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Theory in Biosciences, Theorie in Den Biowissenschaften

Francesco Catania, Ulrich Krohs, Marco Chittò, Diana Ferro, Kevin Ferro, Gildas Lepennetier, Hans-Dieter Görtz, Rebecca S Schreiber, Joachim Kurtz, Jürgen Gadau
Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called 'typical' organisms no longer organisms in their own right? Is the study of the holobiont-host plus its symbiotic microorganisms-no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host's environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont...
December 19, 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
David C Krakauer, Lydia Müller, Sonja J Prohaska, Peter F Stadler
A critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical, and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.
December 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Elham Shamsara, Jamal Shamsara, Zahra Afsharnezhad
In this paper, we consider a four dimensional model of the human immunodeficiency virus-1 (HIV-1) with delay, which is an extension of some three dimensional models. We approach the treatment problem by adding two controllers to the system for inhibiting viral production. The optimal controller [Formula: see text] is considered for vaccine and [Formula: see text] for the drug. The Pontryagin maximum principle with delay is used to characterize these optimal controls. At the end, numerical results are presented to illustrate the optimal solutions...
December 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
N Grosjean, T Huillet, G Rollet
After an introduction to the general topic of models for a given locus of a diploid population whose quadratic dynamics is determined by a fitness landscape, we consider more specifically the models that can be treated using genetic (or train) algebras. In this setup, any quadratic offspring interaction can produce any type of offspring and after the use of specific changes of basis, we study the evolution and possible stability of some examples. We also consider some examples that cannot be treated using the framework of genetic algebras...
December 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Jônata Tyska Carvalho, Stefano Nolfi
In this paper, we show how the development of plastic behaviours, i.e., behaviour displaying a modular organisation characterised by behavioural subunits that are alternated in a context-dependent manner, can enable evolving robots to solve their adaptive task more efficiently also when it does not require the accomplishment of multiple conflicting functions. The comparison of the results obtained in different experimental conditions indicates that the most important prerequisites for the evolution of behavioural plasticity are: the possibility to generate and perceive affordances (i...
December 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Elizabeth Watts, Uwe Hossfeld, Irina Tolstikova, Georgy S Levit
This paper provides a detailed look at how creationism originated in the United States and then explores how this evangelical trend was exported to Russia by American missionaries following the fall of the USSR. The comparison between these two countries is particularly interesting since the rivalry between the US and the USSR during the race to space caused both countries to revamp their science education. Yet, while political interests led both governments to focus on science education, creationist activities were simultaneously focused on diminishing the coverage of evolution in science classrooms...
October 20, 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Karl J Niklas, Ulrich Kutschera
In 1790, the German poet Johann W. v. Goethe (1749-1832) proposed the concept of a hypothetical sessile organism known as the 'Plant Archetype,' which was subsequently reconstructed and depicted by 19th-century botanists, such as Franz Unger (1800-1870) and Julius Sachs (1832-1897), and can be considered one of the first expressions of Evo-Devo thinking. Here, we present the history of this concept in the context of Ernst Haeckel's (1834-1919) biogenetic law espoused in his Generelle Morphologie der Organismen of 1866...
October 18, 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Michal V Simunek, Michael Mielewczik, Georgy S Levit, Uwe Hossfeld
The 'rediscovery' of Mendel's laws in 1900 was a turning point in modern research of heredity/genetics. According to the traditional view, adopted and fostered by many textbooks of genetics, Mendel's principles were presented in the first half of 1900 simultaneously and independently by three biologists (H. de Vries, C. Correns, E. v. Tschermak-Seysenegg). Having thus laid the foundations of further development, the 'rediscovery' continues to attract considerable interest. Since the 1950s, however, serious questions arose concerning both the chronology and specific conceptual achievement of the scientists involved...
October 13, 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Jürgen Jost
No abstract text is available yet for this article.
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Ulrich Kutschera, Karl J Niklas
In his Generelle Morphologie der Organismen (1866), 150 years ago, Ernst Haeckel (1834-1919) combined developmental patterns in animals with the concept of organismic evolution, and 50 years ago, a new era of plant research started when focus shifted from crop species (sunflower, maize etc.) to thale cress (Arabidopsis thaliana) as a model organism. In this contribution, we outline the general principles of developmental evolutionary biology sensu Haeckel and describe the evolutionary genome-to-morphology-plant hormone auxin (IAA, indole-3-acetic acid)-circuit with reference to other phytohormones and a focus on land plants (embryophytes) plus associated epiphytic microbes...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Alessandro Minelli
Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Wolfgang Banzhaf, Bert Baumgaertner, Guillaume Beslon, René Doursat, James A Foster, Barry McMullin, Vinicius Veloso de Melo, Thomas Miconi, Lee Spector, Susan Stepney, Roger White
The open-endedness of a system is often defined as a continual production of novelty. Here we pin down this concept more fully by defining several types of novelty that a system may exhibit, classified as variation, innovation, and emergence. We then provide a meta-model for including levels of structure in a system's model. From there, we define an architecture suitable for building simulations of open-ended novelty-generating systems and discuss how previously proposed systems fit into this framework. We discuss the design principles applicable to those systems and close with some challenges for the community...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Parth Pratim Pandey, Sanjay Jain
Experiments have found that the growth rate and certain other macroscopic properties of bacterial cells in steady-state cultures depend upon the medium in a surprisingly simple manner; these dependencies are referred to as 'growth laws'. Here we construct a dynamical model of interacting intracellular populations to understand some of the growth laws. The model has only three population variables: an amino acid pool, a pool of enzymes that transport an external nutrient and produce the amino acids, and ribosomes that catalyze their own and the enzymes' production from the amino acids...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Luiz R R Faria, Elaine Della Giustina Soares, Eduardo do Carmo, Paulo Murilo Castro de Oliveira
Insects in the order Hymenoptera (bees, wasps and ants) present an haplodiploid system of sexual determination in which fertilized eggs become females and unfertilized eggs males. Under single locus complementary sex-determination (sl-CSD) system, the sex of a specimen depends on the alleles at a single locus: when diploid, an individual will be a female if heterozygous and male if homozygous. Significant diploid male (DM) production may drive a population to an extinction scenario called "diploid male vortex"...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
José F Fontanari, Francisco A Rodrigues
The idea of a collective intelligence behind the complex natural structures built by organisms suggests that the organization of social networks is selected so as to optimize problem-solving competence at the group level. Here we study the influence of the social network topology on the performance of a group of agents whose task is to locate the global maxima of NK fitness landscapes. Agents cooperate by broadcasting messages informing on their fitness and use this information to imitate the fittest agent in their influence networks...
September 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Viner F Khabibullin
Ecologists face an overwhelming diversity of ecological relationships in natural communities. In this paper, I propose to differentiate various types of the interspecific relations on the basis of two factors: relative localization and foraging activity of interacting partners. I advocate recognition of four types of environments: internal, surface, proximate external and distant external. Then I distinguish four types of synoikia-one partner lives in different degree of proximity to another; and four types of synmensalism: one partner forages in different degree of proximity to another...
June 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Lisa Fürtauer, Thomas Nägele
Biochemical regulation in compartmentalized metabolic networks is highly complex and non-intuitive. This is particularly true for cells of higher plants showing one of the most compartmentalized cellular structures across all kingdoms of life. The interpretation and testable hypothesis generation from experimental data on such complex systems is a challenging step in biological research and biotechnological applications. While it is known that subcellular compartments provide defined reaction spaces within a cell allowing for the tight coordination of complex biochemical reaction sequences, its role in the coordination of metabolic signals during metabolic reprogramming due to environmental fluctuations is less clear...
June 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Surama Biswas, Sriyankar Acharyya
Gene regulatory network (GRN) is produced as a result of regulatory interactions between different genes through their coded proteins in cellular context. Having immense importance in disease detection and drug finding, GRN has been modelled through various mathematical and computational schemes and reported in survey articles. Neural and neuro-fuzzy models have been the focus of attraction in bioinformatics. Predominant use of meta-heuristic algorithms in training neural models has proved its excellence. Considering these facts, this paper is organized to survey neural modelling schemes of GRN and the efficacy of meta-heuristic algorithms towards parameter learning (i...
June 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Ping Song, Hongyong Zhao, Xuebing Zhang
In the study, we consider a fractional order delayed predator-prey system with harvesting terms. Our discussion is divided into two cases. Without harvesting, we investigate the stability of the model, as well as deriving some criteria by analyzing the associated characteristic equation. With harvesting, we investigate the dynamics of the system from the aspect of local stability and analyze the influence of harvesting to prey and predator. Finally, numerical simulations are presented to verify our theoretical results...
June 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
Menelaos Apostolou
The model of sexual selection under parental choice has been proposed to account for the control that parents exercise over their children's mating decisions. The present paper attempts to formalize and advance this model with the purpose of providing a better understanding of how parental choice mandates the course of sexual selection. In particular, in the proposed formulation, free mate choice involves an opportunity cost which motivates parents to place their children's mate choices under their control...
June 2016: Theory in Biosciences, Theorie in Den Biowissenschaften
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