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)

While scientific pluralism enjoys widespread popularity within the philosophy of science, a related position, epistemic relativism, does not have much traction. Defenders of scientific pluralism, however, dread the question of whether scientific pluralism entails epistemic relativism. It is often argued that if a scientific pluralist accepts epistemic relativism, she will be unable to pass judgment because she believes that “anything goes”. In this article, I will show this concern to be unnecessary. I will also argue that common strategies to differentiate (...) relativism and pluralism fail. Building upon this analysis, I will propose a new way of looking at both positions’ relations. This article aims to understand what explains the friction between scientific pluralism and epistemic relativism. I will demonstrate that conceptualizing both epistemic relativism and scientific pluralism as “stances” sheds better light on their relation and demonstrates that it is, in principle, possible to support both positions at the same time. Preferred policies and levels of analysis, however, cause friction in practice. (shrink)

In his insightful review, Eugene V. Koonin discusses various aspects of CRISPR-Cas systems with a strong focus on their qualities as "adaptive immune systems". The CRISPR-Cas system is most famous for its application as a gene-editing tool. Koonin provides a deeper insight into its biological function in bacteria, which is to immunize the cell against parasite DNA. I shall comment on one issue discussed in the text, in two steps. First, I shall elaborate on CRISPR-Cas systems and their supposed Lamarckian (...) character. Criteria for calling biological phenomena genuinely Lamarckian will be narrowed down and then applied to the CRISPR-Cas system, considering interference-driven spacer acquisition as an instantiation of a truly Lamarckian paradigm. Second, I shall consider whether Lamarckian and "canonical" instances of inheritance are a case of theoretical pluralism, being two non-reducible, yet interconnected paradigms. (shrink)

In recent years, immune systems have sparked considerable interest within the philosophy of science. One issue that has received increased attention is whether other phyla besides vertebrates display an adaptive immune system. Particularly the discovery of CRISPR-Cas9-based systems has triggered a discussion about how to classify adaptive immune systems. One question that has not been addressed yet is the transgenerational aspect of the CRISPR-Cas9-based response. If immunity is acquired and inherited, how to distinguish evolutionary from immunological adaptation? To shed light (...) on this issue and obtain conceptual clarity, I will investigate the inheritance of small RNA responses to pathogens in the nematode C. elegans as a further potential instantiation of a transgenerational adaptive immune system. I will explore how to make sense of systems that lie at the crossroads between genetic, immunological, and evolutionary spheres and explore the consequences of a transgenerational perspective on immune systems for immunology and its philosophy. (shrink)

In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher’s name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher’s reception in the historiography of genetics. To his critics, Miescher was a “contaminator,” whose preparations were impure. Modern historians portrayed him as a “confuser,” whose misunderstandings delayed the development of molecular biology. Each of (...) these portrayals reflects the disciplinary context in which Miescher’s work was evaluated. Using archival sources to unearth Miescher’s unpublished speculations—including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation—this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago. (shrink)

Fundamental disagreement is at the core of many debates surrounding epistemic relativism. Proponents of epistemic relativism argue that certain disagreements are irresolvable because proponents base their views on fundamentally different epistemic principles and, thus, fundamentally different epistemic systems. Critics of epistemic relativism argue that this analysis is wrong since the particular epistemic principles in question are most of the time derived from or instances of the same, more basic, epistemic principle. With regard to the individuation of epistemic systems, there is, (...) thus, an impasse within the epistemic relativism literature. It is the aim of this article to employ the recently developed notion of ‘situated judgments’ as well as the concepts of ‘world-traveling’ and ‘epistemic friction’ to provide an epistemic agent-based, dynamic account of disagreeing and thereby also contribute to the question of how to individuate an epistemic system. (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)

The “Encyclopedia of DNA Elements” (ENCODE) project was launched by the US National Human Genome Research Institute in the aftermath of the Human Genome Project (HGP). It aimed to systematically map the human transcriptome, and held the promise that identifying potential regulatory regions and transcription factor binding sites would help address some of the perplexing results of the HGP. Its initial results published in 2012 produced a flurry of high-impact publications as well as criticisms. Here we put the results of (...) ENCODE and the work on epigenomics that followed in a broad theoretical and historical context, focusing on three strands of research. The first is the history of thinking about the organization of genomes, both physical and regulatory. The second is the history of ideas about gene regulation, primarily in eukaryotes. Finally, and connecting these two issues, we suggest how to think about the role of genetic material in physiology and development. (shrink)

Scientific pluralism has become a household position within the philosophy of science literature. There are numerous accounts of plurality within various research fields. Most scientific pluralists, however, focus on the plurality of theories, explanations, or mechanisms, while other potential targets of plurality that the philosophy of scientific practice has particularly emphasized have so far not received extensive treatment. How should we approach such practice-based candidates of plurality? And what are potential pluralist positions concerning the objects of scientific practice? In this (...) article, I set out to answer these questions. I combine approaching a widely influential topic within the philosophy of science, scientific pluralism, with social science methodology. Using interview data combined with sociological analysis, I provide a nuanced picture of the dynamics of one particular research field that displays plurality. Focusing on how sociological configurations resonate with intellectual commitments within a research field, I disentangle practice-based from theoretical plurality. I consider how these empirical results should feedback on the scientific pluralism literature. (shrink)