Ard Louis

Abstract:

This chapter will provide an overview of how characterising free energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The landscapes for these complex systems are accessible through the use of accurate coarse-grained descriptions of DNA. Particular foci will be the landscapes associated with DNA self-assembly and mechanical deformation, where the latter can arise from either externally imposed forces or internal stresses.

Abstract:

Engineers routinely design systems to be modular and symmetric in order to increase robustness to perturbations and to facilitate alterations at a later date. Biological structures also frequently exhibit modularity and symmetry, but the origin of such trends is much less well understood. It can be tempting to assume—by analogy to engineering design—that symmetry and modularity arise from natural selection. However, evolution, unlike engineers, cannot plan ahead, and so these traits must also afford some immediate selective advantage which is hard to reconcile with the breadth of systems where symmetry is observed. Here we introduce an alternative nonadaptive hypothesis based on an algorithmic picture of evolution. It suggests that symmetric structures preferentially arise not just due to natural selection but also because they require less specific information to encode and are therefore much more likely to appear as phenotypic variation through random mutations. Arguments from algorithmic information theory can formalize this intuition, leading to the prediction that many genotype–phenotype maps are exponentially biased toward phenotypes with low descriptional complexity. A preference for symmetry is a special case of this bias toward compressible descriptions. We test these predictions with extensive biological data, showing that protein complexes, RNA secondary structures, and a model gene regulatory network all exhibit the expected exponential bias toward simpler (and more symmetric) phenotypes. Lower descriptional complexity also correlates with higher mutational robustness, which may aid the evolution of complex modular assemblies of multiple components.

Abstract:

SignificanceWhy does evolution favor symmetric structures when they only represent a minute subset of all possible forms? Just as monkeys randomly typing into a computer language will preferentially produce outputs that can be generated by shorter algorithms, so the coding theorem from algorithmic information theory predicts that random mutations, when decoded by the process of development, preferentially produce phenotypes with shorter algorithmic descriptions. Since symmetric structures need less information to encode, they are much more likely to appear as potential variation. Combined with an arrival-of-the-frequent mechanism, this algorithmic bias predicts a much higher prevalence of low-complexity (high-symmetry) phenotypes than follows from natural selection alone and also explains patterns observed in protein complexes, RNA secondary structures, and a gene regulatory network.