  In systems biology effective models are widely used due to the complexity of
biological system. They result from a coarse-graining process which employs
specific assumptions. Frequently one does not start with a model taking all
details into account and then performs a coarse-graining process, but rather
one starts right away with the effective equations and often the underlying
assumptions remain hidden or unclear. We exemplify the analysis of an effective
model by analyzing a time delay equation for the JAK/STAT5 signaling pathway
and show how one can avoid wrong conclusions and obtain a deeper understanding
of the biological system . By analyzing the assumptions leading to a
coarse-grained model one might be able to gain new insight into the involved
biological processes. Further, the compliance of the model with experimental
data can be considered as a validation of the assumptions made in the
derivation of the mathematical equations.
