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)

With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...) KM in semantic systems biology. Through an empirical philosophical account of KM-enabled biological research, we argue that KM helps produce new first-order biological knowledge that did not exist before, and which could not have been produced by traditional means. KM work is enabled by conceiving of ‘knowledge’ as an object for computational science: as explicated in the text of biological articles and computable via appropriate data and metadata. However, these founded knowledge concepts enabling computational KM risk focusing on only computationally tractable data as knowledge, underestimating practice-based knowing and its significance in ensuring the validity of ‘manageable’ knowledge as knowledge. (shrink)

A model-theoretic realist account of science places linguistic systems and their corresponding non-linguistic structures at different stages or different levels of abstraction of the scientific process. Apart from the obvious problem of underdetermination of theories by data, philosophers of science are also faced with the inverse (and very real) problem of overdetermination of theories by their empirical models, which is what this article will focus on. I acknowledge the contingency of the factors determining the nature – and choice – of (...) a certain model at a certain time, but in my terms, this is a matter about which we can talk and whose structure we can formalise. In this article a mechanism for tracing "empirical choices" and their particularized observational-theoretical entanglements will be offered in the form of Yoav Shoham's version of non-monotonic logic. Such an analysis of the structure of scientific theories may clarify the motivations underlying choices in favor of certain empirical models (and not others) in a way that shows that "disentangling" theoretical and observation terms is more deeply model-specific than theory-specific. This kind of analysis offers a method for getting an articulable grip on the overdetermination of theories by their models – implied by empirical equivalence – which Kuipers' structuralist analysis of the structure of theories does not offer. (shrink)

In this paper I discuss the rule of inference proposed by Kuipers under the name of Inference to the Best Theory. In particular, I argue that the rule needs to be strengthened if it is to serve realist purposes. I further describe a method for testing, and perhaps eventually justifying, a suitably strengthened version of it.

Se explora la naturaleza de los problemas lacunae a partir del análisis de los conceptos elaborados, respectivamente, por Larry Laudan, Theo Kuipers y Atocha Aliseda. Sugeriré que los problemas lacunae pueden surgir del debilitamiento de la noción de ‘falsación empírica’ y repercutir en la noción de ‘implicación lógica’.

The paper explores the handling of singular analogy in quantitative inductive logics. It concentrates on two analogical patterns coextensive with the traditional argument from analogy: perfect and imperfect analogy. Each is examined within Carnap’s λ-continuum, Carnap’s and Stegmüller’s λ-η continuum, Carnap’s Basic System, Hintikka’s α-λ continuum, and Hintikka’s and Niiniluoto’s K-dimensional system. Itis argued that these logics handle perfect analogies with ease, and that imperfect analogies, while unmanageable in some logics, are quite manageable in others. The paper concludes with a (...) modification of the K-dimensional system that synthesizes independent proposals by Kuipers and Niiniluoto. (shrink)

A critique is given of the attempt by Hettema and Kuipers to formalize the periodic table. In particular I dispute their notions of identifying a naïve periodic table with tables having a constant periodicity of eight elements and their views on the different conceptions of the atom by chemists and physicists. The views of Hettema and Kuipers on the reduction of the periodic system to atomic physics are also considered critically.

This review provides an outline of the collection New Approaches to Scientific Realism, edited by Wenceslao Gonzalez. In particular, it questions whether the contributions to this edition can claim to be novel. The edition includes an introductory chapter and eighteen texts by well-known philosophers, such as Peter Achinstein, Alexander Bird, Donald Gillies, Theo Kuipers, Alan Musgrave, Thomas Nickles, Ilkka Niiniluoto, Howard Sankey, and John Worrall.