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PubMed2002

Spin-flip symmetry and synchronization.

In the context of optimization by evolutionary algorithms (EAs), epistasis, deception, and scaling are well-known examples of problem difficulty characteristics. The presence of one such characteristic in the representation of a search problem indicates a certain type of difficulty the EA is to encounter during its search for globally optimal configurations. In this paper, we claim that the occurrence of symmetry in the representation is another problem difficulty characteristic and discuss one particular form, spin-flip symmetry, characterized by fitness invariant permutations on the alphabet. Its usual effect on unspecialized EAs, premature convergence due to synchronization problems, is discussed in detail. We discuss five different ways to specialize EAs to cope with the symmetry: adapting the genetic operators, changing the fitness function, using a niching technique, using a distributed EA, and attaching a highly redundant genotype-phenotype mapping.

Algorithms↗
PubMed2005

A filter-based evolutionary algorithm for constrained optimization.

We introduce a filter-based evolutionary algorithm (FEA) for constrained optimization. The filter used by an FEA explicitly imposes the concept of dominance on a partially ordered solution set. We show that the algorithm is provably robust for both linear and nonlinear problems and constraints. FEAs use a finite pattern of mutation offsets, and our analysis is closely related to recent convergence results for pattern search methods. We discuss how properties of this pattern impact the ability of an FEA to converge to a constrained local optimum.

Algorithms↗
PubMed2000

Duplication of modules facilitates the evolution of functional specialization.

The evolution of simulated robots with three different architectures is studied in this article. We compare a nonmodular feed-forward network, a hardwired modular, and a duplication-based modular motor control network. We conclude that both modular architectures outperform the non-modular architecture, both in terms of rate of adaptation as well as the level of adaptation achieved. The main difference between the hardwired and duplication-based modular architectures is that in the latter the modules reached a much higher degree of functional specialization of their motor control units with regard to high-level behavioral functions. The hardwired architectures reach the same level of performance, but have a more distributed assignment of functional tasks to the motor control units. We conclude that the mechanism through which functional specialization is achieved is similar to the mechanism proposed for the evolution of duplicated genes. It is found that the duplication of multifunctional modules first leads to a change in the regulation of the module, leading to a differentiation of the functional context in which the module is used. Then the module adapts to the new functional context. After this second step the system is locked into a functionally specialized state. We suggest that functional specialization may be an evolutionary absorption state.

Adaptation, Physiological↗
PubMed2002

Evolvable self-replicating molecules in an artificial chemistry.

This paper gives details of Squirm3, a new artificial environment based on a simple physics and chemistry that supports self-replicating molecules somewhat similar to DNA. The self-replicators emerge spontaneously from a random soup given the right conditions. Interactions between the replicators can result in mutated versions that can outperform their parents. We show how artificial chemistries such as this one can be implemented as a cellular automaton. We concur with Dittrich, Ziegler, and Banzhaf that artificial chemistries are a good medium in which to study early evolution.

Biological Evolution↗
PubMed2003

High-dimensional analysis of evolutionary autonomous agents.

This article presents a new approach to the important challenge of localizing function in a neurocontroller. The approach is based on the basic functional contribution analysis (FCA) presented earlier, which assigns contribution values to the elements of the network, such that the ability to predict the network's performance in response to multi-unit lesions is maximized. These contribution values quantify the importance of each element to the tasks the agent performs. Here we present a generalization of the basic FCA to high-dimensional analysis, using high-order compound elements. Such elements are composed of conjunctions of simple elements. Their usage enables the explicit expression of sets of neurons or synapses whose contributions are interdependent, a prerequisite for localizing the function of complex neurocontrollers. High-dimensional FCA is shown to significantly improve on the accuracy of the basic analysis, to provide new insights concerning the main subsets of simple elements in the network that interact in a complex nonlinear manner, and to systematically reveal the types of interactions that characterize the evolved neurocontroller.

Artificial Intelligence↗
PubMed2006

Exploring the dynamics of adaptation with evolutionary activity plots.

Evolutionary activity statistics and their visualization are introduced, and their motivation is explained. Examples of their use are described, and their strengths and limitations are discussed. References to more extensive or general accounts of these techniques are provided.

Acclimatization↗
PubMed2006

Visualizing coevolution with CIAO plots.

In a previous article, we introduced a number of visualization techniques that we had developed for monitoring the dynamics of artificial competitive coevolutionary systems. One of these techniques involves evaluating the performance of an individual from the current population in a series of trials against opponents from all previous generations, and visualizing the results as a 2D grid of shaded cells or pixels: qualitative patterns in the shading can indicate different classes of coevolutionary dynamics. As this technique involves pitting a current individual against ancestral opponents, we referred to the visualizations as CIAO plots. Since then, a number of other authors studying the dynamics of competitive coevolutionary systems have used CIAO plots or close derivatives to help illuminate the dynamics of their systems, and it has become something of a de facto standard visualization technique. In this very brief article we summarize the rationale for CIAO plots, explain the method of constructing a CIAO plot, and review important recent results that identify significant limitations of this technique.

Artificial Intelligence↗
PubMed2004

Exact solutions for evolutionary strategies on harmonic landscapes.

In this paper two different evolutionary strategies are tested by means of harmonic landscapes. Both strategies are based on ensembles of searchers, spreading over the search space according to laws inspired by nature. The main difference between the two prototypes is given by the underlying selection mechanism, governing the increase or decrease of the local population of searchers in certain regions of the search space. More precisely, we compare a thermodynamic strategy, which is based on a physically motivated local selection criterion, with a biologically motivated strategy, which features a global selection scheme (i.e., global coupling of the searchers). Confining ourselves to a special class of initial conditions, we show that, in the simple case of harmonic test potentials, both strategies possess particular analytical solutions of the same type. By means of these special solutions, the velocities of the two strategies can be compared exactly. In the last part of the paper, we extend the scope of our discussion to a mixed strategy, combining local and global selection.

Biological Evolution↗
PubMed2004

An orthogonal multi-objective evolutionary algorithm for multi-objective optimization problems with constraints.

In this paper, an orthogonal multi-objective evolutionary algorithm (OMOEA) is proposed for multi-objective optimization problems (MOPs) with constraints. Firstly, these constraints are taken into account when determining Pareto dominance. As a result, a strict partial-ordered relation is obtained, and feasibility is not considered later in the selection process. Then, the orthogonal design and the statistical optimal method are generalized to MOPs, and a new type of multi-objective evolutionary algorithm (MOEA) is constructed. In this framework, an original niche evolves first, and splits into a group of sub-niches. Then every sub-niche repeats the above process. Due to the uniformity of the search, the optimality of the statistics, and the exponential increase of the splitting frequency of the niches, OMOEA uses a deterministic search without blindness or stochasticity. It can soon yield a large set of solutions which converges to the Pareto-optimal set with high precision and uniform distribution. We take six test problems designed by Deb, Zitzler et al., and an engineering problem (W) with constraints provided by Ray et al. to test the new technique. The numerical experiments show that our algorithm is superior to other MOGAS and MOEAs, such as FFGA, NSGAII, SPEA2, and so on, in terms of the precision, quantity and distribution of solutions. Notably, for the engineering problem W, it finds the Pareto-optimal set, which was previously unknown.

Algorithms↗
PubMed2006

Connectivity independent protein-structure alignment: a hierarchical approach.

BACKGROUND: Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). RESULTS: We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. alpha-helices and beta-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. CONCLUSION: As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity.

Algorithms↗
PubMed2006

Polymorphism analysis of six selenoprotein genes: support for a selective sweep at the glutathione peroxidase 1 locus (3p21) in Asian populations.

BACKGROUND: There are at least 25 human selenoproteins, each characterized by the incorporation of selenium into the primary sequence as the amino acid selenocysteine. Since many selenoproteins have antioxidant properties, it is plausible that inter-individual differences in selenoprotein expression or activity could influence risk for a range of complex diseases, such as cancer, infectious diseases as well as deleterious responses to oxidative stressors like cigarette smoke. To capture the common genetic variants for 6 important selenoprotein genes (GPX1, GPX2, GPX3, GPX4, TXNRD1, and SEPP1) known to contribute to antioxidant host defenses, a re-sequence analysis was conducted across these genes with particular interest directed at the coding regions, intron-exon borders and flanking untranslated regions (UTR) for each gene in an 102 individual population representative of 4 major ethnic groups found within the United States. RESULTS: For 5 of the genes there was no strong evidence for selection according to the expectations of the neutral equilibrium model of evolution; however, at the GPX1 locus (3p21) there was evidence for positive selection. Strong confirmatory evidence for recent positive selection at the genomic region 3p21 in Asian populations is provided by data from the International HapMap project. CONCLUSION: The SNPs and fine haplotype maps described in this report will be valuable resources for future functional studies, for population specific genetic studies designed to comprehensively explore the role of selenoprotein genetic variants in the etiology of various human diseases, and to define the forces responsible for a recent selective sweep in the vicinity of the GPX1 locus.

Asian People↗
PubMed2001

Functional evolution of two subtly different (similar) folds.

BACKGROUND: The function of proteins is a direct consequence of their three-dimensional structure. The structural classification of proteins describes the ways of folding patterns all proteins could adopt. Although, the protein folds were described in many ways the functional properties of individual folds were not studied. RESULTS: We have analyzed two beta-barrel folds generally adopted by small proteins to be looking similar but have different topology. On the basis of the topology they could be divided into two different folds named SH3-fold and OB-fold. There was no sequence homology between any of the proteins considered. The sequence diversity and loop variability was found to be important for various binding functions. CONCLUSIONS: The function of Oligonucleotide/oligosaccharide-binding (OB) fold proteins was restricted to either DNA/RNA binding or sugar binding whereas the Src homology 3 (SH3) domain like proteins bind to a variety of ligands through loop modulations. A question was raised whether the evolution of these two folds was through DNA shuffling.

Amino Acid Sequence↗
PubMed2025

The impact of the live broadcast of Stromae's song L'enfer on social media publications, calls to the national helpline, and suicide attempt rates in France.

On January 9, 2022, Belgian pop singer Stromae performed his new hit "L'enfer" live on French TV. The song addresses his personal struggles with suicidal ideation. To evaluate the impact of Stromae's performance, we modeled the evolution of hospital admission rates for suicide attempts (SAs) in France, calls to the national suicide prevention helpline (3114), and Twitter publications mentioning the singer or the helpline. We employed the Gombay test to identify change points within each time series. We identified a significant increase in mean SA rates among women aged 20-24 years 6 days after the singer's performance. No similar effect was observed in the general population or other young age groups. The show was immediately followed by a peak in tweets referring to the singer, while Twitter activity related to the 3114 remained modest. We did not observe any increase in calls to the helpline. Celebrity testimonies about suicidal experiences can help alleviate stigma but should be accompanied by prevention messages to reduce the risk of contagion.

Humans↗
PubMed2007

Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes.

Compartmentalized self-replication (CSR) is a novel method for the directed evolution of enzymes and, in particular, polymerases. In its simplest form, CSR consists of a simple feedback loop involving a polymerase that replicates only its own encoding gene (self-replication). Self-replication occurs in discrete, spatially separate, noncommunicating compartments formed by a heat-stable water-in-oil emulsion. Compartmentalization ensures the linkage of phenotype and genotype (i.e., it ensures that each polymerase replicates only its own encoding gene to the exclusion of those in the other compartments). As a result, adaptive gains by the polymerase directly (and proportionally) translate into genetic amplification of the encoding polymerase gene. CSR has proven to be a useful strategy for the directed evolution of polymerases directly from diverse repertoires of polymerase genes. In this chapter, we describe some of the CSR protocols used successfully to evolve variants of T. aquaticus Pol I (Taq) polymerase with novel and useful properties, such as increased thermostability or resistance to the potent inhibitor, heparin, from a repertoire of randomly mutated Taq polymerase genes.

DNA Replication↗
PubMedDate not supplied

Structure of the sodium channel gene SCN11A: evidence for intron-to-exon conversion model and implications for gene evolution.

Exon/intron boundaries in the regions encoding the trans-membrane segments of voltage-gated Na channel genes are conserved, supporting their proposed evolution from a single domain channel, while the exons encoding the cytoplasmic loops are less conserved with their evolutionary heritage being less defined. SCN11A encodes the tetrodotoxin-resistant (TTX-R) sodium channel Nav1.9a/NaN, which is preferentially expressed in nociceptive primary sensory neurons of dorsal root ganglia (DRG) and trigeminal ganglia. SCN11A is localized to human chromosome 3 (3p21-24) close to the other TTX-R sodium channel genes SCN5A and SCN10A. An alternative transcript, Nav1.9b, has been detected in rat DRG and trigeminal ganglion. Nav1.9b is predicted to produce a truncated protein due to a frame-shift, which is introduced by the new sequence of exon 23c (E23c). In human and mouse SCN11A, divergent splicing signals prevent utilization of E23c. Unlike exons 5A/N in genes encoding TTX-sensitive sodium channels, which appear to have resulted from exon duplication, E23c might have evolved from the conversion of an intronic sequence. Although a functional role for Nav1.9b has yet to be established, intron-to-exon conversion may represent a mechanism for ion channels to acquire novel features.

Amino Acid Sequence↗
PubMedDate not supplied

Algorithm for construction of phylogenetic trees.

An algorithm is described for the construction of phylogenetic trees. The algorithm is based on the progressive correction of data along the tree construction. For the correction, the average value of the difference between each pair of neighbour elements to the rest of the table is considered.

Algorithms↗
PubMed2002

The pharmacoeconomic impact of generics: an evolutionary tale.

The very word generics stiffens sinews and tightens lips in the pharma industry. It has been proposed that large profits and much pride are now being lost through the creeping forces of intellectual piracy and generic plagiarism [1-3]. In this article, I will argue against this position. Using models from evolution and modern day complexity theory I will attempt to address some of the fears that surround generic pharmaceutical enterprise and to express my own concerns about some of the overly optimistic thinking that occurs with respect to developing world systems and the HIV virus.

Biological Evolution↗