Robust Multi-Cellular Developmental Design

This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as well as the differentiation value of the cell in the phenotype, are controlled by a Neural Network (the genotype) that takes as inputs the chemicals produced by the neighboring cells at the previous time step. In the proposed model, the number of iterations of the growth process is not pre-determined, but emerges during evolution: only organisms for which the growth process stabilizes give a phenotype (the stable state), others are declared nonviable. The optimization of the controller is done using the NEAT algorithm, that optimizes both the topology and the weights of the Neural Networks. Though each cell only receives local information from its neighbors, the experimental results of the proposed approach on the 'flags' problems (the phenotype must match a given 2D pattern) are almost as good as those of a direct regression approach using the same model with global information. Moreover, the resulting multi-cellular organisms exhibit almost perfect self-healing characteristics

Unsupervised Learning of Echo State Networks: A case study in Artificial Embryogeny.

International audienceEcho State Networks (ESN) have demonstrated their efficiency in supervised learning of time series: a "reservoir" of neurons provide a set of dynamical systems that can be linearly combined to match the target dynamics, using a simple quadratic optimisation algorithm to tune the few free parameters. In an unsupervised learning context, however, another optimiser is needed. In this paper, an adaptive (1+1)-Evolution Strategy as well as the state-of-the-art CMA-ES are used to optimise an ESN to tackle the "flag" problem, a classical benchmark from multi-cellular artificial embryogeny: the genotype is the cell controller of a Continuous Cellular Automata, and the phenotype, the image that corresponds to the fixed point of the resulting dynamical system, must match a given 2D pattern. This approach is able to provide excellent results with few evaluations, and favourably compares to that using the NEAT algorithm (a state-of-the-art neuro-evolution method) to evolve the cell controllers. Some characteristics of the fitness landscape of the ESN-based method are also investigated

Evolutionary Design of Buildable Objects with BlindBuilder : an Empirical Study

In a previous paper, we presented BlindBuilder, a new representation formalism for Evolutionary Design based on construction plans. As for other indirect encoding approaches in the literature, \emph{BlindBuilder} makes it possible to easily represent possible solutions but makes it difficult to perform structural optimization. While satisfying results are provided, it becomes more and more difficult to build larger structures during the course of evolution. This is due to the high disruptive rate of variation operators as construction plans grow. In this paper, we provide an analysis of such a problem and propose new construction operators to avoid this. Then, we perform extensive experiments so as to identify the key parameters and discuss the advantages, limitations and possible perspectives of the indirect enconding approach

L'Islande et sa musique représentées dans le documentaire : entre lieu, scène et insularité

Ce mémoire de maîtrise s’intéresse à la scène musicale islandaise à travers le documentaire. La notion de scène désigne généralement un contexte spatial au sein duquel différents acteurs (musiciens, producteurs, promoteurs, amateurs de musique, etc.) partagent des intérêts à l’égard de la musique. Dans ce mémoire, elle est conceptualisée en combinant d’une part l’approche de Straw (1991) qui met l’accent sur l’aspect interactionnel et réticulaire de la scène et souligne le potentiel d’adaptation au changement de cet espace de sociabilité ; et d’autre part, celle de Bennett et Peterson (2004) qui insistent sur les différences d’échelles auxquelles se déploient les réseaux d’interactions que constituent les scènes locales, trans-locales et virtuelles. L’auteure y intègre aussi une réflexion géographique destinée à problématiser le caractère insulaire de l’Islande en tant qu’élément productif de la scène musicale qui s’y déploie. Pour ce faire, elle a recours aux propositions théoriques de Massey (2005) concernant l’espace comme construit à travers un ensemble hétérogène de trajectoires, des « stories-so-far » dont la co-présence et la simultanéité conférerait au lieu que serait, en l’occurrence, la scène islandaise, sa spécificité. Ce questionnement fait l’objet d’une exploration empirique à travers une série de documentaires s’intéressant, selon des modes différents (Nichols, 2001 ; 2010), à différents visages de la musique locale en Islande. Les représentations visuelles et auditives de l’Islande et de la musique islandaise que produisent ces documentaires constituent le discours qui fait l’objet de l’analyse. Inspirée de la perspective de Hall (1994 ; 1997), le discours est abordé en tant qu’unité significative socio-historiquement ancrée et composée d’énoncés. La démarche méthodologique adoptée consiste à examiner un corpus de documentaires pour en dégager les énoncés et, sur cette base, reconstituer les différentes trajectoires constitutives de la scène musicale islandaise ainsi mise en discours. L’analyse met en évidence cinq trajectoires (Monde ; Affinités ; Filiation ; Stéréotypie et authenticité ; Territorialité) ainsi que les différentes modalités de leur co-occurrence, points de rencontre ou de distanciation, à différentes échelles. Ce sont ces points de (non) rencontre qui constituent le lieu de la scène islandaise.This Masters thesis examines the icelandic music scene as portrayed through documentaries. The notion of scene usually refers to a spatial entity in which different actors (musicians, producers, promoters, fans, etc) share their common interests in music. In this thesis, its conceptualization combines elements drawn from an approach developed by Straw (1991) wich focuses on ideas of interaction and network, and insists on how this space of sociability is formed through adaptation and change ; and from Bennett and Peterson’s (2004) approach which emphasize the difference in scales through which the networks of interactions characteristic of local, trans-local and virtual scenes are deployed. The author also addresses geographical questions as a means to further problematize the insular character of Island construed as one of the elements through which the music scene is produced. She does so by mobilizing Massey’s (2005) theory of space as a coming together of heterogeneous trajectories and "stories-so-far", and argues that it is the copresence and simultaneity of these trajectories that give the icelandic music scene its specificity. This line of investigation is pursued through the empirical exploration of a series of documentaries which address through different modes (Nichols, 2001 ; 2010) various facets of what they construe as local music in Iceland. The visual and aural representations that these documentaries put forth form the discourse that is the object of the analysis. Inspired by Hall (1994 ; 1997) discourse is considered as a meaningful and sociohistorically contingent unit composed of statements. The methodological process that guides the analysis consists in the critical examination of a corpus of documentaries with a view to identifying the statements that they articulate, and, on this basis, to reconstituting the different trajectories that constitute the icelandic music scene discursively produced therein. The analysis brings forth five trajectories (World ; Affinities ; Filiation ; Stereotyping et authenticity ; Territoriality) and discusses their various co-occurrences at different scales. It is these (non-) meeting points which are conceptualized as constituting the place of the icelandic music scene

Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts

Transposable elements (TEs) constitute the majority of plant genomes, but most are epigenetically inactivated by their host. Research over the last decade has elucidated many of the molecular components that are required for TE silencing. In contrast, the evolutionary dynamics between TEs and silencing pathways are less clear. Here, we discuss current information about these dynamics from both mechanistic and evolutionary perspectives. We highlight new evidence that palindromic sequences within TEs may act as signals for host recognition and that cis-regulatory regions of TEs may be sites of ongoing arms races with host defenses. We also discuss patterns of TE aging after they are silenced; while there is not yet a consensus, it appears that TEs are removed more rapidly near genes, such that older TE insertions tend to be farther from genes. We conclude by discussing the energetic costs for maintaining silencing pathways, which appear to be substantive. The maintenance of silencing pathways across many species suggests that epigenetic emergencies are frequent

Evolutionary development of tensegrity structures

Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering

Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified <i>arabidopsis</i> RNA-dependent RNA polymerases RDR2 and RDR6

Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer-independent and primer-dependent RNA polymerase activities with different efficiencies. We further show that RDR2 and RDR6 can initiate dsRNA synthesis either by elongation of 21- to 24- nucleotides RNAs hybridized to complementary RNA template or by elongation of self-primed RNA template. These findings provide new insights into our understanding of the molecular mechanisms of RNA silencing in plants

Toward a Theory of Collective Resource Distribution: A Study of a Dynamic Morphogenesis Controller

Distribution of resources can be a collective decision making process in both natural and artificial systems. The division of a colony into subtasks, the ant trails exploring the environment and connecting the nest to the food sources, and the growth and spread of branches in a tree to optimize the access to light, are different examples of collective distribution processes. In this paper, collective decision on distribution of resource is investigated via an algorithm inspired by plants morphogenesis. The algorithm, called Vascular Morphogenesis Controller (VMC), acts based on the competition of branches in a plant for limited shared resources - water, minerals, etc. The VMC algorithm decides on the changes in the shape of an artificial structure. The structure is a collective entity consisting of several nodes. The nodes act as agents running the algorithm and deciding collectively on the distribution of a shared resource. A change in the distribution of the resource may lead to addition or deletion of nodes and change the morphology of the structure. The system is dynamic and adaptive to variations in the environmental conditions (e.g. light). In this paper, the effects of different parameterizations of the algorithm on the morphology aspects of the collective structure (e.g. asymmetry and dynamicity) are studied analytically and numerically. A set of experiments are presented with the VMC embodied in a physical structure. The structure is made out of modules that hold VMC nodes and can be manually attached or detached following the suggestions of the algorithm. The experiments are performed with various parameters and environmental conditions (e.g. different lighting). The results support the findings of the theoretical study. The paper provides a deeper understanding of the functionalities of VMC and a basis for parameter selection according to desired behaviors. It also indicates similarities in some of the properties of this system and other collective systems suggesting potential benefits of viewing various types of collective systems from the perspective of resource distribution.<br/

Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm

A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental biology as well as for transformative applications in regenerative biomedicine and the engineering of highly fault-tolerant cybernetic systems. Molecular biologists are working to identify the pathways underlying the remarkable regenerative abilities of model species that perfectly regenerate limbs, brains, and other complex body parts. However, a profound disconnect remains between the deluge of high-resolution genetic and protein data on pathways required for regeneration, and the desired spatial, algorithmic models that show how self-monitoring and growth control arise from the synthesis of cellular activities. This barrier to progress in the understanding of morphogenetic controls may be breached by powerful techniques from the computational sciences—using non-traditional modeling approaches to reverse-engineer systems such as planaria: flatworms with a complex bodyplan and nervous system that are able to regenerate any body part after traumatic injury. Currently, the involvement of experts from outside of molecular genetics is hampered by the specialist literature of molecular developmental biology: impactful collaborations across such different fields require that review literature be available that presents the key functional capabilities of important biological model systems while abstracting away from the often irrelevant and confusing details of specific genes and proteins. To facilitate modeling efforts by computer scientists, physicists, engineers, and mathematicians, we present a different kind of review of planarian regeneration. Focusing on the main patterning properties of this system, we review what is known about the signal exchanges that occur during regenerative repair in planaria and the cellular mechanisms that are thought to underlie them. By establishing an engineering-like style for reviews of the molecular developmental biology of biomedically important model systems, significant fresh insights and quantitative computational models will be developed by new collaborations between biology and the information sciences