The Genetic Algorithm (GA) and Simulated Annealing (SA), two techniques for global optimization, were applied to a reduced (simplified) form of the phase problem (RPP) in computational crystallography. Results were compared with those of "enhanced pair flipping" (EPF), a more elaborate problem-specific algorithm incorporating local and global searches. Not surprisingly, EPF did better than the GA or SA approaches, but the existence of GA and SA techniques more advanced than those used in this study suggest that these techniques still (...) hold promise for phase problem applications. The RPP is, furthermore, an excellent test problem for such global optimization methods. (shrink)

This article analyzes the value of geometric models to understand matter with the examples of the Platonic model for the primary four elements (fire, air, water, and earth) and the models of carbon atomic structures in the new science of crystallography. How the geometry of these models is built in order to discover the properties of matter is explained: movement and stability for the primary elements, and hardness, softness and elasticity for the carbon atoms. These geometric models appear to (...) have a double quality: firstly, they exhibit visually the scientific properties of matter, and secondly they give us the possibility to visualize its whole nature. Geometrical models appear to be the expression of the mind in the understanding of physical matter. (shrink)

Scientific models share one central characteristic with fiction: their relation to the physical world is ambiguous. It is often unclear whether an element in a model represents something in the world or presents an artifact of model building. Fiction, too, can resemble our world to varying degrees. However, we assign a different epistemic function to scientific representations. As artifacts of human activity, how are scientific representations allowing us to make inferences about real phenomena? In reply to this concern, philosophers of (...) science have started analyzing scientific representations in terms of fictionalization strategies. Many arguments center on a dyadic relation between the model and its target system, focusing on structural resemblances and “as if” scenarios. This chapter provides a different approach. It looks more closely at model building to analyze the interpretative strategies dealing with the representational limits of models. How do we interpret ambiguous elements in models? Moreover, how do we determine the validity of model-based inferences to information that is not an explicit part of a representational structure? I argue that the problem of ambiguous inference emerges from two features of representations, namely their hybridity and incompleteness. To distinguish between fictional and non-fictional elements in scientific models my suggestion is to look at the integrative strategies that link a particular model to other methods in an ongoing research context. To exemplify this idea, I examine protein modeling through X-ray crystallography as a pivotal method in biochemistry. (shrink)

Several recent studies of early modern natural philosophy have claimed that corpuscularism and experimental philosophy were sharply distinct or even conflicting views. This chapter provides a different perspective on the relation between corpuscularism and experimental philosophy by examining Domenico Guglielmini’s ‘Philosophical Reflections’ on salts (1688). This treatise on crystallography develops a corpuscularist theory and defends it in a way that is in line with the methodological prescriptions, epistemological strictures, and preferred argumentative styles of experimental philosophers. The examination of the (...) ‘Reflections’ shows that early modern philosophers could consistently endorse, at the same time, corpuscularism and experimental philosophy. (shrink)

Mitchell & Gronenborn propose that we account for the presence of multiple models of protein structure, each produced in different contexts, through the framework of integrative pluralism. I argue that two interpretations of this framework are available, neither of which captures the relationship between a model and the protein structure it represents or between multiple models of protein structure. Further, it inclines us toward concluding prematurely that models of protein structure are right in their contexts and makes extrapolation of findings (...) from one context to another seem unwarranted. Instead, protein structure determination ought to be understood as modestly monistic. There is one model for every protein in each physicochemical context, and models of the same protein produced in different contexts are compatible with one another. ‘Integrating’ multiple models amounts to extrapolating from one context to another; this is possible because the effect of context on protein folding is relatively weak and predictable. Modest monism better describes the practice of protein structure determination than integrative pluralism and enables greater attention to how context affects protein folding. (shrink)