Evolution of Memory in Reactive Artificial Neural Networks

In the neuronal circuits of natural and artificial agents, memory is usually implemented with recurrent connections, since recurrence allows past agent state to affect the present, on-going behavior. Here, an interesting question arises in the context of evolution: how reactive agents could have evolved into cognitive ones with internalized memory? This study strives to find an answer to the question by simulating neuroevolution on artificial neural networks, with the hypothesis that internalization of external material interaction can be a plausible evolutionary path leading to a fully internalized memory system. A series of computational experiments were performed to gradually verify the above hypothesis. The first experiment demonstrated the possibility that external materials can be used as memory-aids for a memoryless reactive artificial agents in a simple 1-dimensional environment. Here, the reactive artificial agents used environmental markers as memory references to be successful in the ball-catching task that requires memory. Motivated by the result of the first experiment, an extended experiment was conducted to tackle a more complex memory problem using the same principle of external material interaction. This time, the reactive artificial agents are tasked to remember the locations of food items and the nest in a 2-dimensional environment. Such path-following behavior is a trivial foraging strategy of various lower animals such as ants and fish. The final experiment was designed to show the evolution of internal recurrence. In this experiment, I showed the evolutionary advantage of external material interaction by comparing the results from neural network topology evolution algorithms with and without the material interaction mechanism. The result confirmed that the agents with external material interaction learned to solve the memory task faster and more accurately. The results of the experiments provide insights on the possible evolutionary route to an internalized memory. The use of external material interaction can help reactive artificial agents to go beyond the functionality restricted by their simple network structure. Moreover, it allows much faster convergence with higher accuracy than the topological evolution of the artificial agents. These results suggest one plausible evolutionary path from reactive, through external material interaction, to recurrent structure

DNA Methylation Mechanism

‘Simplicity is the ultimate sophistication’- Leonardo Da Vinci The methylation that occurs simply by attaching one or more methyl molecules to a DNA molecule continues to confuse the scientific world by creating highly complex molecular arrangements. Research on methylation mechanisms have discovered that this simple biochemical event (which adapts to the changing micro/macro environment of the organism, to diseases and even cancerous processes) has shown that it is actually not as simple as it seems. In the last 50 years, our efforts to understand these mechanisms and use them to benefit human beings have continued. With this book called “DNA methylation mechanism”, in which we try to explain the effects on every stage of life, we hope that we have been able to create a resource book for everyone interested in this field, from students who are interested, to amateurs and professionals

The role of genotype in Saccharomyces cerevisiae resistance to 4-methylcyclohexanemethanol

The chemical 4-methylcyclohexanemethanol (MCHM) spilled in the Elk River near Charleston, WV in January 2014, impacting the drinking water of 300,000 residents. Initial studies on MCHM following the spill attempted to characterize its toxicological effects in animals, but largely ignored characterization of its effects on cellular pathways and metabolism. In this study, I used this chemical as a novel stressor for the model eukaryote S. cerevisiae to explore the relationship of genotype and stress phenotypes. Initial exploration characterized the stress phenotype of MCHM in yeast through growth assays, cell cycle analysis, and transcriptomic data. MCHM exposure caused cells to arrest growth in G1, activating a well characterized yeast process called the environmental stress response. Further exploration was carried out using a genetic screen of approximately 5000 haploid gene knockout strains, which combined with the transcriptomic data, revealed that the causes of the stress response in yeast were nutrient deprivation related to amino acid biosynthesis and reactive oxygen species production. A QTL analysis of standing variation between two parental strains with variable resistance uncovered the role of zinc homeostasis and its interaction with the hydrotrope chemical properties of MCHM in protein aggregation as a contributor to resistant phenotypes. Finally, an In-Lab evolution study to produce resistant strains for variant analysis showed mutations in the pleiotropic drug response transcription factor PDR3 cause a reproducible induction of MCHM resistance. These studies combined to characterize cellular changes from MCHM, identify genes required for tolerance, and explore both standing and evolved variation in genotypes that contribute to and produce an MCHM resistant phenotype

Metabolic and molecular adaptation of wine yeasts at low temperature fermentation: strategies for their genetic improvement

La fermentación a baja temperatura incrementa el perfil aromático del vino. Sin embargo presenta algunos inconvenientes: descenso de la tasa de crecimiento, fermentaciones lentas o con paradas. Se comparó el metaboloma de una levadura vínica creciendo a 12 ºC y 28 ºC. Las principales diferencias se observaron en el metabolismo lipídico y en la homeostasis redox. Se comparó el metaboloma de levaduras criotolerantes, Saccharomyces bayanus var. uvarum and Saccharomyces kudriavzevii, con el de S. cerevisiae creciendo a 12 ºC Las principales diferencias se encontraron en el metabolismo de la fructosa. Se analizó la capacidad fermentativa y de crecimiento de cepas mutantes y sobre-expresantes del metabolismo lipídico. El incremento de la dosis génica de los genes PSD1, LCB3 y OLE1mejoraron el crecimiento y la capacidad fermentativa. Se desarrollaron cepas mejor adaptadas al frío mediante evolución dirigida, se analizaron los cambios moleculares, observándose una inducción de 4 genes de la familia DAN/TIR.Low temperature alcoholic fermentations are becoming more frequent as they enhance wine’s aromatic profile but present some disadvantages: reduced growth rate, long lag phase, sluggish or stuck fermentations. We compared the metabolome of wine yeast growing at 12 ºC and 28 ºC in a synthetic must. The main differences were observed in lipid metabolism and redox homeostasis. We also compared the metabolome of the cryotolerant yeasts, Saccharomyces bayanus var. uvarum and Saccharomyces kudriavzevii, growing at 12 ºC to the metabolome of S. cerevisiae. The main differences were found for fructose metabolism. We also analyzed the growth and fermentation capacity of lipid mutants and overexpressing strains. The increase in gene-dosage of PSD1, LCB3 and OLE1 genes improved both growth and fermentation activity. Finally, we developed cold adapted wine yeast strains by evolutionary engineering, and deciphered the underlying changes, resulting in new strain with up-regulation of 4 genes belonging to DAN/TIR family

Fifth Annual Workshop on Space Operations Applications and Research (SOAR 1991), volume 2

Papers given at the Space Operations and Applications Symposium, host by the NASA Johnson Space Center on July 9-11, 1991 are given. The technical areas covered included intelligent systems, automation and robotics, human factors and life sciences, and environmental interactions

Reproductive adaptations to reduce locomotor costs in viviparous fish (Poeciliidae)

Viviparity, a live-bearing mode of reproduction, has evolved over 100 times independently in vertebrate animals. Despite its frequent evolution, viviparity has a number of hypothesised disadvantages compared to the ancestral mode of reproduction, oviparity (egg-laying). One of these disadvantages is a reduction in locomotor performance during pregnancy, the period of internal development of the embryos. Adaptations to a live-bearing reproductive mode could have evolved to reduce these locomotor costs. In this thesis, I aim to find whether matrotrophy, post-fertilization nutrient provisioning (e.g. through a placental structure), and superfetation, the presence of multiple broods of different developmental stages, reduce the locomotor performance decline during pregnancy in the Poeciliidae, live-bearing fishes. In Chapter 2, we review the literature on the effects of pregnancy on morphology, performance and fitness. The biomechanics of each mode of locomotion (walking, swimming or flying) are distinct, and are affected differently by the added mass and volume of pregnancy. Furthermore, we list the possible adaptations that have evolved to reduce the locomotor costs of pregnancy, and divide them into three different categories: adaptations that reduce the locomotor costs of live-bearing, adaptations with which the locomotor costs of live-bearing are avoided, and adaptations to the life history of the animal. Lastly, we discuss hiatuses in the literature and experimental procedures to quantify the hypothesised benefit of adaptations. In Chapter 3, we compare the morphological changes during pregnancy in two closely-related species of live-bearing fish: Poeciliopsis turneri and Poeciliopsis gracilis. These species mainly differ in their mode of nutrient provisioning: P. gracilis is lecithotrophic and P. turneri is an extensive matrotroph. We tracked the morphological changes in 3D using a non-invasive method that creates three-dimensional body models. We find that P. turneri is more slender during the early stages of pregnancy, but increase in size more rapidly. This is in line with the locomotor costs hypothesis, which predicts that matrotrophic fish are more slender during the early stages of pregnancy, but that the difference between the body shapes of lecithotrophic and matrotrophic fish diminishes as pregnancy progresses. Our results indicate that matrotrophy could indeed provide a morphological advantage during pregnancy. Fast-start performance, a manoeuvre fish deploy to escape predatory strikes, is important for individual survival. In Chapter 4, we use state-of-the-art biomechanical methods to, for the first time, quantify this manoeuvre in three-dimensional space in adult fish (Heterandria formosa). We show that fish can orient their escapes in up- and downwards direction, and that this is correlated with a change in pitch angle of the body. Changes in roll angle of the body were not correlated with orientation of the fish. We furthermore demonstrate that stage 1 of the fast start, often described as a preparatory stage, can already contribute to propulsion. The results from Chapter 4 indicate that three-dimensional measurements of fast-start manoeuvres provide novel insights that were often overlooked. Measuring fast starts in three-dimensional space is relevant in determining the adverse effects of pregnancy on locomotor performance. We did this by comparing three species of live-bearing fish: P. turneri, H. formosa and Phalloptychus januarius. In Chapter 5, we show that pregnancy-induced changes in abdominal width are correlated with a reduction in performance in the horizontal plane (maximal horizontal speed, change in yaw angle), but less so in the vertical plane (maximal vertical speed, change in pitch angle). Furthermore, we demonstrate that an increase in abdominal width is correlated with a decrease in abdominal curvature and, for some species, in a decrease in maximal curvature rate in the abdomen. Lastly, we show that the pregnancy-induced morphological changes depend on the level of superfetation: species with a high level of superfetation experience higher frequency, but smaller amplitude changes in the shape of the abdomen. Whether superfetation actually results in a more slender body shape, as predicted by the locomotor costs hypothesis, depends on the level of reproductive investment. In this thesis, I show that pregnancy induces changes in morphology which comes with a cost in fast-start performance. Both matrotrophy and superfetation affect how body shape changes due to pregnancy, but whether the latter provides beneficial changes depends on the level of reproductive investment. Furthermore, I reveal that fast starts can have a substantial three-dimensional component which is relevant both to biomechanicists that aim to understand the physical and physiological mechanisms underlying this manoeuvre and to evolutionary biologists that strive to answer performance-related questions.</p