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Kalhor R, Beslon G, Lafond M, Scornavacca C. A Rigorous Framework to Classify the Postduplication Fate of Paralogous Genes. J Comput Biol 2024. [PMID: 39088355 DOI: 10.1089/cmb.2023.0331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024] Open
Abstract
Gene duplication has a central role in evolution; still, little is known on the fates of the duplicated copies, their relative frequency, and on how environmental conditions affect them. Moreover, the lack of rigorous definitions concerning the fate of duplicated genes hinders the development of a global vision of this process. In this paper, we present a new framework aiming at characterizing and formally differentiating the fate of duplicated genes. Our framework has been tested via simulations, where the evolution of populations has been simulated using aevol, an in silico experimental evolution platform. Our results show several patterns that confirm some of the conclusions from previous studies, while also exhibiting new tendencies; this may open up new avenues to better understand the role of duplications as a driver of evolution.
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Affiliation(s)
- Reza Kalhor
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Manuel Lafond
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Canada
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France
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2
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Hartl B, Risi S, Levin M. Evolutionary Implications of Self-Assembling Cybernetic Materials with Collective Problem-Solving Intelligence at Multiple Scales. ENTROPY (BASEL, SWITZERLAND) 2024; 26:532. [PMID: 39056895 PMCID: PMC11275831 DOI: 10.3390/e26070532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024]
Abstract
In recent years, the scientific community has increasingly recognized the complex multi-scale competency architecture (MCA) of biology, comprising nested layers of active homeostatic agents, each forming the self-orchestrated substrate for the layer above, and, in turn, relying on the structural and functional plasticity of the layer(s) below. The question of how natural selection could give rise to this MCA has been the focus of intense research. Here, we instead investigate the effects of such decision-making competencies of MCA agential components on the process of evolution itself, using in silico neuroevolution experiments of simulated, minimal developmental biology. We specifically model the process of morphogenesis with neural cellular automata (NCAs) and utilize an evolutionary algorithm to optimize the corresponding model parameters with the objective of collectively self-assembling a two-dimensional spatial target pattern (reliable morphogenesis). Furthermore, we systematically vary the accuracy with which the uni-cellular agents of an NCA can regulate their cell states (simulating stochastic processes and noise during development). This allows us to continuously scale the agents' competency levels from a direct encoding scheme (no competency) to an MCA (with perfect reliability in cell decision executions). We demonstrate that an evolutionary process proceeds much more rapidly when evolving the functional parameters of an MCA compared to evolving the target pattern directly. Moreover, the evolved MCAs generalize well toward system parameter changes and even modified objective functions of the evolutionary process. Thus, the adaptive problem-solving competencies of the agential parts in our NCA-based in silico morphogenesis model strongly affect the evolutionary process, suggesting significant functional implications of the near-ubiquitous competency seen in living matter.
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Affiliation(s)
- Benedikt Hartl
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Institute for Theoretical Physics, Center for Computational Materials Science (CMS), TU Wien, 1040 Wien, Austria
| | - Sebastian Risi
- Digital Design, IT University of Copenhagen, 2300 Copenhagen, Denmark;
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Colón-Santos S, Vázquez-Salazar A, Adams A, Campillo-Balderas JA, Hernández-Morales R, Jácome R, Muñoz-Velasco I, Rodriguez LE, Schaible MJ, Schaible GA, Szeinbaum N, Thweatt JL, Trubl G. Chapter 2: What Is Life? ASTROBIOLOGY 2024; 24:S40-S56. [PMID: 38498820 DOI: 10.1089/ast.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.
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Affiliation(s)
- Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A Schaible
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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Fortuna MA, Beslon G, Ofria C. Editorial: Digital evolution: Insights for biologists. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1037040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Smiley P, Levin M. Competition for finite resources as coordination mechanism for morphogenesis: An evolutionary algorithm study of digital embryogeny. Biosystems 2022; 221:104762. [PMID: 36064151 DOI: 10.1016/j.biosystems.2022.104762] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/17/2022] [Indexed: 01/02/2023]
Abstract
The standard view of embryogenesis is one of cooperation driven by the cells' shared genetics and evolutionary interests. However, numerous examples from developmental biology and agriculture reveal a surprising amount of competition among body cells, tissues, and organs for both metabolic and informational resources. To explain the existence of such competition we had hypothesized that evolution uses limiting "reservoirs" of resource molecules as a communication medium - a global scratchpad, to enable tissues across the body to coordinate growth. Here, we test this hypothesis via an evolutionary simulation of embryogeny in silico. Genomes encode state transition rules for cells, such as proliferation, differentiation, and resource use, enabling virtual embryos to develop a specific large-scale morphology. An evolutionary algorithm operates over the genomes, with fitness defined as a function of specific morphological requirements for the final embryo shape. We found that not only does such an algorithm rapidly discover rules for cellular behavior that reliably make embryos with specific anatomical properties, but that it discovers the strategy of using finite resources to coordinate development. Given the option of using finite or infinite reservoirs (which determine cells' ability to carry out specific actions), evolution preferentially uses finite reservoirs, which results in higher fitness and increased consistency (without needing direct selection for morphological invariance). We report aspects of anatomical, physiological/transcriptional, and genomic analysis of evolved virtual embryos that help understand how evolution can use competition among genetically identical subunits within a multicellular body to coordinate reliable, complex morphogenesis. Our results suggest that under some conditions, composite multi-scale systems will promote conflict and artificial scarcity for their components.
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Affiliation(s)
- Peter Smiley
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University and Department of Biology, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
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Information Fragmentation, Encryption and Information Flow in Complex Biological Networks. ENTROPY 2022; 24:e24050735. [PMID: 35626617 PMCID: PMC9141881 DOI: 10.3390/e24050735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023]
Abstract
Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network’s structure as opposed to its function. Here, we introduce a new information-theoretic tool—information fragmentation analysis—that, given full phenotypic data, allows us to localize information in complex networks, determine how fragmented (across multiple nodes of the network) the information is, and assess the level of encryption of that information. Using information fragmentation matrices we can also create information flow graphs that illustrate how information propagates through these networks. We illustrate the use of this tool by analyzing how artificial brains that evolved in silico solve particular tasks, and show how information fragmentation analysis provides deeper insights into how these brains process information and “think”. The measures of information fragmentation and encryption that result from our methods also quantify complexity of information processing in these networks and how this processing complexity differs between primary exposure to sensory data (early in the lifetime) and later routine processing.
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Vostinar AE, Skocelas KG, Lalejini A, Zaman L. Symbiosis in Digital Evolution: Past, Present, and Future. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.739047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
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 in 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.
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Hiebert LS, Vieira LM, Tiozzo S, Simpson C, Grosberg RK, Migotto AE, Morandini AC, Brown FD. From the individual to the colony: Marine invertebrates as models to understand levels of biological organization. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:191-197. [PMID: 33819384 DOI: 10.1002/jez.b.23044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/18/2021] [Indexed: 11/11/2022]
Abstract
The developmental and evolutionary principles of coloniality in marine animals remain largely unexplored. Although many common traits have evolved independently in different groups of colonial animals, questions about their significance for colonial life histories remain unanswered. In 2018 (Nov. 25 - Dec. 8), the inaugural course on the Evolution of Coloniality and Modularity took place at the Center for Marine Biology of the University of São Paulo (CEBIMAR-USP), Brazil. During the intensive two-week graduate-level course, we addressed some of the historical ideas about animal coloniality by focal studies in bryozoans, tunicates, cnidarians, and sponges. We discussed many historical hypotheses and ways to test these using both extant and paleontological data, and we carried direct observations of animal colonies in the different phyla to address questions about coloniality. We covered topics related to multi-level selection theory and studied colonial traits, including modular miniaturization, polymorphism, brooding, and allorecognition. Course participants carried out short research projects using local species of animals to address questions on allorecognition and regeneration in ascidians and sponges, fusion and chimerism in anthoathecate hydrozoans, and evolution of polymorphism in bryozoans. Although many questions remain unanswered, this course served as a foundation to continue to develop a developmental and evolutionary synthesis of clonal and modular development in colonial marine organisms.
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Affiliation(s)
- Laurel S Hiebert
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, Brazil
| | - Leandro M Vieira
- Laboratório de Estudos de Bryozoa (LAEBry), Departamento de Zoologia, Centro de Biociências, UFPE, Cidade Universitária, Recife, Brazil
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Paris, France
| | - Carl Simpson
- Department of Geological Sciences and Museum of Natural History, University of Colorado, Colorado, USA
| | - Richard K Grosberg
- Coastal and Marine Sciences Institute, University of California Davis, Davis, California, USA
| | - Alvaro E Migotto
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, Brazil
| | - Andre C Morandini
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, Brazil
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, Brazil.,Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Bahia, Brazil
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Witkowski O, Ikegami T, Virgo N, Oka M, Iizuka H. Artificial Life Next Generation Perspectives: Echoes from the 2018 Conference in Tokyo. ARTIFICIAL LIFE 2020; 26:1-4. [PMID: 32027533 DOI: 10.1162/artl_e_00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Olaf Witkowski
- Cross Compass Ltd., Cross Labs
- Tokyo Institute of Technology, Earth-Life Science Institute
- Institute for Advanced Study
- University of Tokyo.
| | | | - Nathaniel Virgo
- Institute for Advanced Study
- Max Planck Institute for Mathematics in the Sciences
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