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Dynamical modules in metabolism, cell and developmental biology
Interface Focus ( IF 4.4 ) Pub Date : 2021-04-16 , DOI: 10.1098/rsfs.2021.0011
Johannes Jaeger 1 , Nick Monk 2
Affiliation  

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.



中文翻译:

新陈代谢、细胞和发育生物学中的动态模块

模块化是任何自适应复杂系统的基本特征。表型特征是模块,因为它们具有可区分的结构或功能,可以(准)独立于其上下文而变化。由于所有表型特征都是一些潜在调控动力学的产物,因此构成基因型-表型图谱的生成过程也必须是功能模块化的。传统上,模块化过程已被确定为监管网络中的结构模块。然而,结构只限制而不是决定过程的动态。在这里,我们提出了一种替代方法,将复杂监管系统的行为分解为基本的活动功能。模块化活动可以发生在没有结构模块化的网络中,使动态模块化比结构分解更广泛适用。此外,监管系统的行为密切反映了其对过程结果的功能贡献,这使得动态模块化特别适合功能分解。我们通过研究新陈代谢、细胞过程以及发育和模式形成的大量例子来说明我们的方法。我们认为,动态模块为发育和进化生物学提供了一个共享的概念基础,并作为对过程同源性的新解释的基础,DiFrisco 和 Jaeger 在对该焦点问题的单独贡献中提出了这一点。这使得动态模块化特别适合功能分解。我们通过研究新陈代谢、细胞过程以及发育和模式形成的大量例子来说明我们的方法。我们认为,动态模块为发育和进化生物学提供了一个共享的概念基础,并作为对过程同源性的新解释的基础,DiFrisco 和 Jaeger 在对该焦点问题的单独贡献中提出了这一点。这使得动态模块化特别适合功能分解。我们通过研究新陈代谢、细胞过程以及发育和模式形成的大量例子来说明我们的方法。我们认为,动态模块为发育和进化生物学提供了一个共享的概念基础,并作为对过程同源性的新解释的基础,DiFrisco 和 Jaeger 在对该焦点问题的单独贡献中提出了这一点。

更新日期:2021-04-16
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