Replication, evolution

It follows from our foregoing discussion that such a system must be a culmination of a protracted period of prior evolution. This comprises chemical evolution (the complexification of chemical systems) and evolution by natural selection of chemical replicators of various kinds. It is likely that mineral surfaces have played an important role in precellular evolution (e.g. [9-12]). Surfaces have favourable thermodynamic, kinetic and selective effects on chemical and replicator evolution. Reviews of molecular selection dynamics on surfaces can be found elsewhere [ 13]. We mention this link because effects that surfaces can confer can be conferred even more efficiently by compartments obviously, a reproducing protocell is the strongest form of population structure, conducive to group selection [14,15] of the replicators included within. 

To examine replication of IPBs we made MFKEi-based simulations using the simplest 2D alloy model with the nearest-neighbor interaction. Some results are presented in Figs. 8-10. The lower row in Fig. 10 illustrates possible effects of thermal fluctuations, similar to those discussed in Sec. 3 for the replication of APBs. The figure shows that peculiar features of microstructural evolution are preserved even under rather strong thermal fluctuations used in this simulation. 

The broadest spectrum of antiviral diugs is available against HIV. However, monotherapy with any of these diugs leads to rapid treatment failure due to selection and further evolution of resistant viruses. Since acquisition of resistance mutations requires vims replication,... 

Short replication cycles that may be completed within a few hours, a large amount of viral progeny from one infected host-cell, as well as the general inaccuracy of viral nucleic acid polymerases result in an evolution occurring in fast motion, allowing rapid adaptation of viruses to selective pressures (see chapter by Boucher and Nijhius, this volume). Generalizing, it can be stated that any effective antiviral therapy will lead to the occurrence of resistance mutations. A well studied example... 

Antiviral Resistance and Impact on Viral Replication Capacity Evolution of Viruses Under Antiviral Pressure Occurs in Three Phases... 

Fig. 1 Three phases in viral evolution during suboptimal therapy. The black hne represents wild type virus, whereas the red line represents mutant virus (Res stands for the level of resistance and RC for replication capacity).

The evolution of antiviral resistance for viruses discussed in this chapter (HIV, HBV, HCV, and Influenza virus) shares some common features. Replication in vivo results in the generation of viral variation and selection of preexisting viruses from the population occurs under particular conditions. This will only happen when the escaping viruses have a sufficient level of both resistance and RC. In most cases, the resistance level subsequently increases further by the gradual acquisition of further mutations. Additional compensatory mutations then accumulate that help to restore full RC in the third stage. 

Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, SUiciano RF (2004) Genotypic analysis of HIV-1 drug resistance at the limit of detection virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis 189(8) 1452-1465 Kinoshita S, Su L, Amano M, Timmerman LA, Kaneshima H, Nolan GP (1997) The T cell activation factor NF-ATc positively regulates HIV-1 replication and gene expression in T cells. Immunity 6(3) 235-244... 

Nelson CJ, Carrigan KA, Lysle DT (2000) Naltrexone administration attenuates surgery-induced immune alterations in rats. J Surg Res 94(2) 172-177 Noel RJ Jr, Kumar A (2006) Virus replication and disease progression inversely correlate with SIV tat evolution in morphine-dependent and SIV/SHIV-infected Indian rhesus macaques. Virology 346(1) 127-138... 

How could Dawkins have come up with such an extreme and counterintuitive position The source can be found in his analysis of selection. Dawkins (1976) did not introduce the notion of replicators, but he certainly popularized it. Some entities exhibit structures of the sort that deserves to be termed information . Replication is the transmission of this information from one replicator to the next, copies producing copies. In biological evolution, so Dawkins argues, these replicators are genes. He also introduced a second process (environmental interaction) and corresponding entities (vehicles). As Dawkins sees it, the relation between replicators and vehicles is development. Replicators produce the vehicles in which they reside. Vehicles are clumsy robots, totally governed by the replicators that produce them. 

In the last 20 years, a new problem, the evolutionary origin of levels of organization, or evolutionary transition, has been added to those celebrated since Darwin (Buss, 1987). In their recent book, The Major Transitions in Evolution, Maynard Smith and Szathmary (1995, p. 6) identified what they considered to be eight major originations of new levels of organization (Table 11.1). For most of these, they claimed a common feature . .. entities that were capable of independent replication before the transition... 

In this essay, I argue for a new perspective on units of evolutionary transition. I analyze the process of reproduction, which leads to a conception of units of evolution as reproducers. These units resolve to more familiar ideas of replicators or interactors at levels of spatial organization when explicit spatial and functional models are imposed on abstract reproducers. I also sketch a heuristically promising program of reductionistic research that flows from the new perspective. 

I offer a different and complementary perspective on units which accommodates developmental processes explicitly and which articulates the intimate relationship between units of hereditary transmission and developmental expression. I argue that a process perspective on the temporal dimension of the transition problem, focusing on the propagation of developmental capacities, is a helpful addition to the spatial and functional perspectives. Reproduction is the process that, in general, forms the basis for evolution at a level and also for evolutionary transition to new levels. Processes of inheritance and replication can be understood as special cases of reproduction. In order to formulate a view of how processes of development and hereditary propagation are intertwined in reproduction, let us consider development further. 

After a certain stage in the development and evolution of life, genetic continuity was ensured by RNA replication. 

How can negative fluctuations in entropy production occur or be triggered As Manfred Eigen shows in his evolution theory, fluctuations in entropy production can be caused by the coming into being of a self-replicating molecular species which is capable of selection. Autocatalytically active mutants can also have the same effect. Looked at this way, the phenomenon of evolution consists of a continuous series of instabilities, i.e., collapses of stationary states. 

Szostak et al. worked on the basis of a simple cellular system which can replicate itself autonomously and which is subject to Darwinian evolution. This simple protocell consists of an RNA replicase, which replicates in a self-replicating vesicle. If this system can take up small molecules from its environment (a type of feeding ), i.e., precursors which are required for membrane construction and RNA synthesis, the protocells will grow and divide. The result should be the formation of improved replicases. Improved chances of survival are only likely if a sequence, coded by RNA, leads to better growth or replication of membrane components, e.g., by means of a ribozyme which catalyses the synthesis of amphiphilic lipids (Figs. 10.8 and 10.9). We can expect further important advances in the near future from this combination ( RNA + lipid world ). 

Fig. 10.8 The importance of the vesicle for the Darwinian evolution of a replicase. Compart-mentalisation ensures that related molecules tend to stay together. This permits superior mutant replicases (grey) to replicate more effectively than the parent (black) replicases. The evolutionary advantage spreads in the form of vesicles with superior replicase molecules, leading with a greater probability to vesicles with at least two replicase molecules (or a replicase and a matrix molecule). Vesicles with less than two replicase molecules are struck out their progeny cannot continue the RNA self-replication. Thus, the vesicles with better replicases form the growing fraction of vesicles which carry forward the replicase activity (Szostak et al., 2001)...

Chemical replication of oligonucleotides led to the evolution of self-replicating RNA molecules. 

A catalytic activity must be present that is linked to the replication process, so that variations in replication affect the catalysed reactions. Under such circumstances, variations will change the fitness of the system and lead to evolution. Compartmentalisation of the replicating catalytic system within a membrane-bound volume allows selection of variations, leading to speciation ... 

---