The Origin of Large Molecules in Primordial Autocatalytic Reaction Networks

Abstract

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the ‘food set’, being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying ‘nested ACSs’, a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.

Ecological autocatalysis: a central principle in ecosystem organization?

“…They are often statistically and thermodynamically favored over alternative configurations, and may even explain the origin of life (Eigen and Schuster , Morowitz et al. , Lincoln and Joyce , Giri and Jain ). Hence, they are not trivial or rare structures in biochemical interaction networks.…”

“…Such chemical autocatalytic loops, such as the regular and reverse Krebs cycle, are found at the heart of the intermediate metabolism of all organisms. They are often statistically and thermodynamically favored over alternative configurations, and may even explain the origin of life (Eigen and Schuster 1979, Morowitz et al 2000, Lincoln and Joyce 2009, Giri and Jain 2012. Hence, they are not trivial or rare structures in biochemical interaction networks.…”

“…Throughout this paper, we have reviewed the importance of ecological autocatalysis as a key internal driver of ecosystem organization. Furthermore, we have emphasized that the concept of autocatalytic sets of species roots in biochemistry and systems biology (Eigen and Schuster 1979, Morowitz et al 2000, Lincoln and Joyce 2009, Giri and Jain 2012. This may hint at a basic process that re-emerges across levels of organization, and suggests generality of autocatalytic sets as a driving force of structure across all levels of biological organization (Gadgil and Kulkarni 2009).…”

Optimal size for emergence of self-replicating polymer system

“…In fact, the importance of the transition from the inactive to active state for the emergence of a primitive replicating system has already been pointed out in the seminal work by Dyson [5], while catalytic reaction networks have also been extensively studied [6][7][8][9][10][11]. Here, we study this problem by considering a simple autocatalytic polymerization process, with an aim to obtain the time required for the transition from the inactive to active states.The existence of bistable states and the transition to a catalytically active state has been discussed recently [12,13]. In these studies, the rate equation of the concentrations of the monomers and polymers were often adopted.…”

“…The existence of bistable states and the transition to a catalytically active state has been discussed recently [12,13]. In these studies, the rate equation of the concentrations of the monomers and polymers were often adopted.…”