Biological Polymers: Evolution, Function, and Significance.

Abstract

A holistic description of biopolymers and their evolutionary origins will contribute to our understanding of biochemistry, biology, the origins of life, and signatures of life outside our planet. While biopolymer sequences evolve through known Darwinian processes, the origins of the backbones of polypeptides, polynucleotides, and polyglycans are less certain. We frame this topic through two questions: (i) Do the characteristics of biopolymer backbones indicate evolutionary origins? (ii) Are there reasonable mechanistic models of such pre-Darwinian evolutionary processes? To address these questions, we have established criteria to distinguish chemical species produced by evolutionary mechanisms from those formed by nonevolutionary physical, chemical, or geological processes. We compile and evaluate properties shared by all biopolymer backbones rather than isolating a single type. Polypeptide, polynucleotide, and polyglycan backbones are kinetically trapped and thermodynamically unstable in aqueous media. Each biopolymer forms a variety of elaborate assemblies with diverse functions, a phenomenon we call polyfunction. Each backbone changes structure and function upon subtle chemical changes such as the reduction of ribose or a change in the linkage site or stereochemistry of polymerized glucose, a phenomenon we call function-switching. Biopolymers display homo- and heterocomplementarity, enabling atomic-level control of structure and function. Biopolymer backbones access recalcitrant states, where assembly modulates kinetics and thermodynamics of hydrolysis. Biopolymers are emergent; the properties of biological building blocks change significantly upon polymerization. In cells, biopolymers compose mutualistic networks; a cell is an Amazon Jungle of molecules. We conclude that biopolymer backbones exhibit hallmarks of evolution. Neither chemical, physical, nor geological processes can produce molecules consistent with observations. We are faced with the paradox that Darwinian evolution relies on evolved backbones but cannot alter biopolymer backbones. This Darwinian constraint is underlined by the observation that across the tree of life, ribosomes are everywhere and always have been composed of RNA and protein. Our data suggest that chemical species on the Hadean Earth underwent non-Darwinian coevolution driven in part by hydrolytic stress, ultimately leading to biopolymer backbones. We argue that highly evolved biopolymer backbones facilitated a seamless transition from chemical to Darwinian evolution. This model challenges convention, where backbones are products of direct prebiotic synthesis. In conventional models, biopolymer backbones retain vestiges of prebiotic chemistry. Our findings, however, align with models where chemical species underwent iterative and recursive sculpting, selection, and exaptation. This model supports Orgel's "gloomy" prediction that modern biochemistry has discarded vestiges of prebiotic chemistry. But there is hope. We believe an understanding of biopolymer origins will progress during the challenging and exciting integration of chemical sciences and evolutionary theory. These efforts can provide new perspectives on pre-Darwinian mechanisms and can deepen our understanding of evolution and of chemical sciences. Our working definition of chemical evolution is continuous chemical change with exploration of new chemical spaces and avoidance of equilibrium. In alignment with our model, we observe chemical evolution in complex mixtures undergoing wet-dry cycling, which does appear to undergo continuous chemical change and exploration of new chemical spaces while avoiding equilibrium.