Electronic Supplement for "Evolution of Sustained Foraging in Three-Dimensional Environments with Physics"

Electronic Supplement to the manuscript "Evolution of Sustained Foraging in Three-Dimensional Environments with Physics" in the journal "Genetic Programming and Evolvable Machines". The supplement describes the EVO platform and the genetic language that is used in EVO

Research proposal: Integrating computational science with biology to study collective animal behavior

<p>This is a three-page research proposal that we wrote for funding requests. In this document, we propose an integration of our digital swarm evolution platform with a biological system to study the evolution of simulated prey behavior in response to predation. Particularly, we are looking to establish whether the predator confusion effect exists, and whether it can select for swarming behavior in groups of evolving prey that initially move randomly.</p

Evolution of prey behavior from "outside attack" treatment

<p>Evolution of prey behavior from the "outside attack" treatment in our paper, "Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd" published in the proceedings of GECCO 2013. Each time the simulation resets, 25 generations of evolution have passed and the system is displaying the prey behaviors at the current generation.</p> <p> </p

Evolution of prey behavior from predator-prey coevolution treatment

<p>Evolution of prey behavior from the predator-prey coevolution treatment in our paper, "Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd" published in the proceedings of GECCO 2013. Each time the simulation resets, 50 generations of evolution have passed and the system is displaying the prey behaviors at the current generation.</p

Research proposal: Evolve and Conquer: Using immersive video games to teach Evolution in Action

<p>The Adami Lab studies evolution in many different computational environments, including the popular game development platform Unity3D, which supports our research in 3D virtual physics environ- ments. A group of students in our lab (R. Olson, J. Schossau, and D. Phillips) started a game project with the preliminary title Evolve and Conquer (E&C), a real time strategy game which incorporates the core principles of evolution: inheritance, variation, and natural selection. E&C immerses the player in a world governed by these evolutionary principles, allowing the player to experience evolution in action first-hand as a core aspect of the game mechanics. The player must understand the core principles of evolution in order to prevail and either overcome or learn to coexist with an evolving computer opponent.</p

Research proposal: Evolution of the Dorsal-Ventral gene regulatory network in Drosophila species

<p>Gene regulation in animals is arguably at least as important as the genes that are being regulated. Animal body plans, their structures and in particular the functions that the animal morphology provides, are the consequence over time and space of successive regulatory and developmental processes. Gene regulation in animals is a highly complex process, and can be likened to a computation that the regulatory machinery performs. Often, single genes are regulated by a complex network of genes with activators, repressors, attenuators and the like, and the elucidation of these networks has taken molecular and develop- mental biologists decades. But while we know a tremendous amount about how genes and their associated proteins evolve, much less is known about how regulatory systems evolve. We know the basic building blocks: multiple transcription factor binding sites that regulate the expression of other transcription factors that ultimately lead to the expression of the regulated gene. Each transcription factor has a specific affinity to its binding site, and binding sites can interact either synergistically or antagonistically. If we compare the regulatory regions for the same gene across species in the same family, we can see sometimes significant differences in the regulatory sequence. Are these differences adaptive? How do regulatory networks change in response to changes, either in the environment or in response to a change in body size? In the proposed work, we will analyze the gene regulatory network or “cis-regulatory module” (CRM) that regulates the patterning of a fly embryo in the dorsal-ventral axis. This is a well-studied system for which expression and sequence data is available from the Arnosti lab, and aligned homologous CRMs have been collected. Yet, we do not know in detail how evolution affects such systems. What are the “operators” that evolution uses to change these networks? A computational analysis of the regulatory region of 12 Drosophila species will help us move towards a better understanding of how regulatory systems evolve.</p

Evolution of prey behavior under "random attack" treatment

<p>Evolution of prey behavior from the "random attack" treatment in our paper, "Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd" published in the proceedings of GECCO 2013. Each time the simulation resets, 25 generations of evolution have passed and the system is displaying the prey behaviors at the current generation.</p

Slides for the GECCO 2013 Best Paper Presentation, "Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd"

<p>These are the slides I used for the best paper presentation at GECCO 2013. The talk and associated paper is called, "Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd."</p> <p> </p> <p>The preprint for the paper is available here: http://adamilab.msu.edu/wp-content/uploads/Olson-Critical-Interplay-Between-Density-dependent-Predation-and-Evolution-of-the-Selfish-Herd-2013.pdf</p> <p>and the proceedings are available here: http://www.sigevo.org/gecco-2013/proceedings.html</p

All 914 sequences of self-replicators of length 8 in Avida

An ASCII file of the sequences of self-replicating programs of length eight in the Avida environment, from "Origin of life in a digital microcosm", by Nitash C G, T. LaBar, A. Hintze, and C. Adam

Slides for Behaviour 2013 talk, "Using digital models of evolution to study how animal behavior evolves: a case study with the predator confusion effect"

<p>These are the slides for the talk at the Behaviour 2013 conference entitled, "Using digital models of evolution to study how animal behavior evolves: a case study with the predator confusion effect," presented by Randy Olson.</p> <p>The talk covers much of the work covered in the publication, "Predator confusion is sufficient to evolve swarming behaviour," published in the Proceedings of The Royal Society Interface at http://rsif.royalsocietypublishing.org/content/10/85/20130305.abstract</p> <p>A free preprint of the article is available on the Adami lab web page: http://adamilab.msu.edu/wp-content/uploads/Olson-Predator-confusion-is-sufficient-to-evolve-swarming-behavior-2013.pdf</p