Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state (...) of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo’s description of simulations as “compromises” and “glue”, they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades. (shrink)

The fossil record is paleontology’s great resource, telling us virtually everything we know about the past history of life. This record, which has been accumulating since the beginning of paleontology as a professional discipline in the early nineteenth century, is a collection of objects. The fossil record exists literally, in the specimen drawers where fossils are kept, and figuratively, in the illustrations and records of fossils compiled in paleontological atlases and compendia. However, as has become increasingly clear since the later (...) twentieth century, the fossil record is also a record of data. Paleontologists now routinely abstract information from the physical fossil record to construct databases that serve as the basis for quantitative analysis of patterns in the history of life. What is the significance of this distinction? While it is often assumed that the orientation towards treating the fossil record as a record of data is an innovation of the computer age, it turns out that nineteenth century paleontology was substantially “data driven.” This paper traces the evolution of data practices and analyses in paleontology, primarily through examination of the compendia in which the fossil record has been recorded over the past 200 years. I argue that the transition towards conceptualizing the fossil record as a record of data began long before the emergence of the technologies associated with modern databases (such as digital computers and modern statistical methods). I will also argue that this history reveals how new forms of visual representation were associated with the transition from seeing the fossil record as a record of objects to one of data or information, which allowed paleontologists to make new visual arguments about their data. While these practices and techniques have become increasingly sophisticated in recent decades, I will show that their basic methodology was in place over a century ago, and that, in a sense, paleontology has always been a “data driven” science. (shrink)

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community (...) itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. (shrink)

Recently, biologists have argued that data - driven biology fosters a new scientific methodology; namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data - driven studies can be included into the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful (...) generalizations to complement the procedure of prioritization. Overall this paper aims to shed light on the structure of contemporary research in molecular biology. (shrink)

I argue for the causal character of modeling in data-intensive science, contrary to widespread claims that big data is only concerned with the search for correlations. After discussing the concept of data-intensive science and introducing two examples as illustration, several algorithms are examined. It is shown how they are able to identify causal relevance on the basis of eliminative induction and a related difference-making account of causation. I then situate data-intensive modeling within a broader framework of an epistemology of scientific (...) knowledge. In particular, it is shown to lack a pronounced hierarchical, nested structure. The significance of the transition to such “horizontal” modeling is underlined by the concurrent emergence of novel inductive methodology in statistics such as non-parametric statistics. Data-intensive modeling is well equipped to deal with various aspects of causal complexity arising especially in the higher level and applied sciences. (shrink)

Recent claims, mainly from computer scientists, concerning a largely automated and model-free data-intensive science have been countered by critical reactions from a number of philosophers of science. The debate suffers from a lack of detail in two respects, regarding the actual methods used in data-intensive science and the specific ways in which these methods presuppose theoretical assumptions. I examine two widely-used algorithms, classificatory trees and non-parametric regression, and argue that these are theory-laden in an external sense, regarding the framing of (...) research questions, but not in an internal sense concerning the causal structure of the examined phenomenon. With respect to the novelty of data-intensive science, I draw an analogy to exploratory as opposed to theory-directed experimentation. (shrink)

Agricultural experimentation is a world in constant evolution, spanning multiple scientific domains and affecting society at large. Even though the questions underpinning agricultural experiments remain largely the same, the instruments and practices for answering them have changed constantly during the twentieth century with the advent of new disciplines like molecular biology, genomics, statistics, and computing. Charting this evolving reality requires a mapping of the affinities and antinomies at work within the realm of agricultural research, and a consideration of the practices, (...) tools and social and political structures in which agricultural experiments are grounded. Three main questions will be addressed to provide an overview of the complex world of agricultural research investigated by the special issue: What is an agricultural experiment? Who is an experimenter in agriculture? Where do agricultural experiments take place? It will become apparent that agricultural experiments have a wide relevance for human development as they touch upon concerns related to human health and nutrition, contribute to policy discussions, and can affect the social and political structures in which farming is embedded. (shrink)

Big data techniques, data-driven science and their technological applications raise many serious ethical questions, notably about privacy protection. In this paper, we highlight an entanglement between epistemology and ethics of big data. Discussing the mobilisation of big data in the fields of biomedical research and health care, we show how an overestimation of big data epistemic power – of their objectivity or rationality understood through the lens of neutrality – can become ethically threatening. Highlighting the irreducible non-neutrality at play in (...) big data tools, we insist upon the ethical importance of a critical epistemological approach in which big data are understood as possibly valuable only when coupled with human intelligence and evaluative rationality. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Bioinformatics – the so-called shotgun marriage between biology and computer science – is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised ‘outputs’ in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinary cultures with their own distinct ways of working. Perceived problems of interdisciplinarity include (...) difficulties of making explicit knowledge that is practical, theoretical, or cognitive. But successful interdisciplinary research also depends on an understanding of disciplinary cultures and value systems, often only tacitly understood by members of the communities in question. In bioinformatics, the ‘parent’ disciplines have different value systems; for example, what is considered worthwhile research by computer scientists can be thought of as trivial by biologists, and vice versa. This paper concentrates on the problems of reward and recognition described by scientists working in academic bioinformatics in the United Kingdom. We highlight problems that are a consequence of its cross-cultural make-up, recognising that the mismatches in knowledge in this borderland take place not just at the level of the practical, theoretical, or epistemological, but also at the cultural level too. The trend in big, interdisciplinary science is towards multiple authors on a single paper; in bioinformatics this has created hybrid or fractional scientists who find they are being positioned not just in-between established disciplines but also in-between as middle authors or, worse still, left off papers altogether. (shrink)

Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that (...) they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online. (shrink)

This article examines how the availability of Big Data, coupled with new data analytics, challenges established epistemologies across the sciences, social sciences and humanities, and assesses the extent to which they are engendering paradigm shifts across multiple disciplines. In particular, it critically explores new forms of empiricism that declare ‘the end of theory’, the creation of data-driven rather than knowledge-driven science, and the development of digital humanities and computational social sciences that propose radically different ways to make sense of culture, (...) history, economy and society. It is argued that: Big Data and new data analytics are disruptive innovations which are reconfiguring in many instances how research is conducted; and there is an urgent need for wider critical reflection within the academy on the epistemological implications of the unfolding data revolution, a task that has barely begun to be tackled despite the rapid changes in research practices presently taking place. After critically reviewing emerging epistemological positions, it is contended that a potentially fruitful approach would be the development of a situated, reflexive and contextually nuanced epistemology. (shrink)

Responsible Research and Innovation (‘RRI’) is a cross-cutting priority for scientific research in the European Union and beyond. This paper considers whether the way such research is organised and delivered lends itself to the aims of RRI. We focus particularly on international consortia, which have emerged as a common model to organise large-scale, multi-disciplinary research in contemporary biomedical science. Typically, these consortia operate through fixed-term contracts, and employ governance frameworks consisting of reasonably standard, modular components such as management committees, advisory (...) boards, and data access committees, to co-ordinate the activities of partner institutions and align them with funding agency priorities. These have advantages for organisation and management of the research, but can actively inhibit researchers seeking to implement RRI activities. Conventional consortia governance structures pose specific problems for meaningful public and participant involvement, data sharing, transparency, and ‘legacy’ planning to deal with societal commitments that persist beyond the duration of the original project. In particular, the ‘upstream’ negotiation of contractual terms between funders and the institutions employing researchers can undermine the ability for those researchers to subsequently make decisions about data, or participant remuneration, or indeed what happens to consortia outputs after the project is finished, and can inhibit attempts to make project activities and goals responsive to input from ongoing dialogue with various stakeholders. Having explored these challenges, we make some recommendations for alternative consortia governance structures to better support RRI in future. (shrink)

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

“Ancient DNA Research” is the practice of extracting, sequencing, and analyzing degraded DNA from dead organisms that are hundreds to thousands of years old. Today, many researchers are interested in adapting state-of-the-art molecular biological techniques and high-throughput sequencing technologies to optimize the recovery of DNA from fossils, then use it for studying evolutionary history. However, the recovery of DNA from fossils has also fueled the idea of resurrecting extinct species, especially as its emergence corresponded with the book and movie Jurassic (...) Park in the 1990s. In this paper, I use historical material, interviews with scientists, and philosophical literature to argue that the search for DNA from fossils can be characterized as a data-driven and celebrity-driven practice. Philosophers have recently argued the need to seriously consider the role of data-driven inquiry in the sciences, and likewise, this history highlights the need to seriously consider the role of celebrity in shaping the kind of research that gets pursued, funded, and ultimately completed. On this point, this history highlights that the traditional philosophical and scientific distinctions between data-driven and hypothesis-driven research are not always useful for understanding the process and practice of science. Consequently, I argue that the celebrity status of a particular research practice can be considered as a “serious epistemic strategy” that researchers, as well as editors and funders, employ when making choices about their research and publication processes. This interplay between celebrity and methodology matters for the epistemology of science. (shrink)

This paper uses several case studies to suggest that (1) two prominent definitions of data do not on their own capture how scientists use data and (2) a novel perspectival account of data is needed. It then outlines some key features of what this account could look like. Those prominent views, the relational and representational, do not fully capture what data are and how they function in science. The representational view is insensitive to the scientific context in which data are (...) used. The relational account does not fully account for the empirical nature of data and how it is possible for data to be evidentially useful. The perspectival account surmounts these problems by accommodating a representational element to data. At the same time, data depend upon the epistemic context because they are the product of situated and informed judgements. (shrink)

There are many tangled normative and technical questions involved in evaluating the quality of software used in epidemiological simulations. In this paper we answer some of these questions and offer practical guidance to practitioners, funders, scientific journals, and consumers of epidemiological research. The heart of our paper is a case study of the Imperial College London covid-19 simulator, set in the context of recent work in epistemology of simulation and philosophy of epidemiology.

In science and technology studies today, there is a troubling tendency to portray actors in the biosciences as “cultural dopes” and technology as having monolithic qualities with predetermined outcomes. To remedy this analytical impasse, this article introduces the concept styles of valuation to analyze how actors struggle with valuing technology in practice. Empirically, this article examines how actors in a bioscientific laboratory struggle with valuing the properties and qualities of algorithms in a high-throughput setting and identifies the copresence of several (...) different styles. The question that the actors struggle with is what different configurations of algorithms, devices, and humans are “good bioscience,” that is, what do the actors perform as a good distribution of agency between algorithms and humans? A key finding is that algorithms, robots, and humans are valued in multiple ways in the same setting. For the actors, it is not apparent which configuration of agency and devices is more authoritative nor is it obvious which skills and functions should be redistributed to the algorithms. Thus, rather than tying algorithms to one set of values, such as “speed,” “precision,” or “automation,” this article demonstrates the broad utility of attending to the multivalence of algorithms and technology in practice. (shrink)

ZusammenfassungGenomdaten, Kernstück der 2008 ausgerufenen Big Data-Revolution der Biologie, werden voll automatisiert sequenziert und analysiert. Der Wechsel von der manuellen Laborpraktik der Elektrophorese-Sequenzierung zu DNA-Sequenziermaschinen und softwarebasierten Analyseprogrammen vollzog sich zwischen 1982 und 1992. Erst dieser Wechsel ermöglichte die Flut an Daten, die mit der zweiten und dritten Generation der DNA-Sequenzierer erheblich zunimmt. Doch mit diesem Wechsel verändern sich auch die Validierungsstrategien der Genomdaten. Der Beitrag untersucht beides – die Automatisierung und die damit verbundene Validierungskultur – um ein Bild der (...) Komplexität der Datengenerierung und deren Datenpositivismus zu geben. Leitend ist dabei die Frage, ob dieser Datenpositivismus die Grundlage der aktuell angekündigten Big Data-Revolution der Molekularbiologie ist oder deren Datenhybris. (shrink)

ZusammenfassungGenomdaten, Kernstück der 2008 ausgerufenen Big Data-Revolution der Biologie, werden voll automatisiert sequenziert und analysiert. Der Wechsel von der manuellen Laborpraktik der Elektrophorese-Sequenzierung zu DNA-Sequenziermaschinen und softwarebasierten Analyseprogrammen vollzog sich zwischen 1982 und 1992. Erst dieser Wechsel ermöglichte die Flut an Daten, die mit der zweiten und dritten Generation der DNA-Sequenzierer erheblich zunimmt. Doch mit diesem Wechsel verändern sich auch die Validierungsstrategien der Genomdaten. Der Beitrag untersucht beides – die Automatisierung und die damit verbundene Validierungskultur – um ein Bild der (...) Komplexität der Datengenerierung und deren Datenpositivismus zu geben. Leitend ist dabei die Frage, ob dieser Datenpositivismus die Grundlage der aktuell angekündigten Big Data-Revolution der Molekularbiologie ist oder deren Datenhybris. (shrink)

Philosophers of science diverge on the question what drives the growth of scientific knowledge. Most of the twentieth century was dominated by the notion that theories propel that growth whereas experiments play secondary roles of operating within the theoretical framework or testing theoretical predictions. New experimentalism, a school of thought pioneered by Ian Hacking in the early 1980s, challenged this view by arguing that theory-free exploratory experimentation may in many cases effectively probe nature and potentially spawn higher evidence-based theories. Because (...) theories are often powerless to envisage workings of complex biological systems, theory-independent experimentation is common in the life sciences. Some such experiments are triggered by compelling observation, others are prompted by innovative techniques or instruments, whereas different investigations query big data to identify regularities and underlying organizing principles. A distinct fourth type of experiments is motivated by a major question. Here I describe two question-guided experimental discoveries in biochemistry: the cyclic adenosine monophosphate mediator of hormone action and the ubiquitin-mediated system of protein degradation. Lacking underlying theories, antecedent data bases, or new techniques, the sole guides of the two discoveries were respective substantial questions. Both research projects were similarly instigated by theory-free exploratory experimentation and continued in alternating phases of results-based interim working hypotheses, their examination by experiment, provisional hypotheses again, and so on. These two cases designate theory-free, question-guided, stepwise biochemical investigations as a distinct subtype of the new experimentalism mode of scientific enquiry. (shrink)