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Beyond networks: mechanism and process in evo-devo

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Our ignorance of the laws of variation is profound.

Darwin (1859, 105).

The real goal of evo-devo is to explain evolution as the modification of developmental processes, not merely to demonstrate that evolution has proceeded by modifying development. Although genes are important aspects of the developmental processes, they are not the processes themselves.

Amundson (2005, 247).

Abstract

Explanation in terms of gene regulatory networks (GRNs) has become standard practice in evolutionary developmental biology (evo-devo). In this paper, we argue that GRNs fail to provide a robust, mechanistic, and dynamic understanding of the developmental processes underlying the genotype–phenotype map. Explanations based on GRNs are limited by three main problems: (1) the problem of genetic determinism, (2) the problem of correspondence between network structure and function, and (3) the problem of diachronicity, as in the unfolding of causal interactions over time. Overcoming these problems requires dynamic mechanistic explanations, which rely not only on mechanistic decomposition, but also on dynamic modeling to reconstitute the causal chain of events underlying the process of development. We illustrate the power and potential of this type of explanation with a number of biological case studies that integrate empirical investigations with mathematical modeling and analysis. We conclude with general considerations on the relation between mechanism and process in evo-devo.

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Notes

  1. It is worth noting that the initial formulation was much more modest, and the proposed research program was more precisely circumscribed: “Undoubtedly important regulatory processes occur at all levels of biological organization. We emphasize that this theory is restricted to processes of cell regulation at the level of genomic transcription” (Britten and Davidson 1969, 349).

  2. Independently, Weiss and Fullerton (2000) coined the term “phenogenetic drift” for the same evolutionary process (see also Weiss 2005). This type of phenomenon was first discussed (but not explicitly named) by Schmalhausen (1949).

  3. Probably the most iconic network graph in current evo-devo is the representation of the sea urchin endomesoderm specification network first presented (in parts) in Davidson et al. (2002). This graph is not purely static, given that developmental timing of activation of specific sub-circuits is noted. However, coarse-grained markers of developmental timing are far from capturing the dynamical behaviors of the activated GRNs. An always up-to-date, interactive version of this graph can be found at: http://grns.biotapestry.org/SpEndomes.

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Acknowledgements

We thank two anonymous reviewers and an editor of this journal for insightful comments. Thanks also to audiences at ISHPSSB 2019, the 2019 Venice Summer School in Evo-Devo, the 2019 Summer School in Philosophy of the Life Sciences at University of Rijeka, Institut Monod in Paris, and the EvoDevo Seminar Series in Cambridge for feedback and vigorous discussion. JD thanks the Research Foundation – Flanders (FWO) (Grant No. 12W1818N) and the Konrad Lorenz Institute for Evolution and Cognition Research for financial support.

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  1. Institute of Philosophy, KU Leuven, Leuven, Belgium

    James DiFrisco

  2. Complexity Science Hub, Vienna, Vienna, Austria

    Johannes Jaeger

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DiFrisco, J., Jaeger, J. Beyond networks: mechanism and process in evo-devo. Biol Philos 34, 54 (2019). https://doi.org/10.1007/s10539-019-9716-9

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