The Advantage of Arriving First: Characteristic Times in Finite Size Populations of Error-Prone Replicators

We study the evolution of a finite size population formed by mutationally isolated lineages of error-prone replicators in a two-peak fitness landscape. Computer simulations are performed to gain a stochastic description of the system dynamics. More specifically, for different population sizes, we compute the probability of each lineage being selected in terms of their mutation rates and the amplification factors of the fittest phenotypes. We interpret the results as the compromise between the characteristic time a lineage takes to reach its fittest phenotype by crossing the neutral valley and the selective value of the sequences that form the lineages. A main conclusion is drawn: for finite population sizes, the survival probability of the lineage that arrives first to the fittest phenotype rises significantly

Topological entropy of catalytic sets: Hypercycles revisited

The dynamics of catalytic networks have been widely studied over the last decades because of their implications in several fields like prebiotic evolution, virology, neural networks, immunology or ecology. One of the most studied mathematical bodies for catalytic networks was initially formulated in the context of prebiotic evolution, by means of the hypercycle theory. The hypercycle is a set of self-replicating species able to catalyze other replicator species within a cyclic architecture. Hypercyclic organization might arise from a quasispecies as a way to increase the informational containt surpassing the so-called error threshold. The catalytic coupling between replicators makes all the species to behave like a single and coherent evolutionary multimolecular unit. The inherent nonlinearities of catalytic interactions are responsible for the emergence of several types of dynamics, among them, chaos. In this article we begin with a brief review of the hypercycle theory focusing on its evolutionary implications as well as on different dynamics associated to different types of small catalytic networks. Then we study the properties of chaotic hypercycles with error-prone replication with symbolic dynamics theory, characterizing, by means of the theory of topological Markov chains, the topological entropy and the periods of the orbits of unimodal-like iterated maps obtained from the strange attractor. We will focus our study on some key parameters responsible for the structure of the catalytic network: mutation rates, autocatalytic and cross-catalytic interactions.

Human language as a culturally transmitted replicator

Human languages form a distinct and largely independent class of cultural replicators with behaviour and fidelity that can rival that of genes. Parallels between biological and linguistic evolution mean that statistical methods inspired by phylogenetics and comparative biology are being increasingly applied to study language. Phylogenetic trees constructed from linguistic elements chart the history of human cultures, and comparative studies reveal surprising and general features of how languages evolve, including patterns in the rates of evolution of language elements and social factors that influence temporal trends of language evolution. For many comparative questions of anthropology and human behavioural ecology, historical processes estimated from linguistic phylogenies may be more relevant than those estimated from genes.

Origens da vida

We present a historical perspective about the ideas concerning the origin of life. After displaying the main topics necessary for understanding life's origin, the main characteristics of the present life forms and their relationships are shown, suggesting a common ancestor. The conditions for prebiotic chemistry in terrestrial or interplanetary environments are reviewed. We put in context the arguments about the early origin of replicators versus metabolism. The very narrow window for life settlement in the early Earth is stressed, pointing to the likelihood of life arising in other places in the Universe. Finally, we present the cornerstones of current search for life outside our planet.

Biological evolution of replicator systems: towards a quantitative approach

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312–316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth’s geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

Understanding replication of experiments in software engineering: a classification

Context: Replication plays an important role in experimental disciplines. There are still many uncertain- ties about how to proceed with replications of SE experiments. Should replicators reuse the baseline experiment materials? How much liaison should there be among the original and replicating experiment- ers, if any? What elements of the experimental configuration can be changed for the experiment to be considered a replication rather than a new experiment? Objective: To improve our understanding of SE experiment replication, in this work we propose a classi- fication which is intend to provide experimenters with guidance about what types of replication they can perform. Method: The research approach followed is structured according to the following activities: (1) a litera- ture review of experiment replication in SE and in other disciplines, (2) identification of typical elements that compose an experimental configuration, (3) identification of different replications purposes and (4) development of a classification of experiment replications for SE. Results: We propose a classification of replications which provides experimenters in SE with guidance about what changes can they make in a replication and, based on these, what verification purposes such a replication can serve. The proposed classification helped to accommodate opposing views within a broader framework, it is capable of accounting for less similar replications to more similar ones regarding the baseline experiment. Conclusion: The aim of replication is to verify results, but different types of replication serve special ver- ification purposes and afford different degrees of change. Each replication type helps to discover partic- ular experimental conditions that might influence the results. The proposed classification can be used to identify changes in a replication and, based on these, understand the level of verification.

The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence

Autonomously replicating sequence (ARS) elements, which function as the cis-acting chromosomal replicators in the yeast Saccharomyces cerevisiae, depend upon an essential copy of the 11-bp ARS consensus sequence (ACS) for activity. Analysis of the chromosome III replicator ARS309 unexpectedly revealed that its essential ACS differs from the canonical ACS at two positions. One of the changes observed in ARS309 inactivates other ARS elements. This atypical ACS binds the origin recognition complex efficiently and is required for chromosomal replication origin activity. Comparison of the essential ACS of ARS309 with the essential regions of other ARS elements revealed an expanded 17-bp conserved sequence that efficiently predicts the essential core of ARS elements.

Práticas e características do jornalismo alternativo e contra hegemônico de agência de informação: uma visão a partir da rotina produtiva da Adital

The strong presence of the communication and information technologies (TICs) forced the productive routine of some media vehicles to go through significant changes. The same happened to the alternative agencies segment. Having a scarce literature and sources about this subject, this study’s objective is to understand how the Information Agency Frei Tito for Latin America (Adital) develops its proposal of alternative journalism, within the cyberspace, while aiming a Christian communication. For this finality, the study will describe and explain the practices of journalistic production, identifying the subjects involved and the relations maintained between them in this productive routine. Also, it will trace who and where these content replicators are and/or their online address. At first, it was presented a theoretical discussion about the concepts of “counter-hegemony”, alternative journalism and communicative citizenship, what brings us to the studies of Gramsci (2010), Peruzzo (2011), Moraes (2013), Paiva (2008), Coutinho (2008), Mata (2006), among other authors. Next, it will be approached briefly the historical path of the information agencies around the world and in Latin America, so that the study can focus on authors like Aguiar (2009), Pasti (2013) and Moraes (2010). This piece will draught a “methodologic route” for a qualitative approach with an exploratory and descriptive character. We gave up the etnometodological methods, what allow us to analyze the etnomethods or behavioral groups of action, procedures, activities and knowledge that constitutes these groups, giving them recognition and distinction. (COULON, 1995). To achieve the defined objectives, it was also used a bibliographical and documental research techniques, in addition to subject observation and semi-structured interviews. Finally, we analyze the collected data taking into consideration three pivots: the beginning of Adital; the practices, characteristics and subjects involved in the productive routine of the agency; and who are and where are these content replicators of content produced and transmitted by Adital. We can conclude that the production routine of an alternative agency and the counter-hegemonic of information is marked by some singularities regarding to the organization of the journalistic practice and to the obstacles found on the way. Our data allows us, even if there are still some doubts, to believe that Adital is a sort of independent information agency, alternative and counter-hegemonic, ergo, more close to a proposition of communicative citizenship.

Práticas e características do jornalismo alternativo e contra hegemônico de agência de informação: uma visão a partir da rotina produtiva da Adital

The strong presence of the communication and information technologies (TICs) forced the productive routine of some media vehicles to go through significant changes. The same happened to the alternative agencies segment. Having a scarce literature and sources about this subject, this study’s objective is to understand how the Information Agency Frei Tito for Latin America (Adital) develops its proposal of alternative journalism, within the cyberspace, while aiming a Christian communication. For this finality, the study will describe and explain the practices of journalistic production, identifying the subjects involved and the relations maintained between them in this productive routine. Also, it will trace who and where these content replicators are and/or their online address. At first, it was presented a theoretical discussion about the concepts of “counter-hegemony”, alternative journalism and communicative citizenship, what brings us to the studies of Gramsci (2010), Peruzzo (2011), Moraes (2013), Paiva (2008), Coutinho (2008), Mata (2006), among other authors. Next, it will be approached briefly the historical path of the information agencies around the world and in Latin America, so that the study can focus on authors like Aguiar (2009), Pasti (2013) and Moraes (2010). This piece will draught a “methodologic route” for a qualitative approach with an exploratory and descriptive character. We gave up the etnometodological methods, what allow us to analyze the etnomethods or behavioral groups of action, procedures, activities and knowledge that constitutes these groups, giving them recognition and distinction. (COULON, 1995). To achieve the defined objectives, it was also used a bibliographical and documental research techniques, in addition to subject observation and semi-structured interviews. Finally, we analyze the collected data taking into consideration three pivots: the beginning of Adital; the practices, characteristics and subjects involved in the productive routine of the agency; and who are and where are these content replicators of content produced and transmitted by Adital. We can conclude that the production routine of an alternative agency and the counter-hegemonic of information is marked by some singularities regarding to the organization of the journalistic practice and to the obstacles found on the way. Our data allows us, even if there are still some doubts, to believe that Adital is a sort of independent information agency, alternative and counter-hegemonic, ergo, more close to a proposition of communicative citizenship.

Variable mutation rates as an adaptive strategy in replicator populations

For evolving populations of replicators, there is much evidence that the effect of mutations on fitness depends on the degree of adaptation to the selective pressures at play. In optimized populations, most mutations have deleterious effects, such that low mutation rates are favoured. In contrast to this, in populations thriving in changing environments a larger fraction of mutations have beneficial effects, providing the diversity necessary to adapt to new conditions. What is more, non-adapted populations occasionally benefit from an increase in the mutation rate. Therefore, there is no optimal universal value of the mutation rate and species attempt to adjust it to their momentary adaptive needs. In this work we have used stationary populations of RNA molecules evolving in silico to investigate the relationship between the degree of adaptation of an optimized population and the value of the mutation rate promoting maximal adaptation in a short time to a new selective pressure. Our results show that this value can significantly differ from the optimal value at mutation-selection equilibrium, being strongly influenced by the structure of the population when the adaptive process begins. In the short-term, highly optimized populations containing little variability respond better to environmental changes upon an increase of the mutation rate, whereas populations with a lower degree of optimization but higher variability benefit from reducing the mutation rate to adapt rapidly. These findings show a good agreement with the behaviour exhibited by actual organisms that replicate their genomes under broadly different mutation rates. © 2010 Stich et al.