It is assumed that scientific models contain no superfluous model elements in scientific representation. A representational model is constructed with all the model elements serving the representational purpose. The received view has it that there are no redundant model elements which are non-representational. Contrary to this received view, I argue that there exist some non-representational model elements which are essential in scientific representation. I call them representation-supporting model elements in virtue of the fact that they play the role to support (...) the representational role of representational model elements. Representation-supporting model elements, which have a characteristic of dependability, are not to be eliminated in the process of modeling although they are playing second fiddle to representational model elements in scientific representation. (shrink)

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)

This paper deals with calibration in scientific practices which investigate relatively well-understood natural phenomena by means of already standardized instrumental devices. Calibration is a crucial topic, since it conditions the reliability of instrumental procedures in science. Yet although important, calibration is a relatively neglected topic. We think more attention should be devoted to calibration. The paper attempts to take a step in this direction. The aims are two-fold: (1) to characterize calibration in a relatively simple kind of scientific practices; (2) (...) to provide conceptual and taxonomic tools of broader scope that help to get a better understanding of calibration in more complex cases and other kinds of scientific practices. For this purpose, we first provide indications for why a conceptual framework is needed. Second, a bibliographic survey of works dealing with calibration is attempted. Third, we introduce different tools to enable a better understanding of calibration. Fourth, we turn to the elaboration of what we call a “simple exemplar” of calibration, illustrated through the case of the calibration of an equal-arm balance. Fifth, the tools previously introduced, and the framework of the simple exemplar, are applied to a more complex case of calibration: calibration procedures in X-ray experiments. This serves to show the work accomplished by the simple exemplar and to emphasize features of more complex cases of calibration. Eventually, we revisit and specify the nature, status, scope and value of the proposed framework. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family of proteins (...) acting as molecular chaperones provides information that is complementary to that stored in the nucleic acids, and equally important. A re-evaluation of the role of proteins in the hereditary process is in order away from the gene-centric approach of the information theory of heredity, to which neo-Darwinian evolutionists adhere. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)