Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology

Adaptive Networks at the Crossroad of Artificial Intelligence and Formal, Biological, Medical, and Social Sciences

“…For modeling the cell's metabolic and life processes as biochemical networks within biology, Westerhoff et al [6,7] also point at the importance of such structures, "the dynamic biochemical networks of life", for example: "Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response.…”

“…Accordingly, in more recent times, mathematical formalizations are also playing an important role in other disciplines. This concerns, for example, mathematical descriptions of biochemical processes within a cell addressed in biology and chemistry [5][6][7], of contagion processes addressed within social science and biology [8][9][10], and of processes within the brain addressed within neuroscience [11]; these examples all use concepts and techniques from the areas mentioned above of mathematics.…”

“…The outcomes of such simulated processes for different inputs or parameters can be analyzed using mathematical techniques as well. For example, the processes within a cell are simulated based on a mathematical description of the cell's biochemistry within biology [5][6][7], the processes within the brain are simulated based on a mathematical description of these brain processes within neuroscience [11], and the spread of a virus is simulated based on a mathematical description of the effects of the characteristics of the contact network within social science or biology [8][9][10]. Also, more and more concepts and techniques are applied from artificial intelligence (AI), which can be viewed as an area within informatics or computer science.…”

Ins and Outs of Network-Oriented Modeling

“…In Sect. 2.1 it already was discussed how 'the dynamic biochemical networks of life' (Westerhoff et al 2014a) are fundamental to describe life forms in the biological domain. For the mental domain, the mechanisms found within the area of Cognitive and Social Neuroscience also show how many parts in the brain have connections which are adaptive and often form cyclic pathways; such cycles are assumed to play an important role in many mental processes; see also Bell (1999), Potter (2007.…”

Macromolecular networks and intelligence in microorganisms

“…Designing scaffold proteins in the protein–protein interaction domain has been studied for the control of metabolic flux ( Dueber et al, 2009 ). Recent studies ( He et al, 2013 ; Westerhoff et al, 2014 ) showed that although gene-expression regulation can increase the robustness of an intermediate metabolite concentration, it rarely makes the metabolic pathway infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero-order in the concentration of the protein or the living cell should enter stationary phase after a period of growth.…”