| 1. |
- Adami, C., et al.
(författare)
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Information content of colored motifs in complex networks
- 2011
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1064-5462 .- 1530-9185. ; 17:4, s. 375-390
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Tidskriftsartikel (refereegranskat)abstract
- We study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements. © 2011 Massachusetts Institute of Technology.
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| 2. |
- Gerlee, Philip, 1980, et al.
(författare)
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The Emergence of Overlapping Scale-free Genetic Architecture in
- 2008
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Ingår i: Artificial Life. - 1064-5462 .- 1530-9185. ; 14:3, s. 265-275
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.
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| 3. |
- Gerlee, Philip, 1980, et al.
(författare)
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The Influence of Cellular Characteristics on the Evolution of Shape Homeostasis
- 2017
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Ingår i: Artificial Life. - 1530-9185 .- 1064-5462. ; 23:3, s. 424-448
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Tidskriftsartikel (refereegranskat)abstract
- The importance of individual cells in a developing multicellular organism is well known, but precisely how the individual cellular characteristics of those cells collectively drive the emergence of robust, homeostatic structures is less well understood. For example, cell communication via a diffusible factor allows for information to travel across large distances within the population, and cell polarization makes it possible to form structures with a particular orientation, but how do these processes interact to produce a more robust and regulated structure? In this study we investigate the ability of cells with different cellular characteristics to grow and maintain homeostatic structures. We do this in the context of an individual-based model where cell behavior is driven by an intracellular network that determines the cell phenotype. More precisely, we investigated evolution with 96 different permutations of our model, where cell motility, cell death, long-range growth factor (LGF), short-range growth factor (SGF), and cell polarization were either present or absent. The results show that LGF has the largest positive influence on the fitness of the evolved solutions. SGF and polarization also contribute, but all other capabilities essentially increase the search space, effectively making it more difficult to achieve a solution. By perturbing the evolved solutions, we found that they are highly robust to both mutations and wounding. In addition, we observed that by evolving solutions in more unstable environments they produce structures that were more robust and adaptive. In conclusion, our results suggest that robust collective behavior is most likely to evolve when cells are endowed with long-range communication, cell polarisation, and selection pressure from an unstable environment.
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| 4. |
- Görnerup, Olof, 1977, et al.
(författare)
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Hierarchical self-organization in the finitary process soup
- 2008
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1530-9185 .- 1064-5462. ; 14:3, s. 245-254
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Tidskriftsartikel (refereegranskat)abstract
- Current analyses of genomes from numerous species show that the diversity of their functional and behavioral characters is not proportional to the number of genes that encode the organism. We investigate the hypothesis that the diversity of organismal character is due to hierarchical organization. We do this with the recently introduced model of the finitary process soup, which allows for a detailed mathematical and quantitative analysis of the population dynamics of structural complexity. Here we show that global complexity in the finitary process soup is due to the emergence of successively higher levels of organization, that the hierarchical structure appears spontaneously, and that the process of structural innovation is facilitated by the discovery and maintenance of relatively noncomplex, but general, individuals in a population.
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| 5. |
- Hintze, Arend
(författare)
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Open-endedness for the sake of open-endedness
- 2019
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Ingår i: Artificial Life. - : MIT Press Journals. - 1064-5462 .- 1530-9185. ; 25:2, s. 198-206
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Tidskriftsartikel (refereegranskat)abstract
- Natural evolution keeps inventing new complex and intricate forms and behaviors. Digital evolution and genetic algorithms fail to create the same kind of complexity, not just because we still lack the computational resources to rival nature, but because (it has been argued) we have not understood in principle how to create open-ended evolving systems. Much effort has been made to define such open-endedness so as to create forms of increasing complexity indefinitely. Here, however, a simple evolving computational system that satisfies all such requirements is presented. Doing so reveals a shortcoming in the definitions for open-ended evolution. The goal to create models that rival biological complexity remains. This work suggests that our current definitions allow for even simple models to pass as open-ended, and that our definitions of complexity and diversity are more important for the quest of open-ended evolution than the fact that something runs indefinitely. © 2019 Massachusetts Institute of Technology.
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| 6. |
- Labar, T., et al.
(författare)
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Evolvability tradeoffs in emergent digital replicators
- 2016
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Ingår i: Artificial Life. - : MIT Press Journals. - 1064-5462 .- 1530-9185. ; 22:4, s. 483-498
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Tidskriftsartikel (refereegranskat)abstract
- The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists - one that proceeded from a single self-replicating organism (or a set of replicating hypercycles) to the vast complexity we see today in Earth's biosphere. We know that emergent life has the potential to evolve great increases in complexity, but it is unknown if evolvability is automatic given any self-replicating organism. At the same time, it is difficult to test such questions in biochemical systems. Laboratory studies with RNA replicators have had some success with exploring the capacities of simple self-replicators, but these experiments are still limited in both capabilities and scope. Here, we use the digital evolution system Avida to explore the interplay between emergent replicators (rare randomly assembled self-replicators) and evolvability. We find that we can classify fixed-length emergent replicators in Avida into two classes based on functional analysis. One class is more evolvable in the sense of optimizing the replicators' replication abilities. However, the other class is more evolvable in the sense of acquiring evolutionary innovations. We tie this tradeoff in evolvability to the structure of the respective classes' replication machinery, and speculate on the relevance of these results to biochemical replicators. © 2016 Massachusetts Institute of Technology.
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| 7. |
- Lehman, Joel, et al.
(författare)
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The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities
- 2020
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1530-9185 .- 1064-5462. ; 26:2, s. 274-306
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Tidskriftsartikel (refereegranskat)abstract
- Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an algorithmic process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes, uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This article is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.
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| 8. |
- Liu, Y., et al.
(författare)
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Side Reactions Do Not Completely Disrupt Linear Self-Replicating Chemical Reaction Systems
- 2020
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1064-5462 .- 1530-9185. ; 26:3, s. 327-337
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Tidskriftsartikel (refereegranskat)abstract
- A crucial question within the fields of origins of life and metabolic networks is whether or not a self-replicating chemical reaction system is able to persist in the presence of side reactions. Due to the strong nonlinear effects involved in such systems, they are often difficult to study analytically. There are however certain conditions that allow for a wide range of these reaction systems to be well described by a set of linear ordinary differential equations. In this article, we elucidate these conditions and present a method to construct and solve such equations. For those linear self-replicating systems, we quantitatively find that the growth rate of the system is simply proportional to the sum of all the rate constants of the reactions that constitute the system (but is nontrivially determined by the relative values). We also give quantitative descriptions of how strongly side reactions need to be coupled with the system in order to completely disrupt the system.
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| 9. |
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| 10. |
- Plasson, Raphael, et al.
(författare)
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Autocatalysis : At the Root of Self-Replication
- 2011
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Ingår i: Artificial Life. - : MIT Press - Journals. - 1064-5462 .- 1530-9185. ; 17:3, s. 219-236
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Tidskriftsartikel (refereegranskat)abstract
- Autocatalysis is a fundamental concept, used in a wide range of domains. From its most general definition, that is, a process in which a chemical compound is able to catalyze its own formation, several different systems can be described. We detail the different categories of autocatalyses, and compare them on the basis of their mechanistic, kinetic, and dynamic properties. It is shown how autocatalytic patterns can be generated by different systems of chemical reactions. The notion of autocatalysis covers a large variety of mechanistic realizations with very similar behaviors; it is proposed that its key signature is its kinetic pattern expressed in a mathematical form. This notion, while describing dynamic behaviors at the most fundamental level, is at the basis for developing higher-level concepts towards life: autocatalytic sets and autopoietic systems.
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