Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).
Overview In nature, species do not evolve in isolation but in large networks of interacting species. One of the main goals in evolutionary ecology is to disentangle the evolutionary mechanisms that shape and are shaped by patterns of interaction between species. A particularly important question concerns how coevolution, the reciprocal evolutionary change in local populations of interacting species driven by natural selection, is shaped by the architecture of food webs, plant-animal mutualistic networks, and host-parasite communities. The concept of diffuse coevolution, where adaptation is in response to a suite of biotic interactions, was the first step towards a framework unifying relevant theories in community ecology and coevolution. Understanding how individual interactions within networks influence coevolution, and conversely how coevolution influences the overall structure of networks, requires an appreciation for how pair-wise interactions change due to their broader community contexts as well as how this community context shapes selective pressures. Accordingly, research is now focusing on how reciprocal selection influences and is embedded within the structure of multispecies interactive webs, not only on particular species in isolation.
Coevolution in a community context can be addressed theoretically via mathematical modeling and simulation, by looking at ancient footprints of evolutionary history via ecological patterns that persist and are observable today, and by performing laboratory experiments with microorganisms. In spite of the long time scales involved and the substantial effort that is necessary to isolate and quantify samples, the latter approach of testing biological evolution in the lab has been successful over the last two decades. However, studying the evolution of interspecific interactions, which involves dealing with more complex webs of multiple interacting species, has proven to be a much more difficult challenge. A meta-analysis of host-phage interaction networks, carried out by Weitz and his team, found a striking statistical structure to the patterns of infection and resistance across a wide variety of environments and methods from which the hosts and phage were obtained. However, the ecological mechanisms and evolutionary processes responsible have yet to be unraveled.
Digital ecological networks enable the direct, comprehensive, and real time observation of evolving ecological interactions between antagonistic and/or mutualistic digital organisms that are difficult to study in nature. Research using self-replicating computer programs can help us understand how coevolution shapes the emergence and diversification of coevolving species interaction networks and, in turn, how changes in the overall structure of the web (e.g., through extinction of taxa or the introduction of invasive species) affect the evolution of a given species. Studying the evolution of species interaction networks in these artificial evolving systems also contributes to the development of the field, while overcoming limitations evolutionary biologists may face. For example, laboratory studies have shown that historical contingency can enable or impede the outcome of the interactions between bacteria and phage, depending on the order in which mutations occur: the phage often, but not always, evolve the ability to infect a novel host. Therefore, in order to obtain statistical power for predicting such outcomes of the coevolutionary process, experiments require a high level of replication. This stochastic nature of the evolutionary process was exemplified by Stephen Jay Gould's inquiry ("What would happen if the tape of the history of life were rewound and replayed?"Gould SJ (1990) Wonderful life: the Burgess Shale and the nature of history. W. W. Norton.) Because of their ease in scalability and replication, evolving digital ecological networks open the door to experiments that incorporate this approach of replaying the tape of life. Such experiments allow researchers to quantify the role of historical contingency and repeatability in network evolution, enabling predictions about the architecture and dynamics of large networks of interacting species.
The inclusion of ecological interactions in digital systems enables new research avenues: investigations using self-replicating computer programs complement laboratory efforts by broadening the breadth of viable experiments focused on the emergence and diversification of coevolving interactions in complex communities. This cross-disciplinary research program provides fertile grounds for new collaborations between computer scientists and evolutionary biologists.
History
Coreworld
The field of digital life was inspired by the rampant computer viruses of the 1980s. These viruses were self-replicating computer programs that spread from one computer to another, but they did not evolve. Steen Rasmussen was the first to include the possibility of mutation in self-replicating computer programs by extending the once-popular Core War game, where programs competed in a digital battle ground for the computer's resources. Although Rasmussen observed some interesting evolution, mutations in this early genetic programming language produced many unstable organisms, thus prohibiting scientific experiments. Just one year later, Thomas S. Ray developed an alternative system, Tierra, and performed the first successful experiments with evolving populations of self-replicating computer programs.
Tierra
Thomas S. Ray created a genetic language similar to earlier digital systems, but added several key features that made it more suitable for evolution in his artificial life system, Tierra. Primarily, he prevented instructions from writing beyond the privately allocated memory space, thus limiting the potential for organisms writing over others. The only selective pressure in Tierra was for rapid self-replication. Over the course of evolution, this pressure led to shorter and shorter genomes, reducing the time spent copying instructions during replication. Some individuals even started executing the replication code in other organisms, allowing those "cheaters", which were originally referred to as parasites in Ray's work, to further shrink their genetic programs. This form of cheating was the first evolved ecological interaction between organisms in artificial life software. Ray's cheaters pre-dated the formal study of evolving ecological interactions using Tierra-like digital evolution platforms by 20 years.
Avida
In 1993, Christoph Adami, Charles Ofria, and C. Titus Brown created the artificial life platform AvidaAvida download page () at the California Institute of Technology. They added the ability for digital organisms to obtain bonus CPU cycles for performing computational tasks, like adding two numbers together. In Avida, researchers can define the available tasks and set the consequences for organisms upon successful calculation. When organisms are rewarded with additional CPU cycles, their replication rate increases. Since Avida was designed specifically as a scientific tool, it allows users to collect a comprehensive suite of data about evolving populations. Due to its flexibility and data tracking abilities, Avida has become the most widely used digital system for studying evolution. The DevolabDevolab at the BEACON Center currently continues development of Avida.
Implementation
Digital organisms
Digital organisms in Avida are self-replicating computer programs with a genome composed of assembly-like instructions. The genetic programming language in Avida contains instructions for manipulating values in registers and stacks as well as for control flow and mathematical operations. Each digital organism contains virtual hardware on which its genome is executed. To reproduce, digital organisms must copy their genome instruction by instruction into a new region of memory through a potentially noisy channel that may lead to errors (i.e., mutations). While most mutations are detrimental, mutants will occasionally have higher fitness than their parents, thereby providing the basis for natural selection with all of the necessary components for Darwinian evolution. Digital organisms can acquire random binary numbers from the environment and are able to manipulate them using their genetic instructions, including the logic instruction NAND. With only this instruction, digital organisms can compute any other task by stringing together various operations because NAND is a universal logic function. If the output of processing random numbers from the environment corresponds to the result of a particular logic task, then that task is incorporated into the set of tasks the organism performs, which in turn, defines part of its phenotype.
Digital interactions
Interactions between digital organisms occur through phenotypic matching, which, in the case of task-based phenotypes, results from the performance of overlapping logic functions. Different mechanisms for mapping phenotypic matching to interactions can be implemented, depending on the antagonistic or mutualistic nature of the interaction.
Host-parasite interactions
In host-parasite interactions, the parasite organisms benefits at the expense of the host organisms. Parasites in Avida are implemented just like other self-replicating digital organisms, but they live inside hosts and execute parasitic threads using CPU cycles stolen from their hosts.Zaman, L., Devangam, S, Ofria, C. (2011). Rapid host-parasite coevolution drives the production and maintenance of diversity in digital organisms. Proceedings of the 13th Annual Conference on Genetic and Evolutionary Computation (GECCO), 219-226. Because parasites impose a cost (lost CPU cycles) on hosts, there is selection for resistance, and when resistance starts to spread in a population, there is selective pressure for parasites to infect those new resistant hosts. Infection occurs when both the parasite and host perform at least one overlapping task. Thus a host is resistant to a particular parasite if they do not share any tasks. This mechanism of infection mimics the inverse-gene-for-gene model, in which infection only occurs if a host susceptibility gene (the presence of a logic task) is matched by a parasite virulence gene (a parasite performing the same task). Additional infection mechanisms, such as the matching allele and gene-for-gene models, can also be implemented.