Evolving an ecology of mathematical expressions with grammatical evolution

This is the author’s version of a work that was accepted for publication in Biosystems. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biosystems, 111, 2, (2013) DOI: 10.1016/j.biosystems.2012.12.004This paper describes the use of grammatical evolution to obtain an ecology of artificial beings associated with mathematical functions, whose fitness is also defined mathematically. The system allows “parasite” species and “parasites of parasites” to develop, and supports the simultaneous evolution of several ecological niches. The use of standard measurements makes it possible to explore the influence of the number of niches or the presence of parasites on “biological” diversity and similar functions. Our results suggest that some of the features of biological evolution depend more on the genetic substrate and natural selection than on the actual phenotypic expression of that substrate

Evolving a predator–prey ecosystem of mathematical expressions with grammatical evolution

This article describes the use of grammatical evolution to obtain a predator–prey ecosystem of artificial beings associated with mathematical functions, whose fitness is also defined mathematically. The system supports the simultaneous evolution of several ecological niches and through the use of standard measurements, makes it possible to explore the influence of the number of niches and the values of several parameters on ‘‘biological’’ diversity and similar functions. Sensitivity analysis tests have been made to find the effect of assigning different constant values to the genetic parameters that rule the evolution of the system and the predator–prey interaction or of replacing them by functions of time. One of the parameters (predator efficiency) was found to have a critical range, outside which the ecologies are unstable; two others (genetic shortening rate and predator–prey fitness comparison logistic amplitude) are critical just at one side of the range), the others are not critical. The system seems quite robust, even when one or more parameters are made variable during a single experiment, without leaving their critical ranges. Our results also suggest that some of the features of biological evolution depend more on the genetic substrate and natural selection than on the actual phenotypic expression of that substrate. VC 2014 Wiley Periodicals, Inc. Complexity 20: 66–83, 201

Evolving a predator-prey ecosystem of mathematical expressions with grammatical evolution

This is the accepted version of the following article: Alfonseca, M. and Soler Gil, F. J. (2015), Evolving a predator–prey ecosystem of mathematical expressions with grammatical evolution. Complexity, 20: 66–83, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/cplx.21507/abstractThis article describes the use of grammatical evolution to obtain a predator–prey ecosystem of artificial beings associated with mathematical functions, whose fitness is also defined mathematically. The system supports the simultaneous evolution of several ecological niches and through the use of standard measurements, makes it possible to explore the influence of the number of niches and the values of several parameters on “biological” diversity and similar functions. Sensitivity analysis tests have been made to find the effect of assigning different constant values to the genetic parameters that rule the evolution of the system and the predator–prey interaction or of replacing them by functions of time. One of the parameters (predator efficiency) was found to have a critical range, outside which the ecologies are unstable; two others (genetic shortening rate and predator–prey fitness comparison logistic amplitude) are critical just at one side of the range), the others are not critical. The system seems quite robust, even when one or more parameters are made variable during a single experiment, without leaving their critical ranges. Our results also suggest that some of the features of biological evolution depend more on the genetic substrate and natural selection than on the actual phenotypic expression of that substrat

On environment difficulty and discriminating power

The final publication is available at Springer via http://dx.doi.org/10.1007/s10458-014-9257-1This paper presents a way to estimate the difficulty and discriminating power of any task instance. We focus on a very general setting for tasks: interactive (possibly multiagent) environments where an agent acts upon observations and rewards. Instead of analysing the complexity of the environment, the state space or the actions that are performed by the agent, we analyse the performance of a population of agent policies against the task, leading to a distribution that is examined in terms of policy complexity. This distribution is then sliced by the algorithmic complexity of the policy and analysed through several diagrams and indicators. The notion of environment response curve is also introduced, by inverting the performance results into an ability scale. We apply all these concepts, diagrams and indicators to two illustrative problems: a class of agent-populated elementary cellular automata, showing how the difficulty and discriminating power may vary for several environments, and a multiagent system, where agents can become predators or preys, and may need to coordinate. Finally, we discuss how these tools can be applied to characterise (interactive) tasks and (multi-agent) environments. These characterisations can then be used to get more insight about agent performance and to facilitate the development of adaptive tests for the evaluation of agent abilities.I thank the reviewers for their comments, especially those aiming at a clearer connection with the field of multi-agent systems and the suggestion of better approximations for the calculation of the response curves. The implementation of the elementary cellular automata used in the environments is based on the library 'CellularAutomaton' by John Hughes for R [58]. I am grateful to Fernando Soler-Toscano for letting me know about their work [65] on the complexity of 2D objects generated by elementary cellular automata. I would also like to thank David L. Dowe for his comments on a previous version of this paper. This work was supported by the MEC/MINECO projects CONSOLIDER-INGENIO CSD2007-00022 and TIN 2010-21062-C02-02, GVA project PROMETEO/2008/051, the COST - European Cooperation in the field of Scientific and Technical Research IC0801 AT, and the REFRAME project, granted by the European Coordinated Research on Long-term Challenges in Information and Communication Sciences & Technologies ERA-Net (CHIST-ERA), and funded by the Ministerio de Economia y Competitividad in Spain (PCIN-2013-037).José Hernández-Orallo (2015). On environment difficulty and discriminating power. Autonomous Agents and Multi-Agent Systems. 29(3):402-454. https://doi.org/10.1007/s10458-014-9257-1S402454293Anderson, J., Baltes, J., & Cheng, C. T. (2011). 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Using algorithmic information theory and stochastic modeling to improve classification and evolutionary computation: a dissertation submitted to the department of computer science of the Universidad Autonoma de Madrid in partial fulfillment of the requirements for the degree of doctor of philosophy

Tesis doctoral inédita. Universidad Autónoma de Madrid, Escuela Politécnica Superior, junio de 200

Development of a Yeast-Based Opioid Biosensor by Adaptation of Pheromone Response Pathway

Opioids are simultaneously an essential medicine and a leading cause of death. Metabolic engineering and novel opioids offer solutions to insecure supply chains and harmful side effects but are limited by cost and time required for high throughput screening. We have developed a yeast-based opioid biosensor to accelerate opioid research. Utilizing Homo sapiens µ-opioid receptor as a detector, our biosensor provides a simulacrum of in vivo opioid response while maintaining ease of implementation of a yeast chassis. Functional µ-opioid receptor expression required the introduction of cholesterol biosynthesis as well as pH adjustment. We also identified codon usage as a parameter affecting Homo sapiens melatonin receptor1a function and the properties of the µ-opioid receptor binding. Under optimized conditions our opioid biosensor displayed 157-fold increase in fluorescence after opioid exposure and had µM affinity for opioid peptides and mM affinity for morphine. This opioid biosensor can aid high throughput screening and provides clues for future functional expression of other difficult G-protein coupled receptors

Digital Alchemy: Matter and Metamorphosis in Contemporary Digital Animation and Interface Design

The recent proliferation of special effects in Hollywood film has ushered in an era of digital transformation. Among scholars, digital technology is hailed as a revolutionary moment in the history of communication and representation. Nevertheless, media scholars and cultural historians have difficulty finding a language adequate to theorizing digital artifacts because they are not just texts to be deciphered. Rather, digital media artifacts also invite critiques about the status of reality because they resurrect ancient problems of embodiment and transcendence.In contrast to scholarly approaches to digital technology, computer engineers, interface designers, and special effects producers have invented a robust set of terms and phrases to describe the practice of digital animation. In order to address this disconnect between producers of new media and scholars of new media, I argue that the process of digital animation borrows extensively from a set of preexisting terms describing materiality that were prominent for centuries prior to the scientific revolution. Specifically, digital animators and interface designers make use of the ancient science, art, and technological craft of alchemy. Both alchemy and digital animation share several fundamental elements: both boast the power of being able to transform one material, substance, or thing into a different material, substance, or thing. Both seek to transcend the body and materiality but in the process, find that this elusive goal (realism and gold) is forever receding onto the horizon.The introduction begins with a literature review of the field of digital media studies. It identifies a gap in the field concerning disparate arguments about new media technology. On the one hand, scholars argue that new technologies like cyberspace and digital technology enable radical new forms of engagement with media on individual, social, and economic levels. At the same time that media scholars assert that our current epoch is marked by a historical rupture, many other researchers claim that new media are increasingly characterized by ancient metaphysical problems like embodiment and transcendence. In subsequent chapters I investigate this disparity

Male and Female Reproductive Tactics in Mallards (Anas platyrhynchos L.)

This study examines male and female influence on reproductive success in mallards (Anas platyrhynchos). Chapter One investigates three notable features of the breeding system in wild mallard populations (Lake Starnberg and Lake Ammer, Southern Germany) based on microsatellite analysis of 41 clutches. First, adult populations are male biased, although mallards form social monogamous pairs and unpaired males may suffer reduced reproductive success. We show that this male surplus is already prevalent at egg laying (60% males). Second, egg dumping is a common female strategy in waterfowl and increases reproductive output of parasitic females. We report on high levels of brood parasitism in a mallard population with high nesting density (53%) whereas no egg dumping was observed under low nesting density. Finally, forced extra-pair copulations are commonly pursued by drakes. We assess the level of extra-pair paternity (56% of broods containing extra-pair young), which so far is the highest reported in waterfowl. However extra-pair fertilization was lower than expected from rates of extra-pair copulations described in literature. Chapter Two experimentally examines the relevance of postcopulatory female control of male fertilization success in comparison to sperm competition. By artificially inseminating groups of four sisters with a sperm mixture containing equal sperm numbers of one brother and one unrelated male we did not observe any effect of parental relatedness on gain of paternity. However male reproductive success was significantly influenced by long-term sperm performance (sperm motility, sperm swimming speed). Chapter Three investigates whether the female environment differentially influences sperm activity (concentration of motile sperm, sperm swimming speed). To test sperm activity in different female environment we measured sperm swimming in buffer and added female blood plasma. Again no effect of genetic relatedness was observed, but female reproductive status significantly influenced the amount of motile sperm and sperm SUMMARY 96 swimming speed. Furthermore we observed a strong individual female effect on sperm activity. Chapter Four discusses the relationship between frequent copulations and ejaculate quality (sperm concentration, sperm swimming speed). After males were prevented to copulate with their social partner, sperm concentration and sperm velocity increased significantly. Therefore number of copulations trade against competitiveness of single ejaculates. Chapter Five describes the positive relationship of testis size and circulating levels of testosterone in mallard drakes during the reproductive season