Biomedical subjects

R V Solé

Publications and source records attributed to R V Solé.

14 recordsLinked to original sources

PubMed2001

The small world of human language.

Words in human language interact in sentences in non-random ways, and allow humans to construct an astronomic variety of sentences from a limited number of discrete units. This construction process is extremely fast and robust. The co-occurrence of words in sentences reflects language organization in a subtle manner that can be described in terms of a graph of word interactions. Here, we show that such graphs display two important features recently found in a disparate number of complex systems. (i) The so called small-world effect. In particular, the average distance between two words, d (i.e. the average minimum number of links to be crossed from an arbitrary word to another), is shown to be d approximately equal to 2-3, even though the human brain can store many thousands. (ii) A scale-free distribution of degrees. The known pronounced effects of disconnecting the most connected vertices in such networks can be identified in some language disorders. These observations indicate some unexpected features of language organization that might reflect the evolutionary and social history of lexicons and the origins of their flexibility and combinatorial nature.

Biological Evolution↗

PubMed2001

Field theory for a reaction-diffusion model of quasispecies dynamics.

RNA viruses are known to replicate with extremely high mutation rates. These rates are actually close to the so-called error threshold. This threshold is in fact a critical point beyond which genetic information is lost through a second-order phase transition, which has been dubbed as the "error catastrophe." Here we explore this phenomenon using a field theory approximation to the spatially extended Swetina-Schuster quasispecies model [J. Swetina and P. Schuster, Biophys. Chem. 16, 329 (1982)], a single-sharp-peak landscape. In analogy with standard absorbing-state phase transitions, we develop a reaction-diffusion model whose discrete rules mimic the Swetina-Schuster model. The field theory representation of the reaction-diffusion system is constructed. The proposed field theory belongs to the same universality class as a conserved reaction-diffusion model previously proposed [F. van Wijland et al., Physica A 251, 179 (1998)]. From the field theory, we obtain the full set of exponents that characterize the critical behavior at the error threshold. Our results present the error catastrophe from a different point of view and suggest that spatial degrees of freedom can modify several mean-field predictions previously considered, leading to the definition of characteristic exponents that could be experimentally measurable.

Biophysical Phenomena↗

PubMed2001

Complexity and fragility in ecological networks.

A detailed analysis of three species-rich ecosystem food webs has shown that they display skewed distributions of connections. Such graphs of interaction are, in fact, shared by a number of biological and technological networks, which have been shown to display a very high homeostasis against random removals of nodes. Here, we analyse the responses of these ecological graphs to both random and selective perturbations (directed against the most-connected species). Our results suggest that ecological networks are very robust against random removals but can be extremely fragile when selective attacks are used. These observations have important consequences for biodiversity dynamics and conservation issues, current estimations of extinction rates and the relevance and definition of keystone species.

Ecosystem↗

PubMed2001

Topology of technology graphs: small world patterns in electronic circuits.

Recent theoretical studies and extensive data analyses have revealed a common feature displayed by biological, social, and technological networks: the presence of small world patterns. Here we analyze this problem by using several graphs obtained from one of the most common technological systems: electronic circuits. It is shown that both analogic and digital circuits exhibit small world behavior. We conjecture that the small world pattern arises from the compact design in which many elements share a small, close physical neighborhood plus the fact that the system must define a single connected component (which requires shortcuts connecting different integrated clusters). The degree distributions displayed are consistent with a conjecture concerning the sharp cutoffs associated to the presence of costly connections [Amaral et al., Proc. Natl. Acad. Sci. USA 97, 11 149 (2000)], thus providing a limit case for the classes of universality of small world patterns from real, artificial networks. The consequences for circuit design are outlined.

Journal Article↗

PubMed2000

Gene networks capable of pattern formation: from induction to reaction-diffusion.

One of the main aims of developmental biology is to understand how a single and apparently homogeneous egg cell achieves the intricate complexity of the adult. Here we present two models to explain the generation of developmental patterns through interactions at the gene level. One model considers direct-contact induction between cells while the other takes into account diffusion of hormones. We show that sets of cells involving identical gene networks and communicating through hormones spontaneously exhibit ordered patterns. We have characterized these patterns and the specific networks responsible for them. The models allow to (i) compare diffusion and direct-contact induction processes as mechanisms of pattern generation; (ii) identify the possible range of behaviour of real gene networks and (iii) suggest causal mechanisms to generate known patterns. The evolutionary implications are discussed.

Animals↗

PubMed2000

Self-synchronization and task fulfilment in ant colonies.

Some authors have hypothesized that the observed self-synchronized activity in ant colonies provides some adaptive advantages, and, in particular, it has been suggested that task realization may benefit from this ordered temporal pattern of behaviour (Robinson, 1992, Ann. Rev. Entomol, 37, 637-702; Hatcher et al., 1992, Naturwissenschaften, 79, 32-34). In this paper, we use a model of self-synchronized activity (the fluid neural network) to suggest that with self-synchronized patterns of activity a task may be fulfiled more effectively than with non-synchronized activity, at the same average level of activity per individual.

Animals↗

PubMed2000

Extinctions and taxonomy in a trophic model of coevolution.

We investigate the statistics of extinction sizes and the taxonomy in a trophic model of evolution recently proposed [Phys. Rev. Lett. 82, 652 (1999)]. By further exploring the parameters of this model, we find that the distribution of extinction sizes N(s) shows typically a characteristic maximum before developing the power-law behavior N(s) approximately s(-alpha) with alpha approximately 2, in agreement with empirical observations. Furthermore, the derivation of the alpha=-2 exponent given by Drossel [Phys. Rev. Lett. 81, 5011 (1998)] for this model is completed. The extinction sizes in each trophic level are also analyzed; one finds that at the fourth level and up (l> or =4) the extinction size statistics is a power law with exponent alpha(l) approximately 1.4, and exponential-like at the second level, also in agreement with some empirical data not previously explained by current models. On the other hand, in contrast to the observed power-law distribution of the number of species in genera, numerical simulations yield an exponential law. A modification of the model is presented that provides an approximate potential behavior for taxonomy, and some consequences for future modeling are outlined.

Biological Evolution↗

PubMed2000

Mean-field stochastic theory for species-rich assembled communities.

A dynamical model of an ecological community is analyzed within a "mean-field approximation" in which one of the species interacts with the combination of all of the other species in the community. Within this approximation the model may be formulated as a master equation describing a one-step stochastic process. The stationary distribution is obtained in closed form, and is shown to reduce to a log-series or log-normal distribution, depending on the values that the parameters describing the model take on. A hyperbolic relationship between the connectance of the matrix of interspecies interactions and the average number of species exists for a range of parameter values. The time evolution of the model at short and intermediate times is analyzed using van Kampen's approximation, which is valid when the number of individuals in the community is large. Good agreement with numerical simulations is found. The large time behavior, and the approach to the stationary state, is obtained by solving the equation for the generating function of the probability distribution. The analytical results which follow from the analysis are also in good agreement with direct simulations of the model.

Biophysical Phenomena↗

PubMed2000

Pattern formation and optimization in army ant raids.

Army ant colonies display complex foraging raid patterns involving thousands of individuals communicating through chemical trails. In this article we explore, by means of a simple search algorithm, the properties of these trails in order to test the hypothesis that their structure reflects an optimized mechanism for exploring and exploiting food resources. The raid patterns of three army ant species, Eciton hamatum, Eciton burchelli, and Eciton rapax, are analyzed. The respective diets of these species involve large but rare, small but common, and a combination of large but rare and small but common food sources. Using a model proposed by Deneubourg et al. [4], we simulate the formation of raid patterns in response to different food distributions. Our results indicate that the empirically observed raid patterns maximize return on investment, that is, the amount of food brought back to the nest per unit of energy expended, for each of the diets. Moreover, the values of the parameters that characterize the three optimal pattern-generating mechanisms are strikingly similar. Therefore the same behavioral rules at the individual level can produce optimal colony-level patterns. The evolutionary implications of these findings are discussed.

Algorithms↗

PubMed1999

Red queen dynamics, competition and critical points in a model of RNA virus quasispecies.

RNA viruses offer a unique opportunity for the study of evolution at the molecular level. Recent experiments involving clonal populations of RNA viruses have shown that competition among virus strains of approximately equal relative fitness can result in the eventual competitive exclusion of one of the species. As competition proceeds in time, both the winners and the losers exhibited absolute gains in fitness, consistent with the "Red Queen" hypothesis of evolution. Further experiments involving closely related evolving quasispecies revealed a highly predictable nonlinear behavior suggesting a deterministic component in the underlying quasispecies dynamics. This is apparently in contradiction with the standard view of RNA virus evolution as a highly unpredictable process. In this paper we present a simple model which allows previous hypothesis to be tested and provides an interpretation for the observed experimental results.

Cloning, Molecular↗

PubMed1999

Noise and periodic modulations in neural excitable media.

We have analyzed the interplay between noise and periodic modulations in a mean field model of a neural excitable medium. For this purpose, we have considered two types of modulations, namely, variations of the resistance and oscillations of the threshold. In both cases, stochastic resonance is present, irrespective of whether the system is monostable or bistable.

Biophysical Phenomena↗

PubMed1996

Are critical phenomena relevant to large-scale evolution?

Recent theoretical studies, based on the theory of self-organized critical systems, seem to suggest that the dynamical patterns of macroevolution could belong to such class of critical phenomena. Two basic approaches have been proposed: the Kauffman-Johnsen model (based on the use of coupled fitness landscapes) and the Bak-Sneppen model. Both are reviewed here. These models are oversimplified pictures of biological evolution, but the (possible) validity of them is based on the concept of universality, i.e. that apparently very different systems sharing some few common properties should also behave in a very similar way. In this paper we explore the current evidence from the fossil record, showing that some properties that are suggestive of critical dynamics would also be the result of random phenomema. Some general properties of the large-scale pattern of evolution, which should be reproduced by these models, are discussed.

Biological Evolution↗

PubMedDate not supplied

Phenotypic and dynamical transitions in model genetic networks. I. Emergence of patterns and genotype-phenotype relationships.

Genotype-phenotype interactions during the evolution of form in multicellular organisms is a complex problem but one that can be aided by computational approaches. We present here a framework within which developmental patterns and their underlying genetic networks can be simulated. Gene networks were chosen to reflect realistic regulatory circuits, including positive and negative feedback control, and the exchange of a subset of gene products between cells, or within a syncytium. Some of these networks generate stable spatial patterns of a subset of their molecular constituents, and can be assigned to categories (e.g., "emergent" or "hierarchic") based on the topology of molecular circuitry. These categories roughly correspond to what has been discussed in the literature as "self-organizing" and "programmed" processes of development. The capability of such networks to form patterns of repeating stripes was studied in network ensembles in which parameters of gene-gene interaction were caused to vary in a manner analogous to genetic mutation. The evolution under mutational change of individual representative networks of each category was also simulated. We have found that patterns with few stripes (< or =3) are most likely to originate in the form of a hierarchic network, whereas those with greater numbers of stripes (> or =4) originate most readily as emergent networks. However, regardless of how many stripes it contains, once a pattern is established, there appears to be an evolutionary tendency for emergent mechanisms to be replaced by hierarchic mechanisms. These results have potential significance for the understanding of genotype-phenotype relationships in the evolution of metazoan form.

Biological Evolution↗

PubMedDate not supplied

Phenotypic and dynamical transitions in model genetic networks. II. Application to the evolution of segmentation mechanisms.

Knowledge of the genetic control of segmentation in Drosophila has made insect segmentation a paradigmatic case in the study of the evolution of developmental mechanisms. In Drosophila, the patterns of expression of segmentation genes are established simultaneously in all segments by a complex set of interactions between transcriptional factors that diffuse in a syncytium occupying the whole embryo. Such mechanisms cannot act in short germ-band insects where segments appear sequentially from a cellularized posterior proliferative zone. Here, we compare mechanisms of segmentation in different organisms and discuss how the transition between the different types of segmentation can be explained by small and progressive changes in the underlying gene networks. The recent discovery of a temporal oscillation in expression during somitogenesis of vertebrate homologs of the pair-rule gene hairy enhances the plausibility of an earlier proposal that the evolutionary origin of both the short- and long germ-band modes of segmentation was an oscillatory genetic network (Newman 1993). An implication of this scenario is that the self-organizing, pattern-forming system embodied in an oscillatory network operating in the context of a syncytium (i.e., a reaction-diffusion system)-which is hypothesized to have originated the simultaneous mode of segmentation-must have been replaced by the genetic hierarchy seen in modern-day Drosophila over the course of evolution. As demonstrated by the simulations in the accompanying article, the tendency for "emergent" genetic networks, associated with self-organizing processes, to be replaced through natural selection with hierarchical networks is discussed in relation to the evolution of segmentation.

Animals↗