Evolution of heterogeneous cellular automata in fluctuating environments

The importance of environmental fluctuations in the evolution of living organisms by natural selection has been widely noted by biologists and linked to many important characteristics of life such as modularity, plasticity, genotype size, mutation rate, learning, or epigenetic adaptations. In artificial-life simulations, however, environmental fluctuations are usually seen as a nuisance rather than an essential characteristic of evolution. HetCA is a heterogeneous cellular automata characterized by its ability to generate open-ended long-term evolution and ``evolutionary progress''. In this paper, we propose to measure the impact of different types of environmental fluctuations in HetCA. Our results indicate that environmental changes induce mechanisms analogous to epigenetic adaptation or multilevel selection. This is particularly prevalent in two of the tested fluctuation schemes, which involve a round-robin inhibition of certain cell types, where phenotypic selection seems to occur

Towards Growing Robots: A Piecewise Morphology-Controller Co-adaptation Strategy for Legged Locomotion

Control of robots has largely been based on the assumption of a fixed morphology. Accordingly, robot designs have been stationary in time, except for the case of modular robots. Any drastic change in morphology, hence, requires a remodelling of the controller. This work takes inspiration from developmental robotics to present a piecewise morphology-controller growth/adaptation strategy that facilitates fast and reliable control adaptation to growing robots. We demonstrate our methodology on a simple 3 degree of freedom walking robot with adjustable foot lengths and with varying inertial conditions. Our results show not only the effectiveness and reliability of the piecewise morphology controller co-adaptation (PMCCA) strategy, but also highlight the need for morphological adaptation as a robot design strategy

An integrated modelling framework from cells to organism based on a cohort of digital embryos

We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage. Our resulting artificial prototype was embedded in 3D space by biomechanical agent-based modelling and simulation, which allowed a systematic exploration and optimisation of free parameters to fit the experimental data and test biological hypotheses. The spherical monolayered blastula and the spatial arrangement of its different cell types appeared tightly constrained by cell stiffness, cell-adhesion parameters and blastocoel turgor pressure

Emergent diversity in an open-ended evolving virtual community

Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires speciesʼ characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.This research was partially supported by a grant for the GENEX project (P09-TIC-5123) from the Consejería de Innovación y Ciencia de Andalucía. J.D.F. was supported by a FPU grant from the Spanish Ministerio de Educación. R.D. wishes to thank the Région Ile-de-France for supporting his research position at the Complex Systems Institute, Paris Ile-de-France

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages

Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences

A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations) is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species

From evolutionary computation to the evolution of things

Evolution has provided a source of inspiration for algorithm designers since the birth of computers. The resulting field, evolutionary computation, has been successful in solving engineering tasks ranging in outlook from the molecular to the astronomical. Today, the field is entering a new phase as evolutionary algorithms that take place in hardware are developed, opening up new avenues towards autonomous machines that can adapt to their environment. We discuss how evolutionary computation compares with natural evolution and what its benefits are relative to other computing approaches, and we introduce the emerging area of artificial evolution in physical systems

A reafferent and feed-forward model of song syntax generation in the Bengalese finch

Adult Bengalese finches generate a variable song that obeys a distinct and individual syntax. The syntax is gradually lost over a period of days after deafening and is recovered when hearing is restored. We present a spiking neuronal network model of the song syntax generation and its loss, based on the assumption that the syntax is stored in reafferent connections from the auditory to the motor control area. Propagating synfire activity in the HVC codes for individual syllables of the song and priming signals from the auditory network reduce the competition between syllables to allow only those transitions that are permitted by the syntax. Both imprinting of song syntax within HVC and the interaction of the reafferent signal with an efference copy of the motor command are sufficient to explain the gradual loss of syntax in the absence of auditory feedback. The model also reproduces for the first time experimental findings on the influence of altered auditory feedback on the song syntax generation, and predicts song- and species-specific low frequency components in the LFP. This study illustrates how sequential compositionality following a defined syntax can be realized in networks of spiking neurons