Why network approach can promote a new way of thinking in biology.

Alessandro Giuliani,Simonetta Filippi,Marta Bertolaso

doi:10.3389/fgene.2014.00083

Alessandro Giuliani, Simonetta Filippi + Show 1 more

Open Access

https://doi.org/10.3389/fgene.2014.00083

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Abstract

This work deals with the particular nature of network-based approach in biology. We will comment about the shift from the consideration of the molecular layer as the definitive place where causative process start to the elucidation of the among elements (at any level of biological organization they are located) interaction network as the main goal of scientific explanation. This shift comes from the intrinsic nature of networks where the properties of a specific node are determined by its position in the entire network (top-down explanation) while the global network characteristics emerge from the nodes wiring pattern (bottom-up explanation). This promotes a “middle-out” paradigm formally identical to the time honored chemical thought holding big promises in the study of biological regulation.

Highlights

The classical form in which biological systems are described (being they metabolic charts, gene expression regulation pathways, protein–protein interaction maps, intercellular connections, food webs, and so forth) corresponds to a set of nodes linked by edges in which the nodes are the basic elements of the described system (genes, proteins, metabolites, cells, and so forth) and the edges connecting them some rules of the kind “is transformed into” or “is increased by” or, more in general “is correlated with.”The figures normally present in books and scientific papers implicitly consider these pathways as linear causative chains in which a signal starting from a molecular perturbation, after a sequence of “if-” events, emerges as a biological end-point (Tun et al, 2011)
The classical form in which biological systems are described corresponds to a set of nodes linked by edges in which the nodes are the basic elements of the described system and the edges connecting them some rules of the kind “is transformed into” or “is increased by” or, more in general “is correlated with.”The figures normally present in books and scientific papers implicitly consider these pathways as linear causative chains in which a signal starting from a molecular perturbation, after a sequence of “if-” events, emerges as a biological end-point (Tun et al, 2011)
We will comment about the shift from the consideration of the molecular layer as the definitive place where causative process start to the elucidation of the among elements interaction network as the main goal of scientific explanation

Summary

Introduction

The classical form in which biological systems are described (being they metabolic charts, gene expression regulation pathways, protein–protein interaction maps, intercellular connections, food webs, and so forth) corresponds to a set of nodes linked by edges in which the nodes are the basic elements of the described system (genes, proteins, metabolites, cells, and so forth) and the edges connecting them some rules of the kind “is transformed into” or “is increased by” or, more in general “is correlated with.”The figures normally present in books and scientific papers implicitly consider these pathways as linear causative chains in which a signal starting from a molecular perturbation, after a sequence of “if-” events, emerges as a biological end-point (Tun et al, 2011). For these reasons many authors preferred a purely topological approach to the analysis of biological networks (Nordling et al, 2007; Dehmer et al, 2013) considering the presence of a link between two nodes as a pure yes/no binary relation and limiting themselves to statistical descriptions making use of the so called graph invariants (Watts and Strogatz, 1998).

Results

Conclusion