The Informational Substrate of Chemical Evolution: Implications for Abiogenesis

Abstract

A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.

3D bioprinting of tissue units with mesenchymal stem cells, retaining their proliferative and differentiating potential, in polyphosphate-containing bio-ink

“…A shift in paradigm emerged when it was found that the natural and physiological polymer polyP, with its numerous high-energy phosphoanhydride bonds, stores metabolic energy which is released in the extracellular space during enzymatic degradation of the polymer [17,21]. This metabolic energy is required not only for endergonic biochemical reactions but also for driving energy dissipating compartmentation, protein folding and selfassembly processes [52]. In particular, the energy is needed for the building and maintenance of the organized extracellular fibrillar architecture [21].…”

The protometabolic nature of prebiotic chemistry

“… 53 This, combined with the heterogeneity of the reaction medium, self-assembly and phase separation processes, together with compartmentalization events, would enrich the space of possibilities for the emergence of the first self-sustaining autonomous systems (in a biological/metabolic relevant sense – see again ref. 12 and 24 ). In the context of this tutorial review, where various small cycles with prebiotic relevance have been discussed (see Schemes 4, 8 and 10 ), the networks resulting from their integration could be seen as a funnel that drives energy from abundant, constantly produced and highly reactive one-carbon precursors (formaldehyde, HCN, formamide) into self-sustaining protometabolic cycles of gradually increasing complexities ( Fig.…”

“…This means that, with the help of fuelling molecules to promote the endothermic steps, together with catalysts to facilitate the slowly running ones, the kinetics and thermodynamics of the different reactions constituting the cycle should be coupled, in such a way that allows adapting the matter and energy balance of the system to the state of its close environment. 12,24 In this direction, a revolution is taking place in the capacity of chemists to manage out-of-equilibrium self-assembled systems and networks, [123][124][125][126][127] which makes this challenge potentially solvable in the future. A pertinent question, however, is whether the complexity of the TCA or the glyoxylate cycles would enable achieving an efficient dynamic coupling of their constituent transformations, in order to be run out of equilibrium.…”

“…This requires the establishment of recurrent control and feedback loops (autocatalytic cycles, kinetic and energetic couplings between common intermediates, compartmentalization through membranes or liquid–liquid phase separation to form condensates/aggregates like microdroplets) by which higher-level functional networks and assemblies harness the synthetic pathways that produce their own components. 24 As it has been pointed out by Ruiz-Mirazo and co-workers, 25 there is in that kind of organization a double-way causal connection, upwards and downwards, between the endogenously created control mechanisms and the pathways to synthesize the system's functional molecules. That basic hierarchical relationship defines the minimal condition for a network of reactions to be considered a metabolism (in its most elementary sense), suggesting that the application of an organizational/metabolic perspective is crucial in the search for prebiotic ‘systems principles’.…”

Origin of Life: The Point of No Return

“…Usually, those suggestions explain not only the prebiotic synthesis of RNA and amino acids, but the transfer of information and heredity as a necessary byproduct. In a prebiotic environment, different molecular components possess different functions toward proto-cell formation, organizing itself as an autonomous chemical system(s) capable of chemical evolution [63]. It was demonstrated that mutually catalytic systems (MCS) can emerge and could maintain some structural integrity with oscillatory patterns [64].…”