Modeling Biochemical Pathways - Mathematical Approaches to Polymer Sequence Analysis and Related Problems - page 113

while, at the molecular level, the presence of feedback loops in a biochemical system
can determine oscillations of some of the species concentrations [ 25 ]. The concept
of emergent properties refers to two situations:

Weak emergence : The phenomenon wherein complex, interesting high-level
function is produced as a result of combining simple low-level mechanisms in
simple ways; systems showing this kind of emergence are, for example, the game
of life and biochemical systems [ 5 ]

Strong emergence : A phenomenon that arises from the low-level domain, but
truths concerning that phenomenon are not deducible even in principle from
truths in the low-level domain [ 5 ].

The reductionist approach aims to understand the reality by the study of its
constituents. Reductionism led to remarkable results related to the knowledge
of molecular components of biological systems, such as genes, RNAs, proteins,
metabolites and biochemical reactions. However, properties of many systems resist
to a reductionist explanation [ 23 ], and the failure of the reductionist approach is
mainly related to the complexity of biological systems. Therefore, while the study
of the “building-blocks” is still important, a system level approach, aimed to the
understanding of system structures, system dynamics, the control method and the
design method, is fundamental for a deeper understanding of biological processes
[ 14 ]. Systems biology is the multidisciplinary field which pursues this goal using
knowledge and approaches from a series of disciplines such as biology, chemistry,
physics, computer science, mathematics and engineering. Historically, it is possible
to identify two roots which have led to the approach referred to as systems biology
[ 27 ]: on the one hand, the evolution of molecular biology; on the other hand, the
formal analysis of molecule systems.

6.3 Steps Involved in the Definition of a Kinetic Model

Systems biology studies systems described by means of the interactions of organic
and inorganic components that reside within the cell and its environment. A model
is usually developed by following a process structured in three sequential steps:
1. The definition of the wiring diagram and the structure of the system;
2. The mathematical formulation for the system's dynamics;
3. The identification of a set of proper values for the model parameters, in order to
obtain a behavior comparable to experimental data or to some known dynamics.

It is important to consider that there is no unique correspondence between a
wiring diagram and the mathematical formulation. The same biological mecha-
nism can be represented by different forms of equations. Since these choices are
somewhat arbitrary, there is a hierarchy of assumptions associated with the model
definition, from the assembly of the wiring diagram to the assignment of specific
values to the parameters appearing in the mathematical formulation. Once the model