Computational modeling is one of the primary approaches to constructing protein–protein interfaces in the laboratory. The algorithm-driven computational protein design has been successfully applied to the construction of functional proteins with improved binding affinity and increased thermostability. It is intriguing how a computational protein modeling approach can construct and shape the reality of new functional proteins from scratch. I articulate an account of abstraction and exploration-driven strategies in this computational endeavor. I aim to show that how a computational modelling approach, (...) which is laden with mathematics and algorithms, can have a constructive force on the target protein. (shrink)

Scientific models consist of fictitious elements and assumptions. Various attempts have been made to answer the question of how a model, which is sometimes viewed as a fiction, can explain or predict the target phenomenon adequately. I examine two accounts of models-as-fictions which are aiming at disentangling the myth of representing the reality by fictional models. I argue that both views have their own weaknesses in spite of many virtues. I propose to re-evaluate the problems of representation from a novel (...) perspective in which some of the model representations can be regarded as fictional representations. I argue that this type of model representation is credible despite being a fictional representation of the reality. (shrink)

Reports of quantitative experimental results often distinguish between the statistical uncertainty and the systematic uncertainty that characterize measurement outcomes. This article discusses the practice of estimating systematic uncertainty in high-energy physics. The estimation of systematic uncertainty in HEP should be understood as a minimal form of quantitative robustness analysis. The secure evidence framework is used to explain the epistemic significance of robustness analysis. However, the empirical value of a measurement result depends crucially not only on the resulting systematic uncertainty estimate, (...) but on the learning aims for which that result will be used. Important conceptual and practical questions regarding systematic uncertainty assessment call for further investigation. _1_ Introduction _2_ Systematic Uncertainty: The Very Idea _3_ Systematic Uncertainty in High-Energy Physics _4_ Methodological Debates in High-Energy Physics _5_ The Secure Evidence Framework _6_ Systematic Uncertainty Assessment as Robustness Analysis _7_ Security and Sensitivity _8_ Conclusion Appendix. (shrink)

Convergence of model projections is often considered by climate scientists to be an important objective in so far as it may indicate the robustness of the models’ core hypotheses. Consequently, the range of climate projections from a multi-model ensemble, called “model spread”, is often expected to reduce as climate research moves forward. However, the successive Assessment Reports of the Intergovernmental Panel on Climate Change indicate no reduction in model spread, whereas it is indisputable that climate science has made improvements in (...) its modelling. In this paper, after providing a detailed explanation of the situation, we describe an epistemological setting in which a steady model spread is not doomed to be seen as negative, and is indeed compatible with a desirable evolution of climate models taken individually. We further argue that, from the perspective of collective progress, as far as the improvement of the products of a multi-model ensemble is concerned, reduction of model spread is of lower priority than model independence. (shrink)

For computer simulation models to usefully inform climate risk management, uncertainties in model projections must be explored and characterized. Because doing so requires running the model many ti...

Here I critically assess an argument put forward by Kuorikoski et al. (Br J Philos Sci, 61(3):541–567, 2010) for the epistemic import of model-based robustness analysis. I show that this argument is not sound since the sort of probabilistic independence on which it relies is unfeasible. By revising the notion of probabilistic independence imposed on the models’ results, I introduce a prima-facie more plausible argument. However, despite this prima-facie plausibility, I show that even this new argument is unsound in most (...) if not all cases of model-based robustness analysis. This I do to demonstrate that the epistemic import of model-based robust analysis cannot be satisfactorily defended on the basis of probabilistic independence. (shrink)