According to a widely held view, scientific modelling consists in entertaining a set of model descriptions that specify a model. Rather than studying the phenomenon of interest directly, scientists investigate the phenomenon indirectly via a model in the hope of learning about some of the phenomenon’s features. I call this view the description-driven modelling (DDM) account. I argue that although an accurate description of much of scientific research, the DDM account is found wanting as regards the mechanistic modelling found in (...) many branches of biology. By analysing research practices in cancer immunology concerning the development of mechanistic models of the process of cancer metastasis, this paper presents and argues for a complementary account of scientific modelling, herein called the experimentation-driven modelling (EDM) account. In EDM, scientists investigate a set of experimental systems and then integrate the results obtained from experiments into a mechanistic model. While EDM shares some key features with DDM, the two are epistemically very different approaches to research. (shrink)

One of the foundational problems of biochemistry concerns the conceptualisation of the relationship between the composition, structure and function of macromolecules like proteins. Part of the recent philosophical literature displays a reductionist bias, that is, the endorsement of a form of microstructuralism mirroring an out-dated biochemical conceptualisation. We shall argue that such microstructuralist approaches are ultimately committed to a potentialist form of micro-predeterminism whereby the macrostructure and function of proteins is accounted for solely in terms of the intrinsic properties and (...) potentialities of the components of the primary structure as if they were self-contained or essentially immutable entities. We shall instead suggest that a conceptualisation of the relationship between proteins’ composition, structure and function consistent with contemporary biochemical practice should account also for the causal role of the cellular, organismal and environmental relations in protein development. The analysis of the folding process we propose suggests that microstructure-laden reductionist approaches are ontologically indefensible. Rather than a potentialist form of micro-predeterminism, our analysis ultimately supports a relational-construction-based view of protein development and potentialities formation, which requires an indispensable analysis of the dynamical interplay between the micro-level of the parts and the macro-level of the relational structures of their systems. (shrink)

I argue that diversity and pluralism are valuable not just for science but for philosophy of science. Given the partiality and perspectivism of representation, pluralism preserving integration can...

This essay considers a mixed-effects modeling practice and its implications for the philosophical debate surrounding reductive explanation. Mixed-effects modeling is a species of the multilevel modeling practice, where a single model incorporates simultaneously two levels of explanatory variables to explain a phenomenon of interest. I argue that this practice makes the position of explanatory reductionism held by many philosophers untenable because it violates two central tenets of explanatory reductionism: single-level preference and lower-level obsession.

Since the discovery of dark matter in the 1980s, multiple experiments have been set up to detect dark matter particles through some other mode than gravity. Particle physicists provide detailed jus...

'Structure' and 'function' are both ambiguous terms. Discriminating different meanings of these terms sheds light on research and explanatory practice in molecular biology, as well as clarifying central theoretical concepts in the life sciences like the sequence-structure-function relationship and its corresponding scientific "dogmas". The overall project is to answer three questions, primarily with respect to proteins: What is structure? What is function? What is the relation between structure and function? The results of addressing these questions lead to an answer to (...) the title question, what the statement 'structure determines function' means. (shrink)