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Scharf C, Witkowski O. Rebuilding the Habitable Zone from the Bottom up with Computational Zones. ASTROBIOLOGY 2024; 24:613-627. [PMID: 38853680 DOI: 10.1089/ast.2023.0035] [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: 06/11/2024]
Abstract
Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs and may be a fundamental measure of living systems. The opportunity for biological computation, represented in the propagation and selection-driven evolution of information-carrying organic molecular structures, has been partially characterized in terms of planetary habitable zones (HZs) based on primary conditions such as temperature and the presence of liquid water. A generalization of this concept to computational zones (CZs) is proposed, with constraints set by three principal characteristics: capacity (including computation rates), energy, and instantiation (or substrate, including spatial extent). CZs naturally combine traditional habitability factors, including those associated with biological function that incorporate the chemical milieu, constraints on nutrients and free energy, as well as element availability. Two example applications are presented by examining the fundamental thermodynamic work efficiency and Landauer limit of photon-driven biological computation on planetary surfaces and of generalized computation in stellar energy capture structures (a.k.a. Dyson structures). It is suggested that CZs that involve nested structures or substellar objects could manifest unique observational signatures as cool far-infrared emitters. While these latter scenarios are entirely hypothetical, they offer a useful, complementary introduction to the potential universality of CZs.
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Affiliation(s)
- Caleb Scharf
- NASA Ames Research Center, Moffett Field, California, USA
| | - Olaf Witkowski
- Cross Labs, Cross Compass Ltd., Kyoto, Japan
- College of Arts and Sciences, University of Tokyo, Tokyo, Japan
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2
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Lingam M. Information Transmission via Molecular Communication in Astrobiological Environments. ASTROBIOLOGY 2024; 24:84-99. [PMID: 38109216 DOI: 10.1089/ast.2023.0069] [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: 12/20/2023]
Abstract
The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
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3
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Lingam M, Frank A, Balbi A. Planetary Scale Information Transmission in the Biosphere and Technosphere: Limits and Evolution. Life (Basel) 2023; 13:1850. [PMID: 37763254 PMCID: PMC10532900 DOI: 10.3390/life13091850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Information transmission via communication between agents is ubiquitous on Earth, and is a vital facet of living systems. In this paper, we aim to quantify this rate of information transmission associated with Earth's biosphere and technosphere (i.e., a measure of global information flow) by means of a heuristic order-of-magnitude model. By adopting ostensibly conservative values for the salient parameters, we estimate that the global information transmission rate for the biosphere might be ∼1024 bits/s, and that it may perhaps exceed the corresponding rate for the current technosphere by ∼9 orders of magnitude. However, under the equivocal assumption of sustained exponential growth, we find that information transmission in the technosphere can potentially surpass that of the biosphere ∼90 years in the future, reflecting its increasing dominance.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
- Department of Physics and Institute for Fusion Studies, The University of Texas at Austin, Austin, TX 78712, USA
| | - Adam Frank
- Department of Physics and Astronomy, University of Rochester, Rochester, NY 14620, USA
| | - Amedeo Balbi
- Dipartimento di Fisica, Università di Roma “Tor Vergata”, 00133 Roma, Italy
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4
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Riva F, Graco-Roza C, Daskalova GN, Hudgins EJ, Lewthwaite JM, Newman EA, Ryo M, Mammola S. Toward a cohesive understanding of ecological complexity. SCIENCE ADVANCES 2023; 9:eabq4207. [PMID: 37343095 PMCID: PMC10284553 DOI: 10.1126/sciadv.abq4207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of complex systems is, therefore, critical to progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity and excessive reliance on conventional scientific approaches hamper conceptual advances and synthesis. Ecological complexity may be better understood by following the solid theoretical basis of complex system science (CSS). We review features of ecological systems described within CSS and conduct bibliometric and text mining analyses to characterize articles that refer to ecological complexity. Our analyses demonstrate that the study of complexity in ecology is a highly heterogeneous, global endeavor that is only weakly related to CSS. Current research trends are typically organized around basic theory, scaling, and macroecology. We leverage our review and the generalities identified in our analyses to suggest a more coherent and cohesive way forward in the study of complexity in ecology.
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Affiliation(s)
- Federico Riva
- Geomatics and Landscape Ecology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, Ontario K1S 5B6, Canada
- Insectarium, Montreal Space for Life, 4581 Sherbrooke St E, Montreal, Quebec H1X 2B2, Canada
- Spatial Ecology Group, Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Caio Graco-Roza
- Aquatic Community Ecology Group, Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2, 00560 Helsinki, Finland
- Laboratory of Ecology and Physiology of Phytoplankton, Department of Plant Biology, State University of Rio de Janeiro, Rua São Francisco Xavier 524, PHLC, Sala 511a, 20550-900 Rio de Janeiro, Brazil
| | - Gergana N. Daskalova
- Biodiversity and Ecology Group, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Emma J. Hudgins
- Geomatics and Landscape Ecology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, Ontario K1S 5B6, Canada
| | - Jayme M. M. Lewthwaite
- Marine and Environmental Biology, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA 90089-0371, USA
| | - Erica A. Newman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Masahiro Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Muencheberg, Germany
- Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 03046 Cottbus, Germany
| | - Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00100, Finland
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR), Corso Tonolli, 50, Pallanza 28922, Italy
- National Biodiversity Future Center, Palermo, Italy
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5
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Biology, Buddhism, and AI: Care as the Driver of Intelligence. ENTROPY 2022; 24:e24050710. [PMID: 35626593 PMCID: PMC9140411 DOI: 10.3390/e24050710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022]
Abstract
Intelligence is a central feature of human beings’ primary and interpersonal experience. Understanding how intelligence originated and scaled during evolution is a key challenge for modern biology. Some of the most important approaches to understanding intelligence are the ongoing efforts to build new intelligences in computer science (AI) and bioengineering. However, progress has been stymied by a lack of multidisciplinary consensus on what is central about intelligence regardless of the details of its material composition or origin (evolved vs. engineered). We show that Buddhist concepts offer a unique perspective and facilitate a consilience of biology, cognitive science, and computer science toward understanding intelligence in truly diverse embodiments. In coming decades, chimeric and bioengineering technologies will produce a wide variety of novel beings that look nothing like familiar natural life forms; how shall we gauge their moral responsibility and our own moral obligations toward them, without the familiar touchstones of standard evolved forms as comparison? Such decisions cannot be based on what the agent is made of or how much design vs. natural evolution was involved in their origin. We propose that the scope of our potential relationship with, and so also our moral duty toward, any being can be considered in the light of Care—a robust, practical, and dynamic lynchpin that formalizes the concepts of goal-directedness, stress, and the scaling of intelligence; it provides a rubric that, unlike other current concepts, is likely to not only survive but thrive in the coming advances of AI and bioengineering. We review relevant concepts in basal cognition and Buddhist thought, focusing on the size of an agent’s goal space (its cognitive light cone) as an invariant that tightly links intelligence and compassion. Implications range across interpersonal psychology, regenerative medicine, and machine learning. The Bodhisattva’s vow (“for the sake of all sentient life, I shall achieve awakening”) is a practical design principle for advancing intelligence in our novel creations and in ourselves.
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Probabilistic Inference with Polymerizing Biochemical Circuits. ENTROPY 2022; 24:e24050629. [PMID: 35626513 PMCID: PMC9140500 DOI: 10.3390/e24050629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 03/24/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023]
Abstract
Probabilistic inference—the process of estimating the values of unobserved variables in probabilistic models—has been used to describe various cognitive phenomena related to learning and memory. While the study of biological realizations of inference has focused on animal nervous systems, single-celled organisms also show complex and potentially “predictive” behaviors in changing environments. Yet, it is unclear how the biochemical machinery found in cells might perform inference. Here, we show how inference in a simple Markov model can be approximately realized, in real-time, using polymerizing biochemical circuits. Our approach relies on assembling linear polymers that record the history of environmental changes, where the polymerization process produces molecular complexes that reflect posterior probabilities. We discuss the implications of realizing inference using biochemistry, and the potential of polymerization as a form of biological information-processing.
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7
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Kempes CP, Krakauer DC. The Multiple Paths to Multiple Life. J Mol Evol 2021; 89:415-426. [PMID: 34254169 PMCID: PMC8318961 DOI: 10.1007/s00239-021-10016-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/08/2021] [Indexed: 12/04/2022]
Abstract
We argue for multiple forms of life realized through multiple different historical pathways. From this perspective, there have been multiple origins of life on Earth—life is not a universal homology. By broadening the class of originations, we significantly expand the data set for searching for life. Through a computational analogy, the origin of life describes both the origin of hardware (physical substrate) and software (evolved function). Like all information-processing systems, adaptive systems possess a nested hierarchy of levels, a level of function optimization (e.g., fitness maximization), a level of constraints (e.g., energy requirements), and a level of materials (e.g., DNA or RNA genome and cells). The functions essential to life are realized by different substrates with different efficiencies. The functional level allows us to identify multiple origins of life by searching for key principles of optimization in different material form, including the prebiotic origin of proto-cells, the emergence of culture, economic, and legal institutions, and the reproduction of software agents.
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8
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Moya A, Oliver JL, Verdú M, Delaye L, Arnau V, Bernaola-Galván P, de la Fuente R, Díaz W, Gómez-Martín C, González FM, Latorre A, Lebrón R, Román-Roldán R. Driven progressive evolution of genome sequence complexity in Cyanobacteria. Sci Rep 2020; 10:19073. [PMID: 33149190 PMCID: PMC7643063 DOI: 10.1038/s41598-020-76014-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.
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Affiliation(s)
- Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain.
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain.
| | - José L Oliver
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación, Consejo Superior de Investigaciones Científicas (CSIC), University of València and Generalitat Valenciana, 46113, Valencia, Spain
| | - Luis Delaye
- Department of Genetic Engineering, CINVESTAV, 36821, Irapuato, Mexico
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Pedro Bernaola-Galván
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071, Málaga, Spain
| | - Rebeca de la Fuente
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Balearic Islands, 07122, Palma de Mallorca, Spain
| | - Wladimiro Díaz
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Cristina Gómez-Martín
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | | | - Amparo Latorre
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain
| | - Ricardo Lebrón
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Ramón Román-Roldán
- Department of Applied Physics, University of Granada, 18071, Granada, Spain
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Seoane LF. Fate of Duplicated Neural Structures. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E928. [PMID: 33286697 PMCID: PMC7597184 DOI: 10.3390/e22090928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 01/25/2023]
Abstract
Statistical physics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under specific conditions, self-replicating and computationally complex patterns become favored, yielding life, cognition, and Darwinian evolution. Neurons and neural circuits sit at a crossroads between statistical physics, computation, and (through their role in cognition) natural selection. Can we establish a statistical physics of neural circuits? Such theory would tell what kinds of brains to expect under set energetic, evolutionary, and computational conditions. With this big picture in mind, we focus on the fate of duplicated neural circuits. We look at examples from central nervous systems, with stress on computational thresholds that might prompt this redundancy. We also study a naive cost-benefit balance for duplicated circuits implementing complex phenotypes. From this, we derive phase diagrams and (phase-like) transitions between single and duplicated circuits, which constrain evolutionary paths to complex cognition. Back to the big picture, similar phase diagrams and transitions might constrain I/O and internal connectivity patterns of neural circuits at large. The formalism of statistical physics seems to be a natural framework for this worthy line of research.
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Affiliation(s)
- Luís F. Seoane
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CNB), CSIC, C/Darwin 3, 28049 Madrid, Spain;
- Instituto de Física Interdisciplinar y Sistemas Complejos (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain
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10
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Matthews B, Jokela J, Narwani A, Räsänen K, Pomati F, Altermatt F, Spaak P, Robinson CT, Vorburger C. On biological evolution and environmental solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138194. [PMID: 32251887 PMCID: PMC7118648 DOI: 10.1016/j.scitotenv.2020.138194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 05/22/2023]
Abstract
Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.
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Affiliation(s)
- Blake Matthews
- EAWAG, Department of Fish Ecology and Evolution, Center for Ecology, Evolution, and Biogeochemistry, Seestrasse 79, 6047 Kastanienbaum, Switzerland; EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland.
| | - Jukka Jokela
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | - Anita Narwani
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | - Katja Räsänen
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | - Francesco Pomati
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | - Florian Altermatt
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Piet Spaak
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | | | - Christoph Vorburger
- EAWAG, Department of Aquatic Ecology, Überlandstr. 133, 8600 Dübendorf, Switzerland; Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland.
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11
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Priya M, Jaiswal PK, Shrimali MD. Host-parasite coevolution: Role of selection, mutation, and asexual reproduction on evolvability. CHAOS (WOODBURY, N.Y.) 2020; 30:073103. [PMID: 32752606 DOI: 10.1063/5.0010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The key to the survival of a species lies in understanding its evolution in an ever-changing environment. We report a theoretical model that integrates frequency-dependent selection, mutation, and asexual reproduction for understanding the biological evolution of a host species in the presence of parasites. We study the host-parasite coevolution in a one-dimensional genotypic space by considering a dynamic and heterogeneous environment modeled using a fitness landscape. It is observed that the presence of parasites facilitates a faster evolution of the host population toward its fitness maximum. We also find that the time required to reach the maximum fitness (optimization time) decreases with increased infection from the parasites. However, the overall fitness of the host population declines due to the parasitic infection. In the limit where parasites are considered to evolve much faster than the hosts, the optimization time reduces even further. Our findings indicate that parasites can play a crucial role in the survival of its host in a rapidly changing environment.
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Affiliation(s)
- Madhu Priya
- Department of Physics, Birla Institute of Technology Mesra, Ranchi 835215, Jharkhand, India
| | - Prabhat K Jaiswal
- Department of Physics, Indian Institute of Technology Jodhpur, Karwar 342037, Rajasthan, India
| | - Manish Dev Shrimali
- Department of Physics, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer 305817, Rajasthan, India
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12
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Frieden BR, Gatenby R. Ion-Based Cellular Signal Transmission, Principles of Minimum Information Loss, and Evolution by Natural Selection. Int J Mol Sci 2019; 21:ijms21010009. [PMID: 31861371 PMCID: PMC6982146 DOI: 10.3390/ijms21010009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 11/16/2022] Open
Abstract
The Extreme Physical Information EPI principle states that maximum information transmission or, equivalently, a minimum information loss is a fundamental property of nature. Prior work has demonstrated the universal EPI principle allows derivation of nearly all physical laws. Here, we investigate whether EPI can similarly give rise to the fundamental law of life: Evolution. Living systems require information to survive and proliferate. Heritable information in the genome encodes the structure and function of cellular macromolecules but this information remains fixed over time. In contrast, a cell must rapidly and continuously access, analyze, and respond to a wide range of continuously changing spatial and temporal information in the environment. We propose these two information dynamics are linked because the genes encode the structure of the macromolecules that form information conduits necessary for the dynamical interactions with the external environment. However, because the genome does not have the capacity to precisely locate the time and location of external signals, we propose the cell membrane is the site at which most external information is received and processed. In our model, an external signal is detected by gates on transmembrane ion channel and transmitted into the cytoplasm through ions that flow along pre-existing concentration gradients when the gate opens. The resulting cytoplasmic ion “puff” is localized in both time and space, thus producing spatial and temporal information. Small, localized signals in the cytoplasm are “processed” through alterations in the function and location of peripheral membrane proteins. Larger perturbations produce prolonged or spatially extensive changes in cytoplasmic ion concentrations that can be transmitted to other organelles via ion flows along elements of the cytoskeleton. An evolutionary constraint to the ever-increasing acquisition of environmental information is the cost of doing so. One solution to this trade-off is the evolution of information conduits that minimize signal loss during transmission. Since the structures of these conduits are encoded in the genome, evolution of macromolecular conduits that minimize signal loss is linked to and, in fact, governed by a universal principle, termed extreme physical information (EPI). Mathematical analysis of information dynamics based on the flow of ions through membrane channels and along wire-like cytoskeleton macromolecules fulfills the EPI principle. Thus, the empirically derived model of evolution by natural selection, although uniquely applicable to living systems, is theoretically grounded in a universal principle that can also be used to derive the laws of physics. Finally, if minimization of signal loss is a mechanism to overcome energy constraints, the model predicts increasing information and associated complexity are closely linked to increased efficiency of energy production or improved substrate acquisition.
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Affiliation(s)
- B. Roy Frieden
- College of Optical Sciences, University of Arizona, Tucson, AZ 85721, USA;
| | - Robert Gatenby
- Departments of Radiology and Integrated Mathematical Oncology, Moffitt Cancer Center, 1292 Magnolia Drive, Tampa, FL 33612, USA
- Correspondence:
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13
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Kolchinsky A, Wolpert DH. Semantic information, autonomous agency and non-equilibrium statistical physics. Interface Focus 2018; 8:20180041. [PMID: 30443338 PMCID: PMC6227811 DOI: 10.1098/rsfs.2018.0041] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 01/24/2023] Open
Abstract
Shannon information theory provides various measures of so-called syntactic information, which reflect the amount of statistical correlation between systems. By contrast, the concept of 'semantic information' refers to those correlations which carry significance or 'meaning' for a given system. Semantic information plays an important role in many fields, including biology, cognitive science and philosophy, and there has been a long-standing interest in formulating a broadly applicable and formal theory of semantic information. In this paper, we introduce such a theory. We define semantic information as the syntactic information that a physical system has about its environment which is causally necessary for the system to maintain its own existence. 'Causal necessity' is defined in terms of counter-factual interventions which scramble correlations between the system and its environment, while 'maintaining existence' is defined in terms of the system's ability to keep itself in a low entropy state. We also use recent results in non-equilibrium statistical physics to analyse semantic information from a thermodynamic point of view. Our framework is grounded in the intrinsic dynamics of a system coupled to an environment, and is applicable to any physical system, living or otherwise. It leads to formal definitions of several concepts that have been intuitively understood to be related to semantic information, including 'value of information', 'semantic content' and 'agency'.
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Affiliation(s)
| | - David H. Wolpert
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
- Arizona State University, Tempe, AZ, USA
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14
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Baum DA. The origin and early evolution of life in chemical composition space. J Theor Biol 2018; 456:295-304. [PMID: 30110611 DOI: 10.1016/j.jtbi.2018.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 01/02/2023]
Abstract
Life can be viewed as a localized chemical system that sits in the basin of attraction of a metastable dynamical attractor state that remains out of equilibrium with the environment. To explore the implications of this conception, I introduce an abstract coordinate system, chemical composition (CC Space), which summarizes the degree to which chemical systems are out of equilibrium with the bulk environment. A system's chemical disequilibrium (CD) is defined to be proportional to the Euclidean distance between the composition of a small region of physical space, a pixel, and the origin of CC space. Such a model implies that new living states arise through chance changes in local chemical concentration ("mutations") that cause chemical systems to move in CC space and enter the basin of attraction of a life state. The attractor of a life state comprises an autocatalytic set of chemicals whose essential ("keystone") species are produced at a higher rate than they are lost to the environment by diffusion, such that spatial growth of the life state is expected. This framework suggests that new life states are most likely to form at the interface between different physical phases, where the rate of diffusion of keystone species is tied to the low-diffusion regime, whereas food and waste products are subject to the more diffusive regime. Once life nucleates, for example on a mineral surface, it will tend to grow and generate variants as a result of additional mutations that find alternative life states. By jumping from life state to life state, systems can eventually occupy areas of CC space that are too far out of equilibrium with the environment to ever arise in a single mutational step. Furthermore, I propose that variation in the capacity of different surface associated life states to persist and compete may systematically favor states that have higher chemical disequilibrium. The model also suggests a simple and predictable path from surface-associated life to cell-like individuation. This dynamical systems theoretical framework provides an integrated view of the origin and early evolution of life and supports novel empirical approaches.
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Affiliation(s)
- David A Baum
- Department of Botany and the Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53706, USA.
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15
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Seoane LF, Solé RV. Information theory, predictability and the emergence of complex life. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172221. [PMID: 29515907 PMCID: PMC5830796 DOI: 10.1098/rsos.172221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/24/2018] [Indexed: 05/07/2023]
Abstract
Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the inevitable cost associated with detecting environmental cues and responding to them in adaptive ways, we conjecture that the potential for predicting the environment can overcome the expenses associated with maintaining costly, complex structures. We present a minimal formal model grounded in information theory and selection, in which successive generations of agents are mapped into transmitters and receivers of a coded message. Our agents are guessing machines and their capacity to deal with environments of different complexity defines the conditions to sustain more complex agents.
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Affiliation(s)
- Luís F. Seoane
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard V. Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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16
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Kempes CP, Wolpert D, Cohen Z, Pérez-Mercader J. The thermodynamic efficiency of computations made in cells across the range of life. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160343. [PMID: 29133443 PMCID: PMC5686401 DOI: 10.1098/rsta.2016.0343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/31/2017] [Indexed: 06/01/2023]
Abstract
Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
| | - David Wolpert
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Beyond Center, Arizona State University, Tempe, AZ 85287, USA
| | - Zachary Cohen
- Department of Biology, University of Illinois, Urbana Champagne, Urbana, IL 61801, USA
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
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17
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Bribiesca-Contreras G, Verbruggen H, Hugall AF, O'Hara TD. The importance of offshore origination revealed through ophiuroid phylogenomics. Proc Biol Sci 2017; 284:20170160. [PMID: 28679721 PMCID: PMC5524485 DOI: 10.1098/rspb.2017.0160] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/31/2017] [Indexed: 11/12/2022] Open
Abstract
Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore-offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
- School of Biosciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Heroen Verbruggen
- School of Biosciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrew F Hugall
- Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Timothy D O'Hara
- Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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18
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Abstract
In complex environments, there are costs to both ignorance and perception. An organism needs to track fitness-relevant information about its world, but the more information it tracks, the more resources it must devote to perception. As a first step towards a general understanding of this trade-off, we use a tool from information theory, rate-distortion theory, to study large, unstructured environments with fixed, randomly drawn penalties for stimuli confusion ('distortions'). We identify two distinct regimes for organisms in these environments: a high-fidelity regime where perceptual costs grow linearly with environmental complexity, and a low-fidelity regime where perceptual costs are, remarkably, independent of the number of environmental states. This suggests that in environments of rapidly increasing complexity, well-adapted organisms will find themselves able to make, just barely, the most subtle distinctions in their environment.
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Affiliation(s)
- Sarah E Marzen
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Redwood Center for Theoretical Neuroscience, and Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Simon DeDeo
- Department of Social and Decision Sciences, Carnegie Mellon University, 5000 Forbes Avenue, BP 208, Pittsburgh, PA 15213, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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19
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Kiridena S, Sense A. Profiling Project Complexity: Insights from Complexity Science and Project Management Literature. PROJECT MANAGEMENT JOURNAL 2016. [DOI: 10.1177/875697281604700605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The current understanding of project complexity is limited in that there is neither a widely recognized conceptualization of project complexity nor a convergent view on how to deal with its effects. Drawing on the extant literature concerning project complexity and complexity science, this article develops a coherent and holistic profile of project complexity and provides reflections on its implications for project management theory and practice. This profile serves as a touchstone for practitioners to better understand, assess, and address complexity in their projects and as an aid to researchers in framing their research efforts.
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Affiliation(s)
- Senevi Kiridena
- School of Mechanical, Materials and Mechatronic Engineering, Faculty of Engineering and Information Sciences, University of Wollongong, Australia
| | - Andrew Sense
- School of Management, Operations and Marketing, Faculty of Business, University of Wollongong, Australia
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20
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The Free Energy Requirements of Biological Organisms; Implications for Evolution. ENTROPY 2016. [DOI: 10.3390/e18040138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Caiado CCS, Brock WA, Bentley RA, O'Brien MJ. Fitness landscapes among many options under social influence. J Theor Biol 2016; 405:5-16. [PMID: 26851173 DOI: 10.1016/j.jtbi.2015.12.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022]
Abstract
Cultural learning represents a novel problem in that an optimal decision depends not only on intrinsic utility of the decision/behavior but also on transparency of costs and benefits, the degree of social versus individual learning, and the relative popularity of each possible choice in a population. In terms of a fitness-landscape function, this recursive relationship means that multiple equilibria can exist. Here we use discrete-choice theory to construct a fitness-landscape function for a bi-axial decision-making map that plots the magnitude of social influence in the learning process against the costs and payoffs of decisions. Specifically, we use econometric and statistical methods to estimate not only the fitness function but also movements along the map axes. To search for these equilibria, we employ a hill-climbing algorithm that leads to the expected values of optimal decisions, which we define as peaks on the fitness landscape. We illustrate how estimation of a measure of transparency, a measure of social influence, and the associated fitness landscape can be accomplished using panel data sets.
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Affiliation(s)
| | - William A Brock
- Department of Economics, University of Missouri, Columbia, MO 65211, USA; Department of Economics, University of Wisconsin, Madison, WI 53706, USA
| | - R Alexander Bentley
- Department of Comparative Cultural Studies, University of Houston, Houston, TX 77204, USA.
| | - Michael J O'Brien
- Department of Anthropology, University of Missouri, Columbia, MO 65211, USA
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23
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Kutschera U, Niklas KJ. Darwin-Wallace Demons: survival of the fastest in populations of duckweeds and the evolutionary history of an enigmatic group of angiosperms. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:24-32. [PMID: 24674028 DOI: 10.1111/plb.12171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/23/2014] [Indexed: 05/24/2023]
Abstract
In evolutionary biology, the term 'Darwinian fitness' refers to the lifetime reproductive success of an individual within a population of conspecifics. The idea of a 'Darwinian Demon' emerged from this concept and is defined here as an organism that commences reproduction almost immediately after birth, has a maximum fitness, and lives forever. It has been argued that duckweeds (sub-family Lemnoideae, order Alismatales), a group containing five genera and 34 species of small aquatic monocotyledonous plants with a reduced body plan, can be interpreted as examples of 'Darwinian Demons'. Here we focus on the species Spirodela polyrhiza (Great duckweed) and show that these miniaturised aquatic angiosperms display features that fit the definition of the hypothetical organism that we will call a 'Darwin-Wallace Demon' in recognition of the duel proponents of evolution by natural selection. A quantitative analysis (log-log bivariate plot of annual growth in dry biomass versus standing dry body mass of various green algae and land plants) revealed that duckweeds are thus far the most rapidly growing angiosperms in proportion to their body mass. In light of this finding, we discuss the disposable soma and metabolic optimising theories, summarise evidence for and against the proposition that the Lemnoideae (family Araceae) reflect an example of reductive evolution, and argue that, under real-world conditions (environmental constraints and other limitations), 'Darwin-Wallace Demons' cannot exist, although the concept remains useful in much the same way that the Hardy-Weinberg law does.
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Affiliation(s)
- U Kutschera
- Institute of Biology, University of Kassel, Kassel, Germany
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24
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Abstract
The behavioral sciences have flourished by studying how traditional and/or rational behavior has been governed throughout most of human history by relatively well-informed individual and social learning. In the online age, however, social phenomena can occur with unprecedented scale and unpredictability, and individuals have access to social connections never before possible. Similarly, behavioral scientists now have access to "big data" sets - those from Twitter and Facebook, for example - that did not exist a few years ago. Studies of human dynamics based on these data sets are novel and exciting but, if not placed in context, can foster the misconception that mass-scale online behavior is all we need to understand, for example, how humans make decisions. To overcome that misconception, we draw on the field of discrete-choice theory to create a multiscale comparative "map" that, like a principal-components representation, captures the essence of decision making along two axes: (1) an east-west dimension that represents the degree to which an agent makes a decision independently versus one that is socially influenced, and (2) a north-south dimension that represents the degree to which there is transparency in the payoffs and risks associated with the decisions agents make. We divide the map into quadrants, each of which features a signature behavioral pattern. When taken together, the map and its signatures provide an easily understood empirical framework for evaluating how modern collective behavior may be changing in the digital age, including whether behavior is becoming more individualistic, as people seek out exactly what they want, or more social, as people become more inextricably linked, even "herdlike," in their decision making. We believe the map will lead to many new testable hypotheses concerning human behavior as well as to similar applications throughout the social sciences.
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25
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Baffy G, Loscalzo J. Complexity and network dynamics in physiological adaptation: An integrated view. Physiol Behav 2014; 131:49-56. [DOI: 10.1016/j.physbeh.2014.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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26
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Michel D. Life is a self-organizing machine driven by the informational cycle of Brillouin. ORIGINS LIFE EVOL B 2013; 43:137-50. [PMID: 23625038 DOI: 10.1007/s11084-013-9329-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/04/2013] [Indexed: 01/04/2023]
Abstract
Acquiring information is indisputably energy-consuming and conversely, the availability of information permits greater efficiency. Strangely, the scientific community long remained reluctant to establish a physical equivalence between the abstract notion of information and sensible thermodynamics. However, certain physicists such as Szilard and Brillouin proposed: (i) to give to information the status of a genuine thermodynamic entity (k B T ln2 joules/bit) and (ii) to link the capacity of storing information inferred from correlated systems, to that of indefinitely increasing organization. This positive feedback coupled to the self-templating molecular potential could provide a universal basis for the spontaneous rise of highly organized structures, typified by the emergence of life from a prebiotic chemical soup. Once established, this mechanism ensures the longevity and robustness of life envisioned as a general system, by allowing it to accumulate and optimize microstate-reducing recipes, thereby giving rise to strong nonlinearity, decisional capacity and multistability. Mechanisms possibly involved in priming this cycle are proposed.
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Affiliation(s)
- Denis Michel
- Université de Rennes 1 IRSET U1085 Transcription, Environment and Cancer, Campus de Beaulieu, Bat 13, 35042 Rennes Cedex, France.
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27
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Crutchfield JP, Machta J. Introduction to focus issue on "randomness, structure, and causality: measures of complexity from theory to applications". CHAOS (WOODBURY, N.Y.) 2011; 21:037101. [PMID: 21974664 DOI: 10.1063/1.3643065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We introduce the contributions to this Focus Issue and describe their origin in a recent Santa Fe Institute workshop.
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Affiliation(s)
- James P Crutchfield
- Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, California 95616, USA.
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