Evolution of Resource Competition between Mutually Dependent Digital Organisms

We study the emergence and dynamics of competing strains of digital organisms in a world with two depletable resources. Consumption of one resource produces the other resource as a by-product, and vice versa. As a consequence, two types of mutually dependent organisms emerge that each prey on the waste product of the other. In the absence of mutations, that is, in a purely ecological setting, the abundances of the two types of organisms display a wide range of different types of oscillations, from regular oscillations with large amplitude to irregular oscillations with amplitudes ranging from small to large. In this regime, time-averaged abundance levels seem to be controlled by the relative fitness of the organisms in the absence of resources. Under mutational pressure, on the other hand, populations evolve that seem to avoid the oscillations of intermediate to large amplitudes. In this case, the relative fitness of the organisms in the presence of resources plays an important role in the time-averaged abundance levels as well

Evolution of robustness in digital organisms

We study the evolution of robustness in digital organisms adapting to a high mutation rate. As genomes adjust to the harsh mutational environment, the mean effect of single Imitations decreases, up until the point where a sizable fraction (up to 30% in many cases) of the Imitations are neutral. We correlate the changes in robustness along the line of descent to changes in directional epistasis, and find that increased robustness is achieved by moving from antagonistic epistasis between mutations towards codes where mutations are, on average, independent. We interpret this recoding as a breakup of linkage between vital sections of the genome, up to the point where instructions are maximally independent of each other. While such a recoding often requires sacrificing some replication speed, it is the best strategy for withstanding high rates of mutation

Can Developmental AIS Provides Immunity to a Multi-cellular Robotics System?

The major challenge to multi-cellular robotics system is how to ensure the system is homeostatically stable. This position paper pro- poses a developmental artificial immune system (dev-AIS) framework that tries to provide and maintain homeostasis to the multi-cellular robotics system. If immunity is defined as the ability to maintain home- ostasis; the dev-AIS framework will be designed based on the under- standing and the abstraction of how different organisms attain for this property through evolution and developmental process. Early form of In- nate Immunity evolve from the predator-and-anti prey relationship of the single-celled organism. Progress in evolution drove the evolution of im- munity from this simple relationship to the development of the immune system in multi-cellular organisms

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database

Evolution of plant reproduction: from fusion and dispersal to interaction and communication

Based on the existing data concerning the evolution of the sexual reproduction, it is argued that the processes of sex differentiation and interactions play a key role in evolution. From the beginning environment and organism are unified. In a changing dynamic environment life originates and the interaction between life and environment develops from simple to more complex organisms. Sexual reproduction is introduced after the origin of meiosis and is a key process in evolution. The asexual reproduction process prepares to dispersal. Sexual reproduction process adds the genome renewal and the gamete-gamete interaction. Reproduction and dispersal are connected and the process of reproduction has similarities between asexual and sexual reproduction. Unicellular algae develop the physiological and morphological sex differentiation. Sex differentiation is connected with the way of dispersal. The step to multicellular plants introduces cell isolation after meiosis and by the stay on the mother plant within a cell or organ, plant-cell apoplastic interaction originates and by prolonged stay the plant-plant interaction. This stay influences the type of dispersal. A life cycle with alternation of generations and two moments of dispersal permits plants to go on land. In ferns a shift in the moment of sex differentiation to meiospore happens and the stay of the macrospore leads to the seed plants. In water all types of sexual reproduction, interactions and the alternation of generations are prepared and these are used to conquest land. On land the biotic dispersal is realized. The phylogeny of sexual reproduction reveals that the sex differentiation and interaction are the main causes in the evolution of sexual reproduction. Sexual reproduction shows interactions during gamete fusion, between organism and environment and in multicellular plants between organisms. With respect to other types of interaction as in symbiosis or the nutrient chain, interaction is considered as an important action which is based on a persisting cooperation and points to a push during evolution. The push is expressed as communication: the driving force in the evolution. Based on the interactions between organisms and interactions between organisms and the dynamic environment, communication is considered as a driving force leading to the evolution as explained in the development of plant reproduction. Consequences for reproduction, its regulation and the process of evolution are discusse

Evolution of genetic organization in digital organisms

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of complex, parallel secondary expression patterns. Using principles from information theory, we demonstrate an evolutionary pressure towards overlapping expressions causing variation (and hence further evolution) to sharply drop. Finally, we compare the overlapping sections of dominant genomes to those portions which are singly expressed and observe a significant difference in the entropy of their encoding.Comment: 18 pages with 5 embedded figures. Proc. of DIMACS workshop on "Evolution as Computation", Jan. 11-12, Princeton, NJ. L. Landweber and E. Winfree, eds. (Springer, 1999

The free energy requirements of biological organisms; implications for evolution

Recent advances in nonequilibrium statistical physics have provided unprecedented insight into the thermodynamics of dynamic processes. The author recently used these advances to extend Landauer's semi-formal reasoning concerning the thermodynamics of bit erasure, to derive the minimal free energy required to implement an arbitrary computation. Here, I extend this analysis, deriving the minimal free energy required by an organism to run a given (stochastic) map $\pi$ from its sensor inputs to its actuator outputs. I use this result to calculate the input-output map $\pi$ of an organism that optimally trades off the free energy needed to run $\pi$ with the phenotypic fitness that results from implementing $\pi$. I end with a general discussion of the limits imposed on the rate of the terrestrial biosphere's information processing by the flux of sunlight on the Earth.Comment: 19 pages, 0 figures, presented at 2015 NIMBIoS workshop on "Information and entropy in biological systems

Selected topics on reaction-diffusion-advection models from spatial ecology

We discuss the effects of movement and spatial heterogeneity on population dynamics via reaction-diffusion-advection models, focusing on the persistence, competition, and evolution of organisms in spatially heterogeneous environments. Topics include Lokta-Volterra competition models, river models, evolution of biased movement, phytoplankton growth, and spatial spread of epidemic disease. Open problems and conjectures are presented

Evolutionary cell biology: Functional insight from “Endless forms most beautiful”

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking