With cell and developmental biologist Stuart Newman, Müller co-edited the book Origination of Organismal Form (MIT Press, 2003).

This book on evolutionary developmental biology is a collection of papers on generative mechanisms that were plausibly involved in the origination of disparate body forms during early periods of organismal life.

Together with Eva Jablonka, Kevin Laland,[6] Alex Mesoudi,[7] Stuart Newman, Massimo Pigliucci, Kim Sterelny, John Odling-Smee,[8] Tobias Uller,[9] as well as Denis Noble and others,[10] Gerd Müller is an advocate of an alternative evolutionary framework, one version of which has been termed the Extended Evolutionary Synthesis (EES).

[11][12] In contrast to the Modern Synthesis, the population dynamical model of evolution established in the early twentieth century that had concentrated on the processes of variation and adaptation, the focus of the EES is on the generative properties of evolution, integrating conceptual developments from evolutionary developmental biology, genomics, ecology, and other fields.

It differs from the standard theory in its inclusion of the constructive processes in development, the consideration of reciprocal dynamics of causation, and the relinquishment of a predominantly genetic explanation.