Complex Systems Biology of Networks: The Riddle and the Challenge - Systems Biology of Metabolic and Signaling Networks - page 26

We should also keep in mind that, under oxidative stress, Cys thiols that are not
redox sensors can also become oxidized. Thus, it is important to differentiate true
Cys redox sensors that participate in redox signaling from other Cys that become
oxidized but without biological consequences (Chiu and Dawes 2012 ).
2.3 Complex Systems Biology of Networks
The intricate networks of reactions and processes within living systems (Figs. 2.1 ,
2.2 , and 2.3 ) exhibit complex dynamic behavior (Lloyd and Lloyd 1993 , 1995 ;
Lloyd and Stupfel 1991 ) (see Chaps. 12 , 8 and 5 ). This complexity arises in part
from the existence of multiple topological, structural, as well as functional
interactions among components of these networks organized as molecular
(e.g., enzymes), supra-molecular (e.g., cytoskeleton, respiratory, or enzymatic
supercomplex), and organellar assemblies (e.g., in mitochondria) (see Chaps. 7 ,
8 and 11 ). Consequently, a full description of a biological system involves the
structure , the pattern of organization , and the function (Capra 1996 ; Kitano 2002 ).
Structure refers to the catalog of individual components (e.g., proteins, genes,
enzymes, transcriptional factors); pattern of organization indicates how the
components are wired (linked) and organized (e.g., topological relationships, mor-
phology, feed-forward, and feed-back), and function implies how the ensemble
works, i.e., unfolding in space and time of functional interrelationships,
mass-energy-information fluxes, response to stimuli, growth, division (Figs. 2.2
and 2.3 ).
The collective dynamic function of networks is characterized by novel
properties that cannot be anticipated from the behavior of network components in
isolation. These novel properties are called emergent . As a fundamental trait of
complexity, emergence is a manifestation of the interdependent function of pro-
cesses within cells, organs, organisms (see Chap. 10 ) . Ultimately, what we seek is
to understand how function is coordinated in a cell that exhibits spatially distributed
and compartmentalized subsystems, and the dynamics which unfolds simulta-
neously, although in sequentially consecutive temporal scales. Consequently, in
the following, we attempt to dissect key organizational and functional traits of
living cellular systems.
• Function occurs in spatially distributed, compartmentalized, systems in which
process dynamics unfolds in different successive but overlapping temporal
scales
Processes of different nature occur in distinct compartments connected by
transport mechanisms, temporally unfolding on different timescales from few
milliseconds (electric), hundreds of milliseconds (mechanical) to few seconds
(energetic) (see Chaps. 11 and 5 ).