Abstract
In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule’s prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach—which is based on reverse engineering, simulation, and mathematical analysis—the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.
Highlights
The field of evolutionary developmental biology, or EvoDevo, is experiencing a conceptual crisis on many fronts
In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may take another 100 years
We propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems
Summary
The field of evolutionary developmental biology, or EvoDevo, is experiencing a conceptual crisis on many fronts. What is new is that—for the first time in history—we can combine such theoretical approaches with quantitative empirical evidence, using the data sets and methodologies generated by modern systems biology (Jaeger and Crombach 2012; Jaeger and Sharpe 2014) This allows us to reverse engineer the regulatory networks underlying specific cellular and developmental processes, and to test our models and concepts against detailed and accurate measurements of gene expression pattern or morphological trait characteristics. This opens up exciting novel avenues for research—a new kind of evolutionary systems biology—that may completely transform the fields of EvoDevo and evolutionary biology, and turn them from purely historical into locally predictive branches of science
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