A dynamical systems perspective on inheritance and evolutionary process:
The following papers present a dynamical systems perspective on the evolution of physiological and developmental processes. The aim is to characterise and classify different types of regulatory mechanisms based on the geometry of their phase or state space. This allows us to understand the potential of a system to produce different types of phenotypes, and hence to predict the probability of possible phenotypic transitions.
Jaeger J & Sharpe J (2014). On the concept of mechanism in development. In: Towards a Theory of Development, Minelli A & Pradeau T (eds), Oxford Univ Press, Oxford, UK.
Jaeger J & Monk N (2014). Bioattractors: dynamical systems theory and the evolution of regulatory processes. J Physiol 592: 2267–81.
Jaeger J, Irons D & Monk N (2012). The inheritance of process: a dynamical systems approach. J Exp Zool (Mol Dev Evol) 318B: 591–612.
On the use of reverse-engineering to study evolving developmental systems:
These two reviews present the methodology of reverse-engineering and show how it can be applied to the quantitative study of specific evolving regulatory processes.
Jaeger J & Crombach A (2012). Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology, Soyer O (ed.), Springer, Berlin.
Jaeger J & Monk N (2010). Reverse engineering of gene regulatory networks. In: Learning and Inference in Computational Systems Biology, Lawrence ND, Girolami M, Rattray M & Sanguinetti G (eds), MIT Press, Cambridge, MA.
The limited role of genes and genetic programmes in development and evolution:
The following papers argue against the ‘genetic programme’ metaphor for organismic development, and against genetic determinism in general, and show how development and patterning is governed by feedback driven regulatory dynamics.
Jaeger J & Monk N (2013). Keeping the gene in its place. In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds), Floris Books, Edinburgh, UK.
Jaeger J, Irons D & Monk N (2008). Regulative feedback in pattern formation: towards a general relativistic theory of positional information. Development 135: 3175–83.
Jaeger J & Reinitz J (2006). On the dynamic nature of positional information. BioEssays 28: 1102–11.