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)

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology (...) to become an engineering discipline, that allows that science to slip into the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena. (shrink)

We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not (...) require material manipulation. We also suggest that material manipulation, although still present in in the practice of data mining, fulfill a different epistemic role. (shrink)

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 the prominence and status acquired by data as commodity and recognised output, both within and outside of the scientific community and 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 article 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 needs 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 analysing data given these developments, and the opportunities and worries associated with Big Data discourse and methods. (shrink)

Agricultural Big Data analytics (ABDA) is being proposed to ensure better farming practices, decision-making, and a sustainable future for humankind. However, the use and adoption of these technologies may bring about potentially undesirable consequences, such as exercises of power. This paper will analyse Brey’s five distinctions of power relationships (manipulative, seductive, leadership, coercive, and forceful power) and apply them to the use agricultural Big Data. It will be shown that ABDA can be used as a form of manipulative (...) power to initiate cheap land grabs and acquisitions. Seductive power can be exercised by pressuring farmers into situations they would not have otherwise chosen (such as installing monitors around their farm and limited access to their farm and machinery). It will be shown that agricultural technology providers (ATPs) demonstrate leadership power by getting farmers to agree to use ABDA without informed consent. Coercive power is exercised when ATPs threaten farmers with the loss of ABDA if they do not abide by the policies and requirements of the ATP or are coerced to remain with the ATP because of fear of legal and economic reprisal. ATPs may use ABDA to determine willingness-to-pay rates from farmers, using this information to force farmers into precarious and vulnerable positions. Altogether, this paper will apply these five types of power to the use and implementation of ABDA to demonstrate that it is being used to exercise power in the agricultural industry. (shrink)

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. (shrink)

This paper argues that analyses of the ways in which Big Data has been enacted in other academic disciplines can provide us with concepts that will help understand the application of Big Data to social questions. We use examples drawn from our Science and Technology Studies analyses of -omic biology and high energy physics to demonstrate the utility of three theoretical concepts: primary and secondary inscriptions, crafted and found data, and the locus of legitimate interpretation. These (...) help us to show how the histories, organisational forms, and power dynamics of a field lead to different enactments of big data. The paper suggests that these concepts can be used to help us to understand the ways in which Big Data is being enacted in the domain of the social sciences, and to outline in general terms the ways in which this enactment might be different to that which we have observed in the ‘hard’ sciences. We contend that the locus of legitimate interpretation of Big Data biology and physics is tightly delineated, found within the disciplinary institutions and cultures of these disciplines. We suggest that when using Big Data to make knowledge claims about ‘the social’ the locus of legitimate interpretation is more diffuse, with knowledge claims that are treated as being credible made from other disciplines, or even by those outside academia entirely. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are (...) pragmatic trade-offs between precision and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

As opposed to a ‘one size fits all’ approach, precision medicine uses relevant biological, medical, behavioural and environmental information about a person to further personalize their healthcare. This could mean better prediction of someone’s disease risk and more effective diagnosis and treatment if they have a condition. Big data allows for far more precision and tailoring than was ever before possible by linking together diverse datasets to reveal hitherto-unknown correlations and causal pathways. But it also raises ethical issues relating (...) to the balancing of interests, viability of anonymization, familial and group implications, as well as genetic discrimination. This article analyses these issues in light of the values of public benefit, justice, harm minimization, transparency, engagement and reflexivity and applies the deliberative balancing approach found in theEthical Framework for Big Data in Health and Research to a case study on clinical genomic data sharing. Please refer to that article for an explanation of how this framework is to be used, including a full explanation of the key values involved and the balancing approach used in the case study at the end. Our discussion is meant to be of use to those involved in the practice as well as governance and oversight of precision medicine to address ethical concerns that arise in a coherent and systematic manner. (shrink)

We live in the Age of Big Data. In medicine, artificial intelligence and machine learning algorithms, fueled by big data, promise to change how physicians make diagnoses, determine prognoses, and develop new treatments. An exponential rise in articles on these topics is seen in the medical literature. Recent applications range from the use of deep learning neural networks to diagnose diabetic retinopathy and skin cancer from image databases, to the use of various machine learning algorithms for prognostication in (...) cancer and cardiovascular disease. Many factors are driving the adoption of AI in health care, from... (shrink)

As with many other countries, Malaysia is also developing and promoting biomedical research to increase the understanding of human diseases and possible interventions. To facilitate this development, there is a significant growth of biobanks in the country to ensure continuous collection of biological samples for future research, which contain extremely important personal information and health data of the participants involved. Given the vast amount of samples and data accumulated by biobanks, they can be considered as reservoirs of precious (...) biomedical big data. It is therefore imperative for biobanks to have in place regulatory measures to ensure ethical use of the biomedical big data. Malaysia has yet to introduce specific legislation for the field of biobanking. However, it can be argued that its existing Personal Data Protection Act 2010 has laid down legal principles that can be enforced to protect biomedical big data generated by the biobanks. Consent is a mechanism to enable data subjects to exercise their autonomy by determining how their data can be used and ensure compliance with legal principles. However, there are two main concerns surrounding the current practice of consent in biomedical big data in Malaysia. First, it is uncertain that the current practice would be able to respect the underlying notion of autonomy, and second, it is not in accordance with the legal principles of the PDPA. Scholars have deliberated on different strategies of informed consent, and a more interactive approach has recently been introduced: dynamic consent. It is argued that a dynamic consent approach would be able to address these concerns. (shrink)

In biology—as in other scientific fields—there is a lively opposition between big and small science projects. In this commentary, I try to contextualize this opposition in the field of biomedicine, and I argue that, at least in this context, big science projects should come first.

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in (...) biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

This article provides an ethnographic account of how Big Data biology is produced, interpreted, debated, and translated in a Big Data-driven cancer clinical trial, entitled “Personalized OncoGenomics,” in Vancouver, Canada. We delve into epistemological differences between clinical judgment, pathological assessment, and bioinformatic analysis of cancer. To unpack these epistemological differences, we analyze a set of gazes required to produce Big Data biology in cancer care: clinical gaze, molecular gaze, and informational gaze. We are concerned with (...) the interactions of these bodily gazes and their interdependence on each other to produce Big Data biology and translate it into clinical knowledge. To that end, our central research questions ask: How do medical practitioners and data scientists interact, contest, and collaborate to produce and translate Big Data into clinical knowledge? What counts as actionable and reliable data in cancer decision-making? How does the explicability or translatability of genomic Big Data come to redefine or contradict medical practice? The article contributes to current debates on whether Big Data engenders new questions and approaches to biology, or Big Data biology is merely an extension of early modern natural history and biology. This ethnographic account will highlight how genomic Big Data, which underpins the mechanism of personalized medicine, allows oncologists to understand and diagnose cancer in a different light, but it does not revolutionize or disrupt medical oncology on an institutional level. Rather, personalized medicine is interdependent on different styles of thought, gaze, and practice to be produced and made intelligible. (shrink)

A central theme in western philosophy was to find formal methods that can reliably discover empirical relationships and their explanations from data assembled from experience. As a philosophical project, that ambition was abandoned in the 20th century and generally dismissed as impossible. It was replaced in philosophy by neo-Kantian efforts at reconstruction and justification, and in professional statistics by the more limited ambition to estimate a small number of parameters in pre-specified hypotheses. The influx of “big data” from (...) climate science, neuropsychology, biology, astronomy and elsewhere implicitly called for a revival of the grander philosophical ambition. Search algorithms are meeting that call, but they pose a problem: how are their accuracies to be assessed in domains where experimentation is limited or impossible? Increasingly, the answer is through simulation of data from models of the kind of process in the domain. In some cases, these innovations require rethinking how the accuracy and informativeness of inference methods can be assessed. Focusing on causal inference, we give an example from neuroscience, but to show that the model/simulation strategy is not confined to causal inference, we also consider two classification problems from astrophysics: identifying exoplanets and identifying dark matter concentrations. (shrink)

[Without a theorising], a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!Recent years have seen a steady shift of funding programs in biomedical research towards data collection, analysis, and management and its computational analysis. A sizable majority of new major funding opportunity announcements call for (...) assembling large sample banks and databases of molecular profiles of diseases or for computational tools for analysis, display, and distribution of the data. Large consortium projects, such as the Cancer Genome Atlas, the UK Biobank (Allen... (shrink)

Dominant forms of contemporary big-data based digital citizen science do not question the institutional divide between qualified experts and lay-persons. In our paper, we turn to the historical case of a large-scale amateur project on biogeographical birdwatching in the late nineteenth and early twentieth century to show that networked amateur research can operate in a more autonomous mode. This mode depends on certain cultural values, the constitution of specific knowledge objects, and the design of self-governed infrastructures. We conclude by (...) arguing that the contemporary quest for autonomous citizen science is part of a broader discourse on the autonomy of scientific research in general. Just as the actors in our historical case positioned themselves against the elitism of gentlemen scientists, avant-garde groups of the twenty first century like biohackers and civic tech enthusiasts position themselves against the system of professional science—while “digital citizen science” remains to oscillate between claims for autonomy and realities of heteronomy, constantly reaffirming the classic lay-expert divide. (shrink)

There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a biological cause for (...) phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual’s lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really “new,” or “old wine in new bottles.”. (shrink)

Defense of Scientific Hypothesis: From Reproducibility Crisis to Big Data sets out to explain and defend the scientific hypothesis. Alger's mission is to counteract the misinformation and misunderstanding about the hypothesis that even seasoned scientists have concerning its nature and place in modern science. Most biological scientists receive little or no formal training in scientific thinking. Further, the hypothesis is under attack by critics who claim that it is irrelevant to science. In order to appreciate and evaluate scientific controversies (...) like global climate change, vaccine safety, etc., the public first needs to understand the hypothesis. Defense of Scientific Hypothesis begins by describing and analyzing the scientific hypothesis in depth and examining its relationships to various kinds of science. Alger then guides readers through a review of the hypothesis in the context of the Reproducibility Crisis and presents survey data on how scientists perceive and employ hypotheses. He assesses cognitive factors that influence our ability to use the hypothesis and makes practical and policy recommendations for teaching and learning about it. Finally, Alger considers two possible futures of the hypothesis in science as the Big Data revolution looms: in one scenario, the hypothesis is displaced by the Big Data Mindset that forgoes understanding in favor of correlation and prediction. In the other, robotic science incorporates the hypotheses into mechanized laboratories guided by artificial intelligence. But in his illuminating epilogue, Alger envisions a third way, the Centaur Scientist, a symbiotic relationship between human scientists and computers. (shrink)

Genomic data is generated, processed and analysed at an increasingly rapid pace. This data is not limited to the medical context, but plays an important role in other contexts in society, such as commercial DNA testing, the forensic setting, archaeological research, and genetic surveillance. Genomic information also crosses the borders of these domains, e.g. forensic use of medical genetic information, insurance use of medical genomic information, or research use of commercial genomic data. This paper (1) argues that (...) an informed consent approach for genomic information has limitations in many societal contexts, and (2) seeks to broaden the bioethical debate on genomic information by suggesting an approach that is applicable across multiple societal contexts. I argue that the contextual integrity framework, a theory rooted in information technology and big data ethics, is an effective tool to explore ethical challenges that arise from genomic information within a variety of different contexts. Rather than focusing on individual control over information, the contextual integrity approach holds that information should be shared and protected according to the norms that govern certain distinct social contexts. Several advantages of this contextual integrity approach will be discussed. The paper concludes that the contextual integrity framework helps to articulate and address a broad spectrum of ethical, social, and political factors in a variety of different societal contexts, while giving consideration to the interests of individuals, groups, and society at large. (shrink)

Biomarkers are widely used not only as prognostic or diagnostic indicators, or as surrogate markers of disease in clinical trials, but also to formulate theories of pathogenesis. We identify two problems in the use of biomarkers in mechanistic studies. The first problem arises in the case of multifactorial diseases, where different combinations of multiple causes result in patient heterogeneity. The second problem arises when a pathogenic mediator is difficult to measure. This is the case of the oxidative stress (OS) theory (...) of disease, where the causal components are reactive oxygen species (ROS) that have very short half-lives. In this case, it is usual to measure the traces left by the reaction of ROS with biological molecules, rather than the ROS themselves. Borrowing from the philosophical theories of signs, we look at the different facets of biomarkers and discuss their different value and meaning in multifactorial diseases and system medicine to inform their use in patient stratification in personalized medicine. (shrink)

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. Based on diverse paleontological data and an analogy with macrosociological models, we suggest that (...) the hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

The emergence of systems biology raises many fascinating questions: What does it mean to take a systems approach to problems in biology? To what extent is the use of mathematical and computational modelling changing the life sciences? How does the availability of big data influence research practices? What are the major challenges for biomedical research in the years to come? This book addresses such questions of relevance not only to philosophers and biologists but also to readers interested (...) in the broader implications of systems biology for science and society. The book features reflections and original work by experts from across the disciplines including systems biologists, philosophers, and interdisciplinary scholars investigating the social and educational aspects of systems biology. In response to the same set of questions, the experts develop and defend their personal perspectives on the distinctive character of systems biology and the challenges that lie ahead. Readers are invited to engage with different views on the questions addressed, and may explore numerous themes relating to the philosophy of systems biology. This edited work will appeal to scholars and all levels, from undergraduates to researchers, and to those interested in a variety of scholarly approaches such as systems biology, mathematical and computational modelling, cell and molecular biology, genomics, systems theory, and of course, philosophy of biology. (shrink)

Big dreams are rare but highly memorable dream experiences that make a strong and lasting impact on the dreamer's waking awareness. Moving far beyond "I forgot to study and the finals are today" and other common scenarios, such dreams can include vivid imagery, intense emotions, fantastic characters, and an uncanny sense of being connected to forces beyond one's ordinary dreaming mind. In Big Dreams, Kelly Bulkeley provides the first full-scale cognitive scientific analysis of such dreams, putting forth an original theory (...) about their formation, function, and meaning.Big dreams have played significant roles in religious and cultural history, but because of their infrequent occurrence and fantastical features, they have rarely been studied in light of modern science. We know a great deal about the religious manifestations of big dreams throughout history and around the world, but until now that cross-cultural knowledge has never been integrated with scientific research on their psychological roots in the brain-mind system. In Big Dreams, Bulkeley puts a classic psychological thesis to the scientific test by clarifying and improving it with better data, sharper analysis, and a broader evolutionary framework. He brings evidence from multiple sources, shows patterns of similarity and difference, questions prior assumptions, and provides predictive models that can be applied to new sets of data. The notion of a connection between dreaming and religion has always been intuitively compelling; Big Dreams transforms it into a solid premise of religious studies and brain-mind science. Combining evidence from religious studies, psychology, anthropology, evolutionary biology, and neuroscience, Big Dreams makes a compelling argument that big dreams are a primal wellspring of religious experience. They represent an innate, neurologically hard-wired capacity of our species that regularly provokes greater self-awareness, creativity, and insight into the existential challenges and spiritual potentials of human life. (shrink)

This paper proposes an account of scientific data that makes sense of recent debates on data-driven and ‘big data’ research, while also building on the history of data production and use particularly within biology. In this view, ‘data’ is a relational category applied to research outputs that are taken, at specific moments of inquiry, to provide evidence for knowledge claims of interest to the researchers involved. They do not have truth-value in and of themselves, (...) nor can they be seen as straightforward representations of given phenomena. Rather, they are fungible objects defined by their portability and prospective usefulness as evidence. (shrink)

Modern science’s ability to produce, store, and analyze big datasets is changing the way that scientific research is practiced. Philosophers have only begun to comprehend the changed nature of scientific reasoning in this age of “big data.” We analyze data-focused practices in biology and climate modeling, identifying distinct species of data-centric science: phenomena-laden in biology and phenomena-agnostic in climate modeling, each better suited for its own domain of application, though each entail trade-offs. We argue that (...) data-centric practices in science are not monolithic because the opportunities and challenges presented by big data vary across scientific domains. (shrink)

Both clinical research and basic science rely on the epistemic practice of extrapolation from surrogate models, to the point that explanatory accounts presented in review papers and biology textbooks are in fact composite pictures reconstituted from data gathered in a variety of distinct experimental setups. This raises two new challenges to previously proposed mechanistic-similarity solutions to the problem of extrapolation: one pertaining to the absence of mechanistic knowledge in the early stages of research and the second to the (...) large number of extrapolations underpinning explanatory accounts. An analysis of the strategies deployed in experimental research supports the conclusion that while results from validated surrogate models are treated as a legitimate line of evidence supporting claims about target systems, the overall structure of research projects also demonstrates that extrapolative inferences are not considered definitive or sufficient evidence, but only partially justified hypotheses subjected to further testing. 1 Introduction2 Surrogate Models2.1 What exactly is a surrogate model?2.2 Why use surrogate models?3 Prior Validation of Surrogate Models3.1 The validation and ranking of surrogate models in the early stages of basic research3.2 The validation of surrogate models in later stages of basic research and in clinical research4 ‘Big Picture’ Accounts and the Extrapolations Underpinning Them4.1 The mosaic nature of mechanistic descriptions in basic science4.2 Challenges for mechanistic-similarity-based validation protocols5 Retrospective Testing of Extrapolated Knowledge5.1 Holistic confirmation5.2 Fallback strategies6 Conclusions. (shrink)

ABSTRACT Scientific advances in genetic analysis have been made possible in recent years by technical developments in computational biology, or bioinformatics. Bioinformatics has opened up the human genome to diverse analyses involving automated laboratory hardware and machine learning algorithms and software. As part of an emerging field of social genomics, recent educational genetics studies using big data have begun to raise challenging findings linking DNA to predicted life outcomes. Bioinformatic technologies and techniques including ‘genome-wide association’ and ‘polygenic scoring’ (...) are producing new kinds of genetic biodata and expert knowledge for rethinking the upbringing and education of children. This article takes as an empirical opening a recent epistemic and ethical controversy over the use of biodata to make genetic predictions about educational, socio-economic and life outcomes, detailing the forms of expert knowledge and technologies involved these predictions, and exploring the social and ethical implications of data-intensive bioinformatics. (shrink)

Matrices that cannot be handled using conventional clustering, regression or classification methods are often found in every big data research area. In particular, datasets with thousands or millions of rows and less than a hundred columns regularly appear in biological so-called omic problems. The effectiveness of conventional data analysis approaches is hampered by this matrix structure, which necessitates some means of reduction. An evolutionary method called PreCLAS is presented in this article. Its main objective is to find a (...) submatrix with fewer rows that exhibits some group structure. Three stages of experiments were performed. First, a benchmark dataset was used to assess the correct functionality of the method for clustering purposes. Then, a microarray gene expression data matrix was used to analyze the method’s performance in a simple classification scenario, where differential expression was carried out. Finally, several classification methods were compared in terms of classification accuracy using an RNA-seq gene expression dataset. Experiments showed that the new evolutionary technique significantly reduces the number of rows in the matrix and intelligently performs unsupervised row selection, improving classification and clustering methods. (shrink)

Italian mycologist Pier Andrea Saccardo is best remembered for his monumental Sylloge Fungorum, the first ‘modern’ effort to compile all identified fungi within a single classification scheme. The existing history of mycology is limited and has primarily focused on developments within England, but this article argues that Saccardo and his collaborators on the Sylloge supported a vital transnational expansion of mycological knowledge exchange and played a crucial role in stabilizing the tangled knot of local naming and identification among the world's (...) amateur and professional mycologists. Written in the ‘universal’ scientific language of Latin, the Sylloge served as an early database of fungal knowledge and symbolized a broader unification of mycological inquiry in a moment of expanded scientific correspondence. The article situates this proto-database in broader histories of big data in biology and shows how the Sylloge formed a globalizing foundation for the twentieth century's major collecting and taxonomic advances in mycology. (shrink)

Big Data and biopolitics are two major issues currently attracting attention in public health discourse, but also in sociology of knowledge, STS Studies as well as in philosophy of science and bioethics. The paper considers big data to be a new form and instrument of biopolitics which addresses both the categories of body and space. It is expected to fundamentally transform health care systems, domestic environments and practices of self-observation and reflection. Accordingly the paper points out some problems (...) and pitfalls as well as open questions that have emerged in the field of AAL, which merit more attention in future public and academic debate. (shrink)

Developments in medical big data analytics may bring societal benefits but are also challenging privacy and other ethical values. At the same time, an overly restrictive data protection regime can form a serious threat to valuable observational studies. Discussions about whether data privacy or data solidarity should be the foundational value of research policies, have remained unresolved. We add to this debate with an empirically informed ethical analysis. First, experiences with the implementation of the General (...) class='Hi'>Data Protection Regulation (GDPR) within a European research consortium demonstrate a gap between the aims of the regulation and its effects in practice. Namely, strictly formalised data protection requirements may cause routinisation among researchers instead of substantive ethical reflection, and may crowd out trust between actors in the health data research ecosystem; while harmonisation across Europe and data sharing between countries is hampered by different interpretations of the law, which partly stem from different views about ethical values. Then, building on these observations, we use theory to argue that the concept of trust provides an escape from the privacy-solidarity debate. Lastly, the paper details three aspects of trust that can help to create a responsible research environment and to mitigate the encountered challenges: trust as multi-agent concept; trust as a rational and democratic value; and trust as method for priority setting. Mutual cooperation in research—among researchers and with data subjects—is grounded in trust, which should be more explicitly recognised in the governance of health data research. (shrink)

The most recent tool for acting on the world, the exosomatization of cognitive activities, is often considered an autonomous and objective replacement of knowledge construction. We show the intrinsic limits of the mechanistic myths in AI, from classical to Deep Learning techniques, and its relation to the human construction of sense. Human activities in a changing ecosystem – in their somatic and sensible dimensionalities proper to any living experiences – are at the core of our analysis. By this, we stress (...) the key role of the knowing subject, far away from any allegedly objective big collections of data. The production of organized structures of physics, biology and in societal analysis will be compared and distinguished by trying to set on more robust grounds the constructive as well as the disruptive roles of entropic, negentropic, anti-entropic dynamics that are different concepts in different domains, to be handled with care: the use of machine learning and optimization methods as tools and models to analyse and manage human activities in view of their scientific and political ideology of technoscientific governance. They suppose that which they try to produce is objective, that is, standardized and controllable behaviours. In this dialogue we stress a mirror symmetry between the lack of theoretical interpretation of scientific data and the lack of democracy in this fiction of neutrality. Moreover, bad analogies constitute an obstacle to grasp the anteriority of biological and ecological constraints which enable and limit all artificial products of human intelligence. We will thus stress biological specificity, the role of normativity and constraints in evolution, of labour in structuring the human historical construction of sense by common activities. (shrink)

BackgroundThe success of biobanking is directly linked to the willingness of people to donate their biological materials for research and storage. Ethical issues related to patient consent are an essential component of the current biobanking agenda. The majority of data available are focused on population-based biobanks in USA, Canada and Western Europe. The donation decision process and its ethical applications in clinical populations and populations in countries with other cultural contexts are very limited. This study aimed to evaluate the (...) decision-making experience of the clinical biobank donors, as well as psychological and social motivators and deterrents of this decision and associated ethical risks.MethodsSemi-structured interviews were conducted in two medical institutions, in St Petersburg (Russia), in 2016–2017, among 13 donors of a clinical biobank (pregnant women, cardiac patients, and patients with multiple sclerosis) and three donation organisers—medical specialists involved in recruiting donors for a clinical biobank. Analysis of interview data was based on qualitative content analysis.ResultsDonors of a clinical biobank express beliefs in the absence of risks associated with the donation. The primary motivators for donating to the biobank were: prosocial, indirect reciprocity (response to or anticipation of an act in kind by a third party), intrinsic motivation (to enhance their self-esteem and satisfying their curiosity about the donation process), and comparability with personal values. A high level of trust in biomedical research and the particular physician can contribute to a favourable decision. The overall decision-making process regarding the biobank donation could be described as quick and not based on a careful reading of informed consent documents. The integration of biobank donation decision-making in the process of medical care might prompt patient to donate to biobank without proper consideration. The specific type of therapeutic misconception—the presence of unrealistic hope that donation could provide a direct benefit for a third person in need was discovered.ConclusionsPatients recruited to a clinical biobank in Russia have virtually no concerns as to the storage of their biomaterials. The donation decision is mainly motivated by prosocial attitudes and other factors that are similar to the motivating factors of blood donation. The fact of going through inpatient treatment and poor differentiation between donation for other people's benefit and for research purposes can make the process of obtaining consent more ethically problematic. (shrink)

Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of (...) the Consensus Principle: realist, contextual-best, and coordinative. Contrasted with the realist program of the Open Biomedical Ontologies Foundry, we argue that historical practices in systematic biology provide an important and overlooked alternative based on coordinative consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

Leveraging a massive dataset of over 400 million potential matches between single heterosexuals on a leading mobile dating application we were able to identify numerous characteristics of effective matching. Effective matching is defined as the exchange of contact information with the intent to meet in person. The characteristics of effective match include alignment of psychological traits (i.e. extroversion), physical traits (i.e. height), personal choices (i.e., the relationship type they desired), and shared experiences. For nearly all characteristics, the more similar the (...) individuals were the higher the likelihood of them finding each other desirable and opting to meet in person. The only exception was introversion, where introverts rarely had an effective match with other introverts. Additionally, we investigated the preliminary stages of the choice process. We looked at the consistency between the choice of men/women, the time it took users to make these binary choices and the tendency of yes/no decisions. We used a biologically-inspired choice model to estimate the time allotted to a decision and could predict the decision and response time with nearly 60% accuracy. Given that people make their initial selection within no more than 11 seconds and ultimately converge to a partner who shares numerous attributes with them, we suggest that users are less selective in their early preferences and gradually converge to clusters with high degree of similarity in characteristics during their conversation. (shrink)

The use of molecules and reactions as evidence, markers and/or traits for evolutionary processes has a history more than a century long. Molecules have been used in studies of intra-specific variation and studies of similarity among species that do not necessarily result in the analysis of phylogenetic relations. Promoters of the use of molecular data have sustained the need for quantification as the main argument to make use of them. Moreover, quantification has allowed intensive statistical analysis, as a condition (...) and a product of increasing automation. All of these analyses are subject to the methodological anxiety characteristic of a community in search of objectivity. It is in this context that scientists compared and evaluated protein and nucleic acid sequence data with other types of molecular data – including immunological, electrophoretic and hybridization data. This paper argues that by looking at long-term historical processes, such as the use of molecular evidence in evolutionary biology, we gain valuable insights into the history of science. In that sense, it accompanies a growing concern among historians for big-pictures of science that incorporate the fruitful historical research on local cases of the last decades. (shrink)

The cultural rise of “big data” in the recent years has pressured a number of occupations to make an epistemological shift toward data-driven science. Though expressed as a professional move, this article argues that the push incorporates gendered assumptions that disadvantage women. Using the human resource occupation as an example, I demonstrate how normative perceptions of feminine “soft skills” are seen as irreconcilable with the masculine “hard numbers” of a data-driven epistemology. The history of human resources reflects (...) how assumptions of a biological fit with an occupation limit what women can convincingly describe as her skillsets. However, challenging this cannot stay within the confines of the occupation itself. To undo sexist thinking, it is necessary to understand the broader networks of patriarchal power that dictate how value is defined in corporate environments, especially within other high status professions in business. (shrink)

We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. (...) Natural history and its descendant discipline of biological taxonomy are prime examples of sciences dedicated to creating and managing systems of ordering data. In some sense, the idea of biological taxonomy as an information science is commonplace. Perhaps it is because of its self-evidence that the information science perspective on taxonomy has not been a major theme in the history and philosophy of science. The botanist Vernon Heywood once pointed out that historians of biology, in their ‘preoccupation with the development of the sciences of botany and zoology… [have] diverted attention from the role of taxonomy as an information science’ (Heywood 1985: 11). More specifically, he argued that historians had failed to appreciate how principles and practices that can be traced to Linnaeus constituted ‘a change in the nature of taxonomy from a local or limited folk communication system and later a codified folk taxonomy to a formal system of information science [that] marked a watershed in the history of biology’ (ibid.). A similar observation could be made about twentieth-century philosophy of biology, which mostly skipped over practical and epistemic questions about information management in taxonomy. The taxonomic themes that featured in the emerging philosophy of biology literature in the second half of the twentieth century were predominantly metaphysical in orientation. This is illustrated by what has become known as the ‘essentialism story’: an account about the essentialist nature of pre- Darwinian taxonomy that used to be accepted by many historians and philosophers, and which stimulated efforts to document and interpret shifts in the metaphysical understanding of species and (natural) classification (Richards 2010; Winsor 2003; Wilkins 2009). Although contemporary debates in the philosophy of taxonomy have moved on, much discussion continues to focus on conceptual and metaphysical issues surrounding the nature of species and the principles of classification. Discussions centring on whether species are individuals, classes, or kinds have sprung up as predictably as perennials. Raucous debates have arisen even with the aim of accommodating the diversity of views: is monism, pluralism, or eliminativism about the species category the best position to take? In addition to these, our disciplines continue to interrogate what is the nature of these different approaches to classification: are they representational or inferential roles of different approaches to classification (evolutionary taxonomy, phenetics, phylogenetic systematics)? While there is still much to learn from these discussions—in which we both actively participate—our aim with this topical collection has been to seek different entrypoints and address underexposed themes in the history and philosophy of taxonomy. We believe that approaching taxonomy as an information science prompts new questions and can open up new philosophical vistas worth exploring. A twenty-first century information science turn in the history and philosophy of taxonomy is already underway. In scientific practice and in daily life it is hard to escape the imaginaries of Big Data and the constant threats of being ‘flooded with data’. In the life sciences, these developments are often associated with the socalled bioinformatics crisis that can hopefully be contained by a new, interdisciplinary breed of bioinformaticians. These new concepts, narratives, and developments surrounding the centrality of data and information systems in the biological and biomedical sciences have raised important philosophical questions about their challenges and implications. But historical perspectives are just as necessary to judge what makes our information age different from those that preceded us. Indeed, as the British zoologist Charles Godfray has often pointed out, the piles of data that are being generated in contemporary systematic biology have led to a second bioinformatics crisis, the first being the one that confronted Linnaeus in the mid-18th century (Godfray 2007). Although our aim is to clear a path for new discussions of taxonomy from an information science-informed point of view, we continue where others in the history, philosophy, and sociology of science have already trod. We believe that an appreciation of biological taxonomy as an information science raises many questions about the philosophical, theoretical, material, and practical aspects of the use and revision of biological nomenclatures in different local and global communities of scientists and citizen scientists. In particular, conceiving of taxonomy as an information science directs attention to the temporalities of managing an accumulating data about classified entities that are themselves subject to revision, to the means by which revision is accomplished, and to the semantic, material, and collaborative contexts that mediate the execution of revisions. (shrink)

The COVID-19 pandemic invites a question about how long-standing narratives of alterity and current narratives of disease are entwined and re-enacted in the diagnosis of COVID-19. In this commentary, we discuss two related phenomena that, we argue, should be taken into account in answering this question. First, we address the diffusion of pseudoscientific accounts of minorities’ immunity to COVID-19. While apparently praising minorities’ biological resistance, such accounts rhetorically introduce a distinction between “Us” and “Them,” and in so doing produce new (...) and re-enact old narratives of alterity. Second, these unsubstantiated narratives thrive on fake news and scarcity of data. The second part of this commentary thus surveys the methods through which the COVID-19 test is administered in various countries. We argue that techniques used for data collection have a major role in producing COVID-19 data that render contagion rates among migrants and other minorities invisible. In the conclusion, we provide two recommendations about how COVID-19 data can instead potentially work towards inclusion. (shrink)

This article proposes a new bi-directional way of understanding the convergence of biology and computing. It argues for a reciprocal interaction in which biology and computing have shaped and are currently reshaping each other. In so doing, we qualify both the view of a natural marriage and of a digital shaping of biology, which are common in the literature written by scientists, STS, and communication scholars. The DNA database is at the center of this interaction. We argue (...) that DNA databases are spaces of convergence for computing and biology that change in form, meaning, and function from the 1960s to the 2000s. The first part of the article shows how, in the 1980s, DNA sequencing shifted from passively incorporating computers to be increasingly modeled in digital coding and decoding. Information retrieval algorithms, reciprocally, were altered according to the peculiarities of DNA in the first sequence-storage databases. The second part of the article investigates the impact of these reciprocal interactions and globalization on the organization of research centers, ways of conducting big science, and scientific values. Through convergence and new technologies such as data mining, biology and computing were transformed technologically, institutionally, and culturally into a new bio-data enterprise called genomics. (shrink)

In the big data era, sequencing technology has produced a large number of biological sequencing data. Different views of the cancer genome data provide sufficient complementary information to explore genetic activity. The identification of differentially expressed genes from multiview cancer gene data is of great importance in cancer diagnosis and treatment. In this paper, we propose a novel method for identifying differentially expressed genes based on tensor robust principal component analysis, which extends the matrix method to (...) the processing of multiway data. To identify differentially expressed genes, the plan is carried out as follows. First, multiview data containing cancer gene expression data from different sources are prepared. Second, the original tensor is decomposed into a sum of a low-rank tensor and a sparse tensor using TRPCA. Third, the differentially expressed genes are considered to be sparse perturbed signals and then identified based on the sparse tensor. Fourth, the differentially expressed genes are evaluated using Gene Ontology and Gene Cards tools. The validity of the TRPCA method was tested using two sets of multiview data. The experimental results showed that our method is superior to the representative methods in efficiency and accuracy aspects. (shrink)

Has the rise of data-intensive science, or ‘big data’, revolutionized our ability to predict? Does it imply a new priority for prediction over causal understanding, and a diminished role for theory and human experts? I examine four important cases where prediction is desirable: political elections, the weather, GDP, and the results of interventions suggested by economic experiments. These cases suggest caution. Although big data methods are indeed very useful sometimes, in this paper’s cases they improve predictions either (...) limitedly or not at all, and their prospects of doing so in the future are limited too. (shrink)

ABSTRACT:Technological advances introduce the possibility that, in the future, firms will be able to use big-data analysis to discover and offer consumers their individual reservation price. This can generate some interesting benefits, such as a better state of affairs in terms of equality of both welfare and resources, as well as increased social welfare. However, these benefits are countered by considerations of relational equality. This article takes up the market-failures approach as its basis to demonstrate what is wrong with (...) using big data to personalize prices. The article offers an improvement to the market-failures approach and argues that what is wrong with using big data to personalize prices is that it unfairly undermines consumers’ ability to benefit from the market, which is the very point of having a market. (shrink)

Between 2006 and 2011, humanity accumulated 1,600 EB of data. As a result of this growth, there is now more data produced than available storage. This article explores the problem of “Big Data,” arguing for an epistemological approach as a possible solution to this ever-increasing challenge.