Abstract

Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype–phenotype map must also be functionally modular. Traditionally, modular processes have been identified as structural modules in regulatory networks. However, structure only constrains, but does not determine, the dynamics of a process. Here, we propose an alternative approach that decomposes the behaviour of a complex regulatory system into elementary activity-functions. Modular activities can occur in networks that show no structural modularity, making dynamical modularity more widely applicable than structural decomposition. Furthermore, the behaviour of a regulatory system closely mirrors its functional contribution to the outcome of a process, which makes dynamical modularity particularly suited for functional decomposition. We illustrate our approach with numerous examples from the study of metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue.

Highlights

  • Modularity is an essential feature of any adaptive complex system

  • We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue

  • The kind of argument we have presented here can be straightforwardly extended from core regulatory complex (CoRC) to character identity networks (ChINs), genetic signatures that are supposed to define the identity of morphological traits [39,40]

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Summary

Introduction: the modular epigenotype

Organisms are characterized by distinguishable metabolic, physiological, developmental, morphological and behavioural traits These phenotypic traits are modular, able to evolve in a quasi-independent manner (figure 1a [1]) (see [2,3]). All biological traits are generated by some underlying regulatory dynamics [12,13,14] These generative processes constitute the epigenotype of the organism [15,16,17,18,19], which is often represented as a complex mapping from genotype to phenotype (figure 1b) [20,21,22]. We conclude by discussing some of the wider implications of dynamical modularity, especially in evolutionary biology

Kinds of modules
Variational modules
Functional modules
Structural modules
Regulatory modules
Dynamical modularity
Modular metabolism
Dynamical modules of the cell
Morphogenetic fields as dynamical developmental modules
Conclusion
78. Bar-Joseph Z et al 2003 Computational discovery of
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