Statistical Physics of Self-Replication

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.Comment: 4+ pages, 1 figur

Does self-replication imply evolvability?

The most prominent property of life on Earth is its ability to evolve. It is often taken for granted that self-replication--the characteristic that makes life possible--implies evolvability, but many examples such as the lack of evolvability in computer viruses seem to challenge this view. Is evolvability itself a property that needs to evolve, or is it automatically present within any chemistry that supports sequences that can evolve in principle? Here, we study evolvability in the digital life system Avida, where self-replicating sequences written by hand are used to seed evolutionary experiments. We use 170 self-replicators that we found in a search through 3 billion randomly generated sequences (at three different sequence lengths) to study the evolvability of generic rather than hand-designed self-replicators. We find that most can evolve but some are evolutionarily sterile. From this limited data set we are led to conclude that evolvability is a likely--but not a guaranteed-- property of random replicators in a digital chemistry.Comment: 8 pages, 5 figures. To appear in "Advances in Artificial Life": Proceedings of the 13th European Conference on Artificial Life (ECAL 2015

Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes

The emergence of replicases that can replicate themselves is a central issue in the origin of life. Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be replicable by the ribozyme and if these fragments self-assemble into a functional ribozyme. However, the continued self-replication of such replicases requires that the production of every essential fragment be balanced and sustained. Here, we use mathematical modeling to investigate whether and under what conditions fragmented replicases achieve continued self-replication. We first show that under a simple batch condition, the replicases fail to display continued self-replication owing to positive feedback inherent in these replicases. This positive feedback inevitably biases replication toward a subset of fragments, so that the replicases eventually fail to sustain the production of all essential fragments. We then show that this inherent instability can be resolved by small rates of random content exchange between loose compartments (i.e., horizontal transfer). In this case, the balanced production of all fragments is achieved through negative frequency-dependent selection operating in the population dynamics of compartments. This selection mechanism arises from an interaction mediated by horizontal transfer between intracellular and intercellular symmetry breaking. The horizontal transfer also ensures the presence of all essential fragments in each compartment, sustaining self-replication. Taken together, our results underline compartmentalization and horizontal transfer in the origin of the first self-replicating replicases.Comment: 14 pages, 4 figures, and supplemental materia

Mechanosensitive Self-Replication Driven by Self-Organization

Self-replicating molecules are likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. We report here two self-replicating peptide-derived macrocycles that emerge from a small dynamic combinatorial library and compete for a common feedstock. Replication is driven by nanostructure formation, resulting from the assembly of the peptides into fibers held together by β sheets. Which of the two replicators becomes dominant is influenced by whether the sample is shaken or stirred. These results establish that mechanical forces can act as a selection pressure in the competition between replicators and can determine the outcome of a covalent synthesis.

Self Replication and Signalling

It is known that if one could clone an arbitrary quantum state one could send signal faster than the speed of light. However it remains interesting to see that if one can perfectly self replicate an arbitrary quantum state, does it violate the no signalling principle? Here we see that perfect self replication would also lead to superluminal signalling.Comment: Modified version of quant-ph/0510221, Accepted in International Journal of Theoretical Physic

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required