Thread by @yoginho

Our second paper on dynamical modularity, "Dynamical Modules in Metabolism, Cell and Developmental Biology" by @NickMonk14 & myself is now available as a preprint: osf.io/rydbn via @OSFramework /1

It complements our earlier evolutionary perspective on the subject (osf.io/vfz4t) with its more regulation-based approach and a long list of practical examples that illustrate our novel conceptual framework for the dynamical decomposition of complex systems. /2

Just like our earlier paper, the argument starts with the following observation: modular phenotypic traits imply that the underlying regulatory processes—the epigenotype of the organism—must be dissociable as well. How to decompose them, however, is not a trivial task. /3

We review the different kinds of modules—variational, functional, structural, and regulatory—that have been used for the functional decomposition of regulatory processes. Regulatory modules (co-regulated synexpression groups) belong to a wider class of dynamical modules. /4

Dynamical modules are elementary activities that constitute the more complex behaviour of a complex regulatory system. We show how such activities can be formally defined & detected in discrete network models. /5

Detecting them in continuous systems is more difficult. In the easiest case, a regulatory network is multifunctional, & we can decompose it according to the different activity-functions it implements. These activities can map to structural modules, but they don't have to. /6

There are many multifunctional networks that are not structurally modular at all. These are called emergent networks. They are the most interesting cases for the application of dynamical modularity. /7

We discuss the problems of context & feedback (retroactivity) for the analysis of metabolic function, and show how metabolic supply-and-demand analysis corresponds to our dynamical approach. /8

We then show how the eukaryotic cell cycle can be decomposed into modular checkpoint regulation, demonstrating that dynamical modularity can apply to processes with a seemingly unified temporal activity-function. /9

Another obvious field of application is cell-cell signalling, where the importance of dynamics & context are increasingly recognised. Or cell differentiation, where different cell types need not be characterised by distinct genetic regulatory signatures. /10

In dev biology, dynamical modules correspond to the morphogenetic fields of classical embryology. The gap gene network in Drosophila is a good example, where it is possible to decompose the system into subprocesses that don't map on any particular set of structural components./11

Other examples of dynamical modularity come from vertebrate neural tube patterning and somitogenesis. /12

Finally, we show that Turing systems are dynamical modules. A good example is the Turing module involved in the fin-to-limb transition in vertebrate evolution (great work by @koh_onimaru @MarconSBSLab @_JamesSharpe & others), showing how activity is shaped by tissue context. /13

We conclude by discussing some evolutionary implications, not least the fact that dynamical modules provide the substrate for our new approach to process homology (work with James DiFrisco, to appear soon in J Roy Soc Interface; preprint to follow). 14

It is a rare privilege to be at a stage of your thinking, where all kinds of things just naturally seem to come together. It seems I'm at such a stage right now, not least due to the many wonderful collaborations I've been involved in over the past few years. /15

Tagging: @briscoejames @AOates1 @_JamesSharpe @koh_onimaru @MarconSBSLab @BertaVerd @NickMonk14… and all those whose work we mention but who are not on Twitter, or who I forgot. 🤓