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  1. Abstract

    Genetic programming and artificial life systems commonly use tag matching to decide interactions between system components. However, the implications of criteria used to determine affinity between tags with respect evolutionary dynamics have not been directly studied. We investigate differences between tag-matching criteria with respect to geometric constraint and variation generated under mutation. In experiments, we find that tag-matching criteria can influence the rate of adaptive evolution and the quality of evolved solutions. Better understanding of the geometric, variational, and evolutionary properties of tag-matching criteria will facilitate more effective incorporation of tag matching into genetic programming and artificial life systems. By showing that tag-matching criteria influence connectivity patterns and evolutionary dynamics, our findings also raise fundamental questions about the properties of tag-matching systems in nature.

  2. Humans have long known how to co-opt evolutionary processes for their own benefit. Carefully choosing which individuals to breed so that beneficial traits would take hold, they have domesticated dogs, wheat, cows and many other species to fulfil their needs. Biologists have recently refined these ‘artificial selection’ approaches to focus on microorganisms. The hope is to obtain microbes equipped with desirable features, such as the ability to degrade plastic or to produce valuable molecules. However, existing ways of using artificial selection on microbes are limited and sometimes not effective. Computer scientists have also harnessed evolutionary principles for their own purposes, developing highly effective artificial selection protocols that are used to find solutions to challenging computational problems. Yet because of limited communication between the two fields, sophisticated selection protocols honed over decades in evolutionary computing have yet to be evaluated for use in biological populations. In their work, Lalejini et al. compared popular artificial selection protocols developed for either evolutionary computing or work with microorganisms. Two computing selection methods showed promise for improving directed evolution in the laboratory. Crucially, these selection protocols differed from conventionally used methods by selecting for both diversity and performance, rather than performance alone. These promising approachesmore »are now being tested in the laboratory, with potentially far-reaching benefits for medical, biotech, and agricultural applications. While evolutionary computing owes its origins to our understanding of biological processes, it has much to offer in return to help us harness those same mechanisms. The results by Lalejini et al. help to bridge the gap between computational and biological communities who could both benefit from increased collaboration.« less
    Free, publicly-accessible full text available August 2, 2023
  3. Short Abstract for evolutionary computing community on selection schemes working for directed evolution experiments in microbes.
    Free, publicly-accessible full text available July 9, 2023
  4. Symbiosis, the living together of unlike organisms as symbionts, is ubiquitous in the natural world. Symbioses occur within and across all scales of life, from microbial to macro-faunal systems. Further, the interactions between symbionts are multimodal in both strength and type, can span from parasitic to mutualistic within one partnership, and persist over generations. Studying the ecological and evolutionary dynamics of symbiosis in natural or laboratory systems poses a wide range of challenges, including the long time scales at which symbioses evolve de novo , the limited capacity to experimentally control symbiotic interactions, the weak resolution at which we can quantify interactions, and the idiosyncrasies of current model systems. These issues are especially challenging when seeking to understand the ecological effects and evolutionary pressures on and of a symbiosis, such as how a symbiosis may shift between parasitic and mutualistic modes and how that shift impacts the dynamics of the partner population. In digital evolution, populations of computational organisms compete, mutate, and evolve in a virtual environment. Digital evolution features perfect data tracking and allows for experimental manipulations that are impractical or impossible in natural systems. Furthermore, modern computational power allows experimenters to observe thousands of generations of evolution inmore »minutes (as opposed to several months or years), which greatly expands the range of possible studies. As such, digital evolution is poised to become a keystone technique in our methodological repertoire for studying the ecological and evolutionary dynamics of symbioses. Here, we review how digital evolution has been used to study symbiosis, and we propose a series of open questions that digital evolution is well-positioned to answer.« less
  5. We introduce and experimentally demonstrate the utility of tag-based genetic regulation, a new genetic programming (GP) technique that allows programs to dynamically adjust which code modules to express.Tags are evolvable labels that provide a flexible mechanism for referencing code modules. Tag-based genetic regulation extends existing tag-based naming schemes to allow programs to “promote” and “repress” code modules in order to alter expression patterns. This extension allows evolution to structure a program as a gene regulatory network where modules are regulated based on instruction executions. We demonstrate the functionality of tag-based regulation on a range of program synthesis problems. We find that tag-based regulation improves problem-solving performance on context-dependent problems; that is, problems where programs must adjust how they respond to current inputs based on prior inputs. Indeed, the system could not evolve solutions to some context-dependent problems until regulation was added. Our implementation of tag-based genetic regulation is not universally beneficial, however. We identify scenarios where the correct response to a particular input never changes, rendering tag-based regulation an unneeded functionality that can sometimes impede adaptive evolution. Tag-based genetic regulation broadens our repertoire of techniques for evolving more dynamic genetic programs and can easily be incorporated into existing tag-enabled GPmore »systems.« less
  6. Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypicmore »plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.« less
  7. We present SignalGP, a new genetic programming (GP) technique designed to incorporate the event-driven programming paradigm into computational evolution's toolbox. Event-driven programming is a software design philosophy that simplifies the development of reactive programs by automatically triggering program modules (event-handlers) in response to external events, such as signals from the environment or messages from other programs. SignalGP incorporates these concepts by extending existing tag-based referencing techniques into an event-driven context. Both events and functions are labeled with evolvable tags; when an event occurs, the function with the closest matching tag is triggered. In this work, we apply SignalGP in the context of linear GP. We demonstrate the value of the event-driven paradigm using two distinct test problems (an environment coordination problem and a distributed leader election problem) by comparing SignalGP to variants that are otherwise identical, but must actively use sensors to process events or messages. In each of these problems, rapid interaction with the environment or other agents is critical for maximizing fitness. We also discuss ways in which SignalGP can be generalized beyond our linear GP implementation.
  8. Lexicase selection has been proven highly successful for finding effective solutions to problems in genetic programming, especially for test-based problems where there are many distinct test cases that must all be passed. However, lexicase (as with most selection schemes) requires all prospective solutions to be evaluated against most test cases each generation, which can be computationally expensive. Here, we propose reducing the number of per-generation evaluations required by applying random subsampling: using a subset of test cases each generation (down-sampling) or by assigning test cases to subgroups of the population (cohort assignment). Tests are randomly reassigned each generation, and candidate solutions are only ever evaluated on test cases that they are assigned to, radically reducing the total number of evaluations needed while ensuring that each lineage eventually encounters all test cases. We tested these lexicase variants on five different program synthesis problems, across a range of down-sampling levels and cohort sizes. We demonstrate that these simple techniques to reduce the number of per-generation evaluations in lexicase can substantially improve overall performance for equivalent computational effort.
  9. Fine-scale evolutionary dynamics can be challenging to tease out when focused on broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic metrics that operate on lineages and phylogenies in digital evolution experiments with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: depth of the most-recent common ancestor, phylogenetic richness, phylogenetic divergence, and phylogenetic regularity. We demonstrate the use of each metric on a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, confirming our intuitions about what they can tell us about evolutionary dynamics.
  10. As the field of Artificial Life advances and grows, we find ourselves in the midst of an increasingly complex ecosystem of software systems. Each system is developed to address particular research objectives, all unified under the common goal of understanding life. Such an ambitious endeavor begets a variety of algorithmic challenges. Many projects have solved some of these problems for individual systems, but these solutions are rarely portable and often must be re-engineered across systems. Here, we propose a community-driven process of developing standards for representing commonly used types of data across our field. These standards will improve software re-use across research groups and allow for easier comparisons of results generated with different artificial life systems. We began the process of developing data standards with two discussion-driven workshops (one at the 2018 Conference for Artificial Life and the other at the 2018 Congress for the BEACON Center for the Study of Evolution in Action). At each of these workshops, we discussed the vision for Artificial Life data standards, proposed and refined a standard for phylogeny (ancestry tree) data, and solicited feedback from attendees. In addition to proposing a general vision and framework for Artificial Life data standards, we release andmore »discuss version 1.0.0 of the standards. This release includes the phylogeny data standard developed at these workshops and several software resources under development to support our proposed phylogeny standards framework.« less