Pablo Funes

Signal analysis of behavioral and molecular cycles.

BackgroundCircadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities.ResultsWe demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase.ConclusionUsing data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.

Evolutionary Body Building: Adaptive Physical Designs for Robots

Creating artificial life forms through evolutionary robotics faces a chicken and egg problem: Learning to control a complex body is dominated by problems specific to its sensors and effectors, while building a body that is controllable assumes the pre-existence of a brain. The idea of coevolution of bodies and brains is becoming popular, but little work has been done in evolution of physical structure because of the lack of a general framework for doing it. Evolution of creatures in simulation has usually resulted in virtual entities that are not buildable, while embodied evolution in actual robotics is constrained by the slow pace of real time. The work we present takes a step in addressing the problem of body evolution by applying evolutionary techniques to the design of structures assembled out of elementary components that stick together. Evolution takes place in a simulator that computes forces and stresses and predicts stability of three-dimensional brick structures. The final printout of our program is a schematic assembly, which is then built physically. We demonstrate the functionality of this approach to robot body building with many evolved artifacts.

Advanced analysis of a cryptochrome mutation's effects on the robustness and phase of molecular cycles in isolated peripheral tissues of Drosophila

BackgroundPreviously, we reported effects of the cryb mutation on circadian rhythms in period and timeless gene expression within isolated peripheral Drosophila tissues. We relied on luciferase activity driven by the respective regulatory genomic elements to provide real-time reporting of cycling gene expression. Subsequently, we developed a tool kit for the analysis of behavioral and molecular cycles. Here, we use these tools to analyze our earlier results as well as additional data obtained using the same experimental designs.ResultsIsolated antennal pairs, heads, bodies, wings and forelegs were evaluated under light-dark cycles. In these conditions, the cryb mutation significantly decreases the number of rhythmic specimens in each case except the wing. Moreover, among those specimens with detectable rhythmicity, mutant rhythms are significantly weaker than cry+ controls. In addition, cryb alters the phase of period gene expression in these tissues. Furthermore, peak phase of luciferase-reported period and timeless expression within cry+ samples is indistinguishable in some tissues, yet significantly different in others. We also analyze rhythms produced by antennal pairs in constant conditions.ConclusionsThese analyses further show that circadian clock mechanisms in Drosophila may vary in a tissue-specific manner, including how the cry gene regulates circadian gene expression.

Three generations of automatically designed robots

The difficulties associated with designing, building, and controlling robots have led their development to a stasis: Applications are limited mostly to repetitive tasks with predefined behavior. Over the last few years we have been trying to address this challenge through an alternative approach: Rather than trying to control an existing machine or create a general-purpose robot, we propose that both the morphology and the controller should evolve at the same time. This process can lead to the automatic design of special-purpose mechanisms and controllers for specific short-term objectives. Here we provide a brief review of three generations of our recent research, which underlies the robots shown on the cover of this issue: Automatically designed static structures, automatically designed and manufactured dynamic electromechanical systems, and modular robots automatically designed through a generative DNA-like encoding.

Evolutionary Techniques in Physical Robotics

Evolutionary and coevolutionary techniques have become a popular area of research for those interested in automated design. One of the cutting edge issues in this field is the ability to apply these techniques to real physical systems with all the complexities and affordances that such systems present. Here we present a selection of our work each of which advances the richness of the evolutionary substrate in one or more dimensions. We overview research in four areas: a) High part-count static structures that are buildable, b) The use of commercial CAD/CAM systems as a simulated substrate, c) Dynamic electromechanical systems with complex morphology that can be built automatically, and d) Evolutionary techniques distributed in a physical population of robots.

Computer Creativity in the Automatic Design of Robots

This article demonstrates the possibility that robotic systems can automatically design robots with complex morphologies and tightly adapted control systems at a low cost. These automatic designs are inspired by nature and achieved through an artificial coevolutionary process to adapt the bodies and brains of artificial life-forms simultaneously through interaction with a simulated reality. Through the use of rapid manufacturing, these evolved designs can be transferred from virtual to true reality. The artificial evolution process embedded in realistic physical simulation can create simple designs often recognizable from the history of biology or engineering. This paper provides a brief review of three generations of these robots, from automatically designed LEGO structures, through the GOLEM project of electromechanical systems based on truss structures, to new modular designs that make use of a generative, DNA-like representation.

Co-evolution, Determinism and Robustness

Robustness has long been recognised as a critical issue for coevolutionary learning. It has been achieved in a number of cases, though usually in domains which involve some form of non-determinism. We examine a deterministic domain - a pseudo real-time two-player game called Tron - and evolve a neural network player using a simple hill-climbing algorithm. The results call into question the importance of determinism as a requirement for successful co-evolutionary learning, and provide a good opportunity to examine the relative importance of other factors.

The Spirit of Bolivia: Complex Behavior Through Minimal Control

The “Spirit of Bolivia” is a robotic soccer team which demonstrates minimally comprehensive team behavior. By this we mean that each member of the team makes progress towards team goals, and obstructs progress of the opponent, by interacting constructively with team-mates and in a sportsmanlike manner with opposing players. This complex behavior is achieved with simple on-board processors running very small behavior-based control programs; team behaviors are achieved without explicit communication. Externalization — the use of the environment as its own best model — and tolerance — a bias towards reducing the need for accurate information rather than attempting to recognize or correct noisy information — are the keys to robustness and sophistication of team behavior.

First Three Generations of Evolved Robots

The field of robotics today faces an economic predicament: most problems in the physical world are too difficult for the current state of the art. The difficulties associated with designing, building and controlling robots have led to a stasis, and robots in industry are only applied to simple and highly repetitive manufacturing tasks. Over the last few years we have been trying to address this challenge through an alternative approach: Rather than a seeking an intelligent general-purpose robot, we are seeking the process that can automatically design and fabricate special purpose mechanisms and controllers to achieve specific short-term objectives. This short paper provides a brief review of three generations of our research results. Automatically designed high part-count static structures that are buildable, automatically designed and manufactured dynamic electromechanical systems, and modular robots automatically designed through generative encoding. We expect that with continued improvement in simulation, manufacturing, and transfer, we will achieve the ability to automatically design and fabricate custom machinery for short-term deployment on specific tasks.