Causality and independence in perfectly adapted dynamical systems

Perfect adaptation in a dynamical system is the phenomenon that one or more variables have an initial transient response to a persistent change in an external stimulus but revert to their original value as the system converges to equilibrium. With the help of the causal ordering algorithm, one can construct graphical representations of dynamical systems that represent the causal relations between the variables and the conditional independences in the equilibrium distribution. We apply these tools to formulate sufficient graphical conditions for identifying perfect adaptation from a set of first-order differential equations. Furthermore, we give sufficient conditions to test for the presence of perfect adaptation in experimental equilibrium data. We apply this method to a simple model for a protein signalling pathway and test its predictions in both simulations and using real-world protein expression data. We demonstrate that perfect adaptation can lead to misleading orientation of edges in the output of causal discovery algorithms.