The replication paradigm

The discovery of viruses made an enormous impression on biologists, because it proved that something much smaller than a cell maintained the ability to replicate, the most quintessential of life s properties. Haldane knew only too well that viruses are totally dependent on cells for their replication, and therefore that they could have evolved only after cells, but those tiny proliferating crystals in the interior of huge cellular structures appeared to state a deeper truth that replication is simpler than metabolism. This was the concept that struck Haldane, and from that came the idea that everything started when the first molecular replicators appeared on the primitive Earth. 

A different solution has been proposed by Joyce, Schwartz, Orgel and Miller (1987) with the idea that the first nucleotides were simpler than modern ones, while Wachtershauser (1992) has suggested that they were tribonucleic acids , double-helical molecules that could have been formed on pyrite surfaces. Today there still is no satisfactory solution for the origin of nucleic acids, and the fact that they are objectively difficult molecules remains a serious obstacle for the replication paradigm, but it may not be impossible to overcome it. 

Let us come therefore to the basic concept of the paradigm, i.e. to the idea that the smallest replicative system is simpler that the smallest metabolic system. This is the problem that we need to address, and in order to do so we must first answer a preliminary question what is the smallest system that allows the replication of RNAs The answer has come from two classic experiments, one by Sol Spiegelman in 1967 and the other by Manfred Eigen in 1971. In both cases the environmental conditions were simplified to the highest degree, and the experiments were performed in solutions containing free nucleotides and RNA-replicase enzymes. 

Spiegelman decided to study the replication of a well-known nucleic acid, and chose the RNA of the virus Qp, a chain of 4500 nucleotides that contains the coding instructions for all viral proteins, including the enzyme that replicates its own RNA. Spiegelman removed all proteins, put the viral RNA in solution, and observed that for a certain period it was faithfully replicated. Soon, however, a mutant appeared that by chance had lost the genes of some proteins that were not contributing to in vitro replication, and were therefore totally useless. Being shorter, the 

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We can say therefore that the metabolism-firsti ta. (the metabolism paradigm) goes back to Oparin, while the replication-first concept (the replication paradigm) goes back to Haldane. And since metabolism is based on proteins, and replication on nucleic acids, Oparin s paradigm is equivalent to saying that proteins (the hardware) came first, whereas Haldane s paradigm maintains that it was nucleic acids (the software) that had priority. 

The fact that ribozymes came before protein enzymes does not mean that replication came before metabolism, but it is an historical fact that this is precisely the meaning that was given, almost universally, to the discovery of ribozymes. With very few exceptions, the RNA world has been interpreted with the logic of the replication paradigm if RNAs could behave as genes and as enzymes, then they did it immediately, at the very beginning, and became the first replicators in the history of life. 

Primitive RNAs, in conclusion, could certainly behave both as genes and enzymes, but this does not save the replication paradigm, because it cannot avoid the various catastrophes that necessarily affect all replicators. 

We conclude that the replication paradigm has not been able, so far, to account for chemical evolution, but could be valid for postchemical evolution, and this, it will be remembered, is also Dyson s hypothesis (metabolism first, replication second). Let us examine therefore the evolutionary potential of primitive vesicles containing RNAs that could behave both as genes and enzymes. 

The replication paradigm requires that protein enzymes were not present at the beginning, and RNA replication was therefore performed by ribozymes. Some RNAs can in fact behave as polymerases and replicases, but they are far less efficient than the corresponding protein enzymes, and the accuracy of their replications was necessarily very low. The experimental measures, obtained from interacting coupled nucleotides, have shown that without protein enzymes the replication error e cannot be less than 0.01, which means, from formula 5.1, that primitive RNAs could not have, as an order of magnitude, more than 100 nucleotides (Maynard Smith and Szathmary, 1995). 

We are bound to conclude that the replication paradigm does not offer a plausible model even for postchemical evolution. Of course we cannot exclude that future discoveries might modify such a conclusion, but it would be necessary to discover, among other things, that primitive ribozymes were making replication errors comparable to those of protein enzymes, and this is extremely unlikely. 

Let us now come to the second part of postchemical evolution, the stage that was destined to lead to the origin of the first cells. It is in this stage that we must look for an answer to the problem that the replication paradigm has been unable to solve how did primitive systems manage to increase their complexity without being destroyed by error catastrophes The ribotype answer is based on three points. 

Donachie WD, Blakely GW (2003) Coupling the initiation of chromosome replication to cell size in Escherichia coli. Curr Opin Microbiol 6 146-150 Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284 601-603... 

The inclusion of noise factors is one of the unique and important contributions of Taguchi. We illustrate the important role that noise factors can play and explore the relative advantages of the different paradigms in Section 2. The first paradigm, simple replication, leads largely to standard designs and analyses, and this approach is treated only briefly in Section 3 of this chapter. We discuss methods for analyzing experiments with noise factors in Section 4. Much of the research in this area has focused on what can be accomplished with no replication and these methods are presented in Section 5. We discuss some examples in Section 6 and summarize the ideas in Section 7. 

Our studies have revealed that the structures of aromatic amine-DNA adducts are determined primarily by their size and coplanarity, as well as the nature of the adduct linkage (C8, N2, etc). It has been shown that aromatic amine lesions exist primarily in three well-defined conformational categories (S, B, W) and their population balance is strongly influenced by the sequences surrounding the lesion site. It is believed that the S/B/W ratios of aromatic amine adducts, not the subtle structural differences at the lesion site (e.g., rotamers, C8 versus N2 linkage, etc), determine the nature of the conformation-specific repair and mutational outcomes. As such, the available data points towards a new paradigm lesion bypass (either error-free or error-prone) depends on various factors, including the thermodynamic and conformational characteristics of the lesion at the replication fork,... 

The problem of origin of life on Earth (abiogenesis) remains one of the central and most intractable problems of modern biology. The current hypotheses cluster either around the replication first paradigm or the metabolism first concept, see [1-10] for consideration of the controversy between the two concepts. The... 

Templates are synonymous with the proliferation of life in biological systems. There is no need here to detail the way that DNA and RNA work to template their own formation. Suffice to say that they are the paradigm of a linear template, whereby not only the length of the replicated strand is determined by the template strand but also the sequence of the nucleic bases is strictly reproduced. This naturally occurring system is also exploitable for the preparation of entirely synthetic systems of varying complexity using the same nucleic acid building blocks, which are reviewed elsewhere in this volume (see Self-Assembly of Nucleic Acids, Self-Processes). 

The establishment of validity in qualitative research rests on assumptions about - and acceptance of - the knowledge and insights of informants, and the issue of reliability is complex. Some claim that the notion of reliability in qualitative research is a misnomer, misappropriating a concept from the normative paradigm. For there is no expectation that qualitative data will be reliable in the sense meant in quantitative research the assumption is that in a small, local situation knowledge is specific and findings are not necessarily replicable. However, it may be that there are different sides to the story , and in this seirse data and analysis from only one source may indeed constitute a distorted picture. 

A common problem experienced under the current automation paradigm, with the demand for greater results in shorter iteration cycles (1-2 weeks), is that screeners are required to collect data from several single assay workstations, often run on different software platforms. With the demand for results on more compounds per week, the screeners must process more samples through the assays, each with fewer data points and replicates. This trade off in quality for quantity can result in lower overall data fidelity. 

AIDS does not fit the paradigm for classical vaccines for a number of reasons. The classical preventive vaccines enhance natural immunity against microbes that change a little or none at all, whereas HIV mutates. There is some level of initial replication and dispersal at the point of entry before the virus reaches its target... 

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