Biology Reference
In-Depth Information
questions related to intra- and intercellular processes within a cell and in cell
populations:
How do the components within a cell interact, so as to bring about its structure
and realise its functioning?
How do cells interact, so as to develop and maintain higher levels of structural
and functional organisation?
A defining feature of systems biology is the role that mathematical modelling
plays. As indicated above, for mathematical modelling to be employed we require
a certain level of complexity that is necessary to convince the nonmathematician
of its usefulness. In systems biology, complexity emerges as
•
A property of an encoding, e.g. a larger number of variables that determine
the behaviour of a system.
•
An attribute of the natural system under consideration, e.g. the connectivity,
nonlinearity of relationships.
•
As related to the technologies by which we take measurements and generate
experimental data, e.g. limited precision and accuracy.
•
Associated with uncertainty arising from the methodologies employed to
investigate and model the system. For instance, the choice of a conceptual
framework, i.e. whether differential equations, automata, etc. are employed.
It is clear that a model of a cell, cell function or pathway, is conceptual - not
reality. All theoretical results are derived within a chosen conceptual framework,
thus formulated to correspond in some useful way to the real world, as it
presents itself to us in experiments. A pathway is an interpretation of observable
facts, in the light of biological and mathematical concepts that we ourselves
construct using natural language, drawings, images and formal, mathematical
methods.
The definition of a pathway usually starts with a selection of proteins and their
modified forms. This choice should be determined by the function the pathway
realises in the cell but is often also determined by the costs and logistics of
time-consuming experiments that can be conducted to investigate the pathway.
In any case, the selected components of a pathway should display some autonomy
or robustness in the sense that their interactions and the resulting behaviour is
to a large degree independent of other components that are not included in its
definition. By defining a pathway, we therefore isolate it from other components
of the cell. This suggests that the concept of 'cross-talk' among pathways is
contradicting the common definition of a pathway, because if two pathways
interact to an extent that they cannot be looked at in isolation, all components
