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At least 415 records · Page 23Linked to original sources
arXiv2000

Microscopic Discrete Proliferating Components Cause the Self-Organized Emergence of Macroscopic Adaptive Features in Biological Systems

We study the emergence of the collective spatio-temporal macroscopic properties of the immune system, by representing individually the elementary interactions between its microscopic components (antibodies, antigens, cytokines). The results of this detailed explicit analysis are compared with the traditional procedure of averaging over individuals and representing the collective dynamics in terms of densities that obey partial differential equations (PDE). The simulations show even for very simple elementary reactions the spontaneous emergence of localized complex structures. In turn the effective dynamics of these structures affects the average behavior of the system in a very decisive way: systems which would according to the differential equations approximation die, display in reality a very lively behavior. Our conclusions are supported both by explicit microscopic simulations and by analytic calculations. As the optimal method we propose a mixture of microscopic simulation (MS) systems describing each reaction separately, and average methods describing the average behavior of the agents.

nlin.AO↗
arXiv2000

Effect of Mutation and Recombination on the Genotype-Phenotype Map

The effect of genetic operators other than selection, such as mutation and recombination, on the genotype-phenotype map is considered. In particular, when the genotypic fitness landscape exhibits a ``symmetry'', i.e. many genotypes corresponding to the same phenotype have equal fitness values, it is shown that such operators can break this symmetry. The consequences of this ``induced symmetry breaking'' are investigated. Specifically, it is shown that it generically leads to an increase in order or self-organization in the system and to the phenomenon of orthogenesis. Additionally, it is shown that it potentially leads to a more robust evolution circumventing some of the problems of brittleness. The above points are supported by explicit, analytic results associated with some simple one and two-locus models and also by some much more complicated numerical simulations.

nlin.AO↗
arXiv2000

Theory of Robustness of Irreversible Differentiation in a Stem Cell System: Chaos hypothesis

Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell systems - stochastic differentiation of stem cells and the robustness of a system due to regulation of this differentiation - are found to be general properties of a system of interacting cells exhibiting chaotic intra-cellular reaction dynamics and cell division, whose presence does not depend on the detail of the model. It is found that stem cells differentiate into other cell types stochastically due to a dynamical instability caused by cell-cell interactions, in a manner described by the Isologous Diversification theory. This developmental process is shown to be stable not only with respect to molecular fluctuations but also with respect to removal of cells. With this developmental process, the irreversible loss of multipotency accompanying the change from a stem cell to a differentiated cell is shown to be characterized by a decrease in the chemical diversity in the cell and of the complexity of the cellular dynamics. The relationship between the division speed and this loss of multipotency is also discussed. Using our model, some predictions that can be tested experimentally are made for a stem cell system.

nlin.AO↗
arXiv2000

Diversity patterns from ecological models at dynamical equilibrium

We study a dynamic model of ecosystems where immigration plays an essential role both in assembling the species community and in mantaining its biodiversity. This framework is particularly relevant for insular ecosystems. Population dynamics is represented either as an individual based model or as a set of deterministic equations for population abundances. Local extinctions and immigrations balance in a statistically stationary state where biodiversity fluctuates around a constant mean value. At stationarity, biodiversity increases as a power law of the immigration rate. Our model yields almost power law species area relationships, with a range of effective exponents in agreement with that observed for biodiversity of whole archipelagos. We also observe broad distributions for species abundances and species lifetimes and a small number of trophic levels, limited by the immigration rate. These results are rather robust with respect to change of description level, as well as change of population dynamic equations, from prey dependent to ratio dependent.

nlin.AO↗
arXiv2000

Evolution of genetic code through isologous diversification of cellular states

Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for the different choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA-amino acid complex in a cell is introduced and numerically studied. It is shown that the biochemical states of cells are differentiated by cell-cell interaction, and each differentiated type takes to use different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. Relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory for the evolution of genetic code is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes, and later with the mutation in genotype, the genotype also differentiates into discrete types, while maintaining the `symbiotic' relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.

nlin.AO↗
arXiv2003

A Theory of Pragmatic Information and Its Application to the Quasispecies Model of Biological Evolution

"Standard" information theory says nothing about the semantic content of information. Nevertheless, applications such as evolutionary theory demand consideration of precisely this aspect of information, a need that has motivated a largely unsuccessful search for a suitable measure of an "amount of meaning". This paper represents an attempt to move beyond this impasse, based on the observation that the meaning of a message can only be understood relative to its receiver. Positing that the semantic value of information is its usefulness in making an informed decision, we define pragmatic information as the information gain in the probability distributions of the receiver's actions, both before and after receipt of a message in some pre-defined ensemble. We then prove rigorously that our definition is the only one that satisfies obvious desiderata, such as the additivity of information from logically independent messages. This definition, when applied to the information "learned" by the time evolution of a process, defies the intuitions of the few previous researchers thinking along these lines by being monotonic in the uncertainty that remains after receipt of the message, but non-monotonic in the Shannon entropy of the input ensemble. It then follows that the pragmatic information of the genetic "messages" in an evolving population is a global Lyapunov function for Eigen's quasi-species model of biological evolution. A concluding section argues that a theory such as ours must explicitly acknowledge purposeful action, or "agency", in such diverse fields as evolutionary theory and finance.

nlin.AO↗
arXiv2001

Competing Populations in Flows with Chaotic Mixing

We investigate the effects of spatial heterogeneity on the coexistence of competing species in the case when the heterogeneity is dynamically generated by environmental flows with chaotic mixing properties. We show that one of the effects of chaotic advection on the passively advected species (such as phytoplankton, or self-replicating macromolecules) is the possibility of coexistence of more species than that limited by the number of niches they occupy. We derive a novel set of dynamical equations for competing populations.

nlin.CD↗
arXiv2001

Self-localization of laser induced tumor coagulation limited by heat diffusion through active tissue

We analyze the necrosis growth due to thermal coagulation induced by laser light absorption and limited by heat diffusion into the surrounding live tissue. The tissue is assumed to contain a certain tumor in the undamaged tissue whereof the blood perfusion rate does not change during the action. By contrast, the normal tissue responds strongly to increase in the tissue temperature and the blood perfusion rate can grow by tenfold. We study in detail the necrosis formation under conditions typical for a real course of thermal therapy treatment, the duration of the action is taken about 5 minutes when a necrosis domain of size about or above 1 cm is formed. In particular, if the tumor size is sufficiently large, it exceeds 1 cm, and the tissue response is not too delayed, the delay time does not exceed 1 min, then there are conditions under which the relative volume of the damaged normal tissue is small in comparison with the tumor volume after the tumor is coagulated totally.

nlin.AO↗
arXiv2001

Complex Systems As Fundamental Theory Of Sports Coaching?

We argue that traditional Western science cannot adequately describe sports and other types of human behavior. Then we make an argument why a complex adaptive systems approach has the potential to provide the foundation for such a theory. We claim that a special role will be played by biological quantum computation in the human brain that should have emerged through biological evolution. Biological quantum computation could have provided evolutionary advantages in the area of decision-making and fast motor responses, when a number of potential actions -represented as a set of points in a high dimensional state-space- are available to the agent. While for animals and early humans these rapid, coordinated motor activities had direct survival value, today they are mostly manifested in competitive sports events. We suggest that entanglement can be facilitated by systematic sports coaching.

nlin.AO↗
arXiv2002

Modelling Food Webs

We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species according to some simple rule. The second class are dynamical models, which include the population dynamics of several interacting species. We focus on the question of the stability of such webs. The third class are species assembly models and evolutionary models, which build webs starting from a few species by adding new species through a process of "invasion" (assembly models) or "speciation" (evolutionary models). Evolutionary models are found to be capable of building large stable webs.

nlin.AO↗
arXiv2002

Neutrality: A Necessity for Self-Adaptation

Self-adaptation is used in all main paradigms of evolutionary computation to increase efficiency. We claim that the basis of self-adaptation is the use of neutrality. In the absence of external control neutrality allows a variation of the search distribution without the risk of fitness loss.

nlin.AO↗
arXiv2002

Spatial Patterns in Chemically and Biologically Reacting Flows

We present here a number of processes, inspired by concepts in Nonlinear Dynamics such as chaotic advection and excitability, that can be useful to understand generic behaviors in chemical or biological systems in fluid flows. Emphasis is put on the description of observed plankton patchiness in the sea. The linearly decaying tracer, and excitable kinetics in a chaotic flow are mainly the models described. Finally, some warnings are given about the difficulties in modeling discrete individuals (such as planktonic organisms) in terms of continuous concentration fields.

nlin.CD↗
arXiv2002

Mating Instabilities Lead to Sympatric Speciation

One of the most challenging issues of evolutionary biology concerns speciation, the emergence of new species from an initial one. The huge amount of species found in nature demands a simple and robust mechanism. Yet, no consensus has been reached concerning a reasonable disruptive selection mechanism that prevents mixing genes among the emerging species, especially when they live in sympatry. Usually it is assumed that females select males according to their displaying traits, but males perform no selection on female traits. However, recent experimental evidence accumulates towards the existence of male choice. Here we propose a robust mechanism for sympatric speciation, based on the assumption that sexual selection operates in two directions: selection of males by females and of females by males. Complex mating instabilities emerge, creating differential fitness depending on the individuals displaying traits and preferences. When a secondary sexual trait is introduced in a population, due to mutations, the activation of previously neutral genes or due to a different perception of already existent displaying traits, sympatric speciation may result (together with a species recognition system) from a competitive exclusion principle. We suggest that potential candidates to test our theory could be yeasts.

nlin.AO↗
arXiv2002

Exact Solutions and hypothesis on Phase Transition in the Polyelectrolite Model of DNA

The two-dimensional generalization of the Polyelectolite model of DNA is proposed. It is reduced to the boundary problem for nonlinear completely integrable equation $\sh$-Gordon. In the linearisible version the exact solution is constructed and its asymptotic is found. The soliton solutions of nonlinear equation are calculated that allowed tells about the possibility of the structural phase transition in the considered system (DNA+polyelectrolite) on the temperature.

nlin.SI↗
arXiv2002

Dynamic Relationship between Diversity and Plasticity of Cell types in Multi-cellular State

Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species space' to model intra-cellular chemical reaction dynamics. Then, by considering the cell division and death of such cells, developmental process from a single cell is studied. Cell differentiation process is found to occur through instability in transient dynamics and cell-cell interaction. In a long time behavior, extinction of multiple cells is repeated, which leads to itinerancy over successive quasi-stable multi-cellular states consisting of different types of cells. By defining the plasticity of a cellular state, it is shown that the plasticity of cells decreases before the large extinction, from which diversity and plasticity are recovered. After this switching, decrease of plasticity again occurs, leading to the next extinction of multiple cells. This cycle is repeated. Relevance of our results to the development, evolution is briefly discussed.

nlin.AO↗
arXiv2002

The Phase Information Associated to Synchronized Electronic Fireflies

An electronic implementation referring to fireflies ensembles flashing in synchrony in a self-organization mode, shows the details of the phase-locking mechanism and how the phases between the electronic oscillators are related to their common period. Quantitative measurements of the timing signals link the limits of a steadily established synchronization to the physics of the electronic circuit. Preliminary observations suggest the existence of bifurcation-like phenomena.

nlin.AO↗
arXiv2002

Adaptive learning and coloniality in birds

We introduce here three complementary models to analyze the role of predation pressure in avian coloniality. Different explanations have been proposed for the existence of colonial breeding behavior in birds, but field studies offer no conclusive results. We first propose a learning model in which the decision of birds are taken according to the collective performance. The properties of the system are then studied according to a model in which birds choose according to their individual experience, and the agreement of the introduction of spatial structure with field data are then shown.

nlin.AO↗