54 research outputs found

    The Emergence of Canalization and Evolvability in an Open-Ended, Interactive Evolutionary System

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    Natural evolution has produced a tremendous diversity of functional organisms. Many believe an essential component of this process was the evolution of evolvability, whereby evolution speeds up its ability to innovate by generating a more adaptive pool of offspring. One hypothesized mechanism for evolvability is developmental canalization, wherein certain dimensions of variation become more likely to be traversed and others are prevented from being explored (e.g. offspring tend to have similarly sized legs, and mutations affect the length of both legs, not each leg individually). While ubiquitous in nature, canalization almost never evolves in computational simulations of evolution. Not only does that deprive us of in silico models in which to study the evolution of evolvability, but it also raises the question of which conditions give rise to this form of evolvability. Answering this question would shed light on why such evolvability emerged naturally and could accelerate engineering efforts to harness evolution to solve important engineering challenges. In this paper we reveal a unique system in which canalization did emerge in computational evolution. We document that genomes entrench certain dimensions of variation that were frequently explored during their evolutionary history. The genetic representation of these organisms also evolved to be highly modular and hierarchical, and we show that these organizational properties correlate with increased fitness. Interestingly, the type of computational evolutionary experiment that produced this evolvability was very different from traditional digital evolution in that there was no objective, suggesting that open-ended, divergent evolutionary processes may be necessary for the evolution of evolvability.Comment: SI can be found at: http://www.evolvingai.org/files/SI_0.zi

    Design for an Increasingly Protean Machine

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    Data-driven, rather than hypothesis-driven, approaches to robot design are becoming increasingly widespread, but they remain narrowly focused on tuning the parameters of control software (neural network synaptic weights) inside an overwhelmingly static and presupposed body. Meanwhile, an efflorescence of new actuators and metamaterials continue to broaden the ways in which machines are free to move and morph, but they have yet to be adopted by useful robots because the design and control of metamorphosing body plans is extremely non-intuitive. This thesis unites these converging yet previously segregated technologies by automating the design of robots with physically malleable hardware, which we will refer to as protean machines, named after Proteus of Greek mythology. This thesis begins by proposing an ontology of embodied agents, their physical features, and their potential ability to purposefully change each one in space and time. A series of experiments are then documented in which increasingly more of these features (structure, shape, and material properties) were allowed to vary across increasingly more timescales (evolution, development, and physiology), and collectively optimized to facilitate adaptive behavior in a simulated physical environment. The utility of increasingly protean machines is demonstrated by a concomitant increase in both the performance and robustness of the final, optimized system. This holds true even if its ability to change is temporarily removed by fabricating the system in reality, or by “canalization”: the tendency for plasticity to be supplanted by good static traits (an inductive bias) for the current environment. Further, if physical flexibility is retained rather than canalized, it is shown how protean machines can, under certain conditions, achieve a form of hyper-robustness: the ability to self-edit their own anatomy to “undo” large deviations from the environments in which their control policy was originally optimized. Some of the designs that evolved in simulation were manufactured in reality using hundreds of highly deformable silicone building blocks, yielding shapeshifting robots. Others were built entirely out of biological tissues, derived from pluripotent Xenopus laevis stem cells, yielding computer-designed organisms (dubbed “xenobots”). Overall, the results shed unique light on questions about the evolution of development, simulation-to-reality transfer of physical artifacts, and the capacity for bioengineering new organisms with useful functions

    A feedback mechanism controls rDNA copy number evolution in yeast independently of natural selection

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    Ribosomal DNA (rDNA) is the genetic loci that encodes rRNA in eukaryotes. It is typically arranged as tandem repeats that vary in copy number within the same species. We have recently shown that rDNA repeats copy number in the yeast Saccharomyces cerevisiae is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). The UAF strongly binds the rDNA gene promoter, but is also able to repress SIR2 deacetylase gene transcription that, in turn, represses rDNA amplification. In this way, the cells with a smaller DNA copy number than what is optimal evolve to increase that copy number until they reach a number that sequestrates free UAF and provokes SIR2 derepression that, in turn, blocks rDNA amplification. Here we propose a mathematical model to show that this evolutionary process can amplify rDNA repeats independently of the selective advantage of yeast cells having bigger or smaller rDNA copy numbers. We test several variants of this process and show that it can explain the observed experimental results independently of natural selection. These results predict that an autoregulated feedback circuit may, in some instances, drive to non Darwinian deterministic evolution for a limited time period

    Probabilidades Variacionales y Propensiones del Desarrollo: Un Estudio Filosófico del Azar en la Variación Evolutiva

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    Tesis inédita de la Universidad Complutense de Madrid, Facultad de Filosofía, leída el 09/11/2020The ongoing debate over a possible extension of the explanatory corpus of evolutionary biology touches many aspects of philosophical interest, among which is the role that chance plays in its models and explanations. In particular, how evolutionary variation relates to chance seems to differ under the classical and the evo-devo perspectives. While some tools of the philosophy of probability and chance have been incorporated into important aspects of evolutionary biology, this discrepancy has not been considered from this perspective. In this dissertation, Iintend to bridge part of this gap by endorsing a conception of chance in the generation of evolutionary variation that is the result of incorporating several conceptual tools from the philosophy of probability and chance into different views over the nature of evolutionary variation. My aim is to clarify the distinct roles that chance in variation plays in the field of evo-devo as compared with classical evolutionary genetics. I depart from the construction of a suitable philosophical framework about the representative role of probabilities in evolutionary disciplines and the type of explanatory causes that are responsible for them...El actual debate sobre una posible extensión del corpus explicativo de la biología evolutiva recoge muchos aspectos de interés filosófico, entre los que se encuentra el rol del azar en sus modelos y explicaciones. En particular, la relación entre la variación evolutiva y el azar parece ser muy distinto bajo las perspectivas clásica y dela evo-devo. Mientras que algunas herramientas de la filosofía de la probabilidad y el azar han sido incorporadas en aspectos importantes de la biología evolutiva, esta disparidad no ha sido considerada desde esta perspectiva. En esta tesis, mi intención es aliviar parcialmente esta carencia defendiendo una noción de azar en la generación de la variación evolutiva que es el resultado de incorporar varias herramientas conceptuales de la filosofía de la probabilidad a distintas perspectivas sobre su naturaleza. Mi objetivo es clarificar los distintos roles que el azar en la variación juega en el campo de la evo-devo en comparación con la genética evolutiva clásica. Comienzo con la construcción de un marco filosófico que considera el rol representativo de la probabilidad en las disciplinas evolutivas y el tipo de causas explicativas que son responsables de ella...Fac. de FilosofíaTRUEunpu

    Evolution of reproductive isolation in sympatric Arctic charr morphs (Salvelinus alpinus)

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    The theory of divergence by trophic polymorphism, an important part of diversification in vertebrates, has recently been extended to encompass the interplay of developmental, ecological and evolutionary processes (Eco-Evo-Devo dynamics). However, this extended theory doesn’t thoroughly explain the evolution of reproductive isolation, which is unfortunate considering the recent advances from the field of speciation. In this thesis, I argue that the Arctic charr morphs of Thingvallavatn are an ideal system to study how reproductive isolation is embedded within the theory of divergence by resource polymorphism, which I present through five papers. First, I focused on two sympatric morphs, the small-benthic (SB) and the planktivorous (PL) charr. Common-garden experiments showed limited evidence for hybridization to affect the structure of trait covariance in both morphs, regarding morphology, developmental timing and feeding behaviour (Paper I), and personality traits (Paper II). However, information on gene expression variability in embryos indicated that hybridization might influence evolvability (Paper III). Multiple reproductive barriers between the two morphs, involving habitat use, assortative mating and hybrid development were also assessed (Paper IV). Finally, Paper V combines field studies and rearing experiments to explore the interplay between habitat choice and offspring development in the large-benthic (LB) charr, which spawns earlier in the season than the other morphs. The results suggested that LB-charr favour temperature conditions that may delay offspring development. Altogether, these findings provide an overview on reproductive isolation among the Arctic charr morphs of Thingvallavatn and constitute a primer to study speciation in an Eco-Evo-Devo context
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