The Sum of the Parts: Large-Scale Modeling in Systems Biology

Download Edit this record How to cite View on PhilPapers
Abstract
Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts.
PhilPapers/Archive ID
GROTSO-22
Revision history
Archival date: 2017-08-07
View upload history
References found in this work BETA

View all 24 references / Add more references

Citations of this work BETA

No citations found.

Add more citations

Added to PP index
2017-06-10

Total views
147 ( #22,150 of 43,831 )

Recent downloads (6 months)
33 ( #21,140 of 43,831 )

How can I increase my downloads?

Downloads since first upload
This graph includes both downloads from PhilArchive and clicks to external links.