An Introduction To Systems Biology Uri Alon Pdf 153 [TOP]

Systems thinking by contrast views biological systems asbased on simplifying assumptions about non-linear interactions amongcomponents (Bechtel and Richardson 1993). In a systems-modelingapproach these assumptions are explicitly formulated as functions,and the model is then used to analyze the properties of the system. Asystems model-based approach has been successfully applied to diversesetups in systems biology, ranging from a block of biochemical reactionsto a complete developmental program (e.g., Hermsen et al. 2014).In this approach, models of biological systems are used to makepredictions and explanations (Section 5.3). The systems approach hasbeen associated with different schools of thinking about complex systemsbiology (e.g., Calvert 2010). For example, the systemic organizationof biological systems has been associated with the field of systemsdynamics and complexity theory (Waldrop 1992; Batte et al.2011; von Caemmerer & Liebig 2013). Molecular biology and systemsbiology are thus often associated with the idea that biology is anopen, complex, and dynamic system.

One of the hallmarks of systemic thinking, and one that is takenup in this book, is that biological systems are not passive recipients ofthe environment, but that they actively shape their environments (Batte etal. 2011; von Caemmerer & Liebig 2013). This idea of a biologicalself-organizing system is incorporated in the term self-organization(Batte et al. 2011). Self-organization has been applied to biology inseveral contexts. Self-organization has been used to describe thedevelopmental organization of entire multicellular organisms. It is used,for example, in developmental biology to describe the processin which a fertilized egg becomes a multicellular organism withtissues and organs, and to describe the emergence of physiologicalfunctions such as vision (developmental biology). The idea ofself-organization has also been used in evolutionary biology toaccount for the recurring emergence of novel biological functions (e.g., Darwin's theory of evolution).

Such non-linearity and multilayeredness in biological networks raisesquestions about the empirical plausibility of scale-free and bow-tie networkstructures. Moreover, it can be hard to establish how generic suchstructures are across biological settings, and how generalizable theempirical models of biological systems are.

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