Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)
This article responds to two problems confronting social and human sciences: how to relate to digital data, inasmuch as it challenges established social science methods; and how to relate to life sciences, insofar as they produce knowledge that impinges on our own ways of knowing. In a case study of proteomics, we explore how digital devices grapple with large-scale multiples – of molecules, databases, machines and people. We analyse one particular visual device, a cluster-heatmap, produced by scientists by mining data (...) from a large number of experiments on human blood plasma proteins. These proteins make up a myriad multiple whose identity shifts in many ways. Rather than displaying data about proteins, the heatmap constructs a view of the differences and similarities between experiments. We find this attempt to construct a view on many things at once instructive in thinking about multiples more generally. Instead of flattening molecular ‘life itself’, this visual device superimposes layers of digital devices and techniques from a wide variety of disciplines. This layering suggests a different way of relating to the life sciences more generally: rather than what they know, how they know might be of use to social and human sciences when attending to multiplicities. (shrink)
This paper analyses the topic of representation since the point of view of ethnomethodology and sociology of scientific knowledge. It starts out by discussing the “standard image of representation” and the constructivist proposition of that image. Then, a case of study is presented to suggest how practices for collecting and analyzing forensic evidence in criminal law, can contribute to understand representational adequacy. The aim of this paper is to think differently about representantion considering how it is produced, managed and deconstructed. (...) Since this point of view, the propositions is to consider representation not only as a problematic epistemological concept but also as a practical accomplishment in specific epistemic cultures. (shrink)
Scientific knowledge is the outcome of a collective, for example, of experts, methods, equipment, and experimental sites. The configuration of the collective shapes the scientific findings, allowing some interactions to become visible and meaningful at the expense of others. PROTEE is a methodology that aims to increase the reflexivity of research and innovation projects by helping to sensitize practitioners to the demarcations their projects enact and to think through how these may affect the relevance of the outcomes. We used PROTEE (...) to structure a series of dialogues with a research project that wanted its findings to make a contribution to the heated debate on transgenic trees. Through this process, the project did indeed become more articulated while we ourselves became engaged with the project in a very particular way, by becoming loyal to it. The dialogues also made the risks that engagement with public debate entails for scientists very apparent. Like us, the scientific project chose its loyalties, but what PROTEE did was to help make these explicit. (shrink)
This paper examines the English case, Regina v Adams in which the difference between "scientific reason" and "common sense" was explicitly at stake in the use of DNA evidence. In its decision the Appellate Court reinstated a boundary between "scientific" and "common sense" evidence, arguing that this boundary was necessary to preserve the jury's role as trier of fact. The paper's discussion of the court's work of demarcation addresses the unresolved problems with the place of probability estimates in jury trials.
A controversial question among contemporary scholars is whether advanced industrial societies are still in modernity, or whether they are on the threshold of, or even have entered, a new postmodern order. In The Consequences of Modernity Anthony Giddens writes: ‘Beyond modernity, we can perceive a new and different order, which is “post-modern”, but this is quite distinct from what is at the moment called by many “post-modernity”’. However, he does recognize that there is something perceptibly different about the present, which (...) he characterizes as ‘late modernity’, an era in which the consequences of modernity are more radicalized and globalized than before. (shrink)
Recent accounts of “the biological” emphasize its thoroughgoing transformation. Accounts of biomedicalization, biotechnology, biopower, biocapital, and bioeconomy tend to agree that twentieth- and twenty-first-century life sciences transform the object of biology, the biological. Amidst so much transformation, we explore attempts to stabilize the biological through standards. We ask: how do standards handle the biological in transformation? Based on ethnographic research, the article discusses three contemporary postgenomic standards that classify, construct, or identify biological forms: the Barcoding of Life Initiative, the BioBricks (...) Assembly Standard, and the Proteomics Standards Initiative. We rely on recent critical analyses of standardization to suggest that any attempt to attribute a fixed property to the biological actually multiplies dependencies between values, materials, and human and nonhuman agents. We highlight ways in which these biological standards cross-validate life forms with forms of life such as publics, infrastructures, and forms of disciplinary compromise. Attempts to standardize the biological, we suggest, offer a good way to see how a life form is always also a form of life. (shrink)
The theme of the third annual Spring workshop of the HUPO-PSI was proteomics and beyond and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment data (...) model and Functional Genomics Ontology ontologies. (shrink)