Behavior finding: Morphogenetic Designs Shaped by Function

Evolution has shaped an incredible diversity of multicellular living organisms, whose complex forms are self-made through a robust developmental process. This fundamental combination of biological evolution and development has served as an inspiration for novel engineering design methodologies, with the goal to overcome the scalability problems suffered by classical top-down approaches. Top-down methodologies are based on the manual decomposition of the design into modular, independent subunits. In contrast, recent computational morphogenetic techniques have shown that they were able to automatically generate truly complex innovative designs. Algorithms based on evolutionary computation and artificial development have been proposed to automatically design both the structures, within certain constraints, and the controllers that optimize their function. However, the driving force of biological evolution does not resemble an enumeration of design requirements, but much rather relies on the interaction of organisms within the environment. Similarly, controllers do not evolve nor develop separately, but are woven into the organism’s morphology. In this chapter, we discuss evolutionary morphogenetic algorithms inspired by these important aspects of biological evolution. The proposed methodologies could contribute to the automation of processes that design “organic” structures, whose morphologies and controllers are intended to solve a functional problem. The performance of the algorithms is tested on a class of optimization problems that we call behavior-finding. These challenges are not explicitly based on morphology or controller constraints, but only on the solving abilities and efficacy of the design. Our results show that morphogenetic algorithms are well suited to behavior-finding

Automated processing of zebrafish imaging data: a survey

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines

Morphogenesis in robot swarms

Morphogenesis allows millions of cells to self-organize into intricate structures with a wide variety of functional shapes during embryonic development. This process emerges from local interactions of cells under the control of gene circuits that are identical in every cell, robust to intrinsic noise, and adaptable to changing environments. Constructing human technology with these properties presents an important opportunity in swarm robotic applications ranging from construction to exploration. Morphogenesis in nature may use two different approaches: hierarchical, top-down control or spontaneously self-organizing dynamics such as reaction-diffusion Turing patterns. Here, we provide a demonstration of purely self-organizing behaviors to create emergent morphologies in large swarms of real robots. The robots achieve this collective organization without any self-localization and instead rely entirely on local interactions with neighbors. Results show swarms of 300 robots that self-construct organic and adaptable shapes that are robust to damage. This is a step toward the emergence of functional shape formation in robot swarms following principles of self-organized morphogenetic engineering

Design for an Increasingly Protean Machine

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

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 371)

This publication is a cumulative index to the abstracts contained in Supplements 359 through 370 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number, and accession number

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 358)

This publication is a cumulative index to the abstracts contained in Supplements 346 through 357 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number and accession number

Neurofly 2008 abstracts : the 12th European Drosophila neurobiology conference 6-10 September 2008 Wuerzburg, Germany

This volume consists of a collection of conference abstracts

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 319)

This publication is a cumulative index to the abstracts contained in Supplements 307 through 318 of Aerospace Medicine and Biology: A Continuing Bibliography. Seven indexes are included -- subject, personal author, corporate source, foreign technology, contract number, report number and accession number