prominent infrastructures set up to organise and interpret such data; and examine the wealth and diversity of expertise, resources and conceptual scaffolding that such databases draw upon. This illuminates some of the conditions under which big data need to be curated to support processes of discovery across biological subfields, which in turn highlights the difficulties caused by the lack of adequate curation for the vast majority of data in the life sciences. In closing, I reflect on the difference that data quantity is making to contemporary biology, the methodological and epistemic challenges of identifying and analyzing data given these developments, and the opportunities and worries associated to big data discourse and methods.

The perils and promises of microbial abundance: novel natures and model ecosystems, from artisanal cheese to alien seas

Microbial life has been much in the news. From outbreaks of Escherichia coli to discussions of the benefits of raw and fermented foods to recent reports of life forms capable of living in extreme environments, the modest microbe has become a figure for thinking through the presents and possible futures of nature, writ large as well as small. Noting that dominant representations of microbial life have shifted from an idiom of peril to one of promise, we argue that microbes--especially when thriving as microbial communities--are being upheld as model ecosystems in a prescriptive sense, as tokens of how organisms and human ecological relations with them could, should, or might be. We do so in reference to two case studies: the regulatory politics of artisanal cheese and the speculative research of astrobiology. To think of and with microbial communities as model ecosystems offers a corrective to the scientific determinisms we detect in some recent calls to attend to the materiality of scientific objects.

Why the Current Insistence on Open Access to Scientific Data? Big Data, Knowledge Production, and the Political Economy of Contemporary Biology

The collection and dissemination of data on human and nonhuman organisms has become a central feature of 21st-century biology and has been endorsed by funding agencies in the United States and Europe as crucial to translating biological research into therapeutic and agricultural innovation. Large molecular data sets, often referred to as “big data,” are increasingly incorporated into digital databases, many of which are freely accessible online. These data have come to be seen as resources that play a key role in mediating global market exchange, thus achieving a prominent social and economic status well beyond science itself. At the same time, calls to make all such data publicly and freely available have garnered strength and visibility, most prominently in the form of the Open Data movement. I discuss these developments by considering the conditions under which data journey across the communities and institutions implicated in globalized biology and biomedicine, and what this indicates about how Internet-based communication and the use of online databases affect scientific research and its role within contemporary society.