The Downs and Ups of Mechanistic Research: Circadian Rhythm Research as an Exemplar

Studies in History and Philosophy of Science Part C: Studies in

2013

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models-which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism's ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation.

Section: Synchronized Oscillations: the Vertebrate Segmentation Clockmentioning

confidence: 99%

Systems biology and the integration of mechanistic explanation and mathematical explanation

Studies in History and Philosophy of Science Part C: Studies in

2013

“…Craver also points out that accounts focusing on reduction (and thus addressing relations among different levels) have overlooked the prevalence of integration among approaches addressing the same level, such as the fruitful interaction of neuroanatomy (studying the structure of neuronal circuits) and electrophysiology (studying the function of neuronal connections). His most important point is the need to take into account the historical dynamics of mechanistic research (see also Bechtel 2010). Accounts asserting reduction in neuroscience (e.g., Bickle 2003) have exclusively focused on finished reductive explanations, which ignores the methodological assumptions and explanatory agendas by which scientists actually discover those explanations.…”

mentioning

confidence: 99%

Explanation in Biology: Reduction, Pluralism, and Explanatory Aims

2011

Sci & Educ

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims.

“…In the present context, beyond analyzing explanatory theories, this involves philosophically studying how scientists develop and use explanations. Accounts of mechanistic explanation are already tied to the process of discovery by paying attention to the discovery of mechanisms and the shifts between reductive research episodes and integrative strategies (Bechtel 2006(Bechtel , 2010Craver 2005;Craver and Darden 2013;Darden 2006). In my argument that some mathematical models are explanatory, I have heeded Carl Craver's admonition that not every representation is an explanation.…”

Section: A Broader Philosophical Conception Of Mechanisms and Mechanimentioning

confidence: 99%

“…Thereby philosophical accounts of mechanistic explanation offer a model of epistemic integration as opposed to the traditional idea of reduction (Brigandt 2013a;Brigandt and Love 2012b;Craver 2005;Craver and Darden 2013;Darden 2005). 1 And rather than just analyzing the result of science (reductive or integrative explanations), such philosophical approaches also take into account the process of scientific research, such as the change between reductive episodes and integrative strategies (Bechtel 2010;Craver 2005).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation

History, Philosophy and Theory of the Life Sciences

2015

Evolutionary developmental biology (evo-devo) is considered a 'mechanistic science,' in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a broadened philosophical conception of mechanisms and mechanistic explanation.Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation.