Biosystems最新文献

{"title":"The concepts of code biology","authors":"Marcello Barbieri","doi":"10.1016/j.biosystems.2025.105400","DOIUrl":"10.1016/j.biosystems.2025.105400","url":null,"abstract":"<div><div>Today there are two dominant paradigms in Biology: the idea that ‘<em>Life is Chemistry</em>’ and the idea that ‘<em>Life is Chemistry plus Information</em>’. There is also a third paradigm, the idea that ‘<em>Life is Chemistry, Information and Meaning</em>’ but today this is a minority view, despite the fact that meaning is produced by codes and there is ample experimental evidence that hundreds of codes exist in living systems. This is because that evidence has not yet reached the university books, but what exists in nature is bound to exist, one day, also in our books and at that point the codes will become an integral part of biology. This paper is a brief description of the key concepts of that third paradigm that has become known as <em>Code Biology</em>.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105400"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear quantum effects explain chemiosmosis: The power of the proton","authors":"Chika Edward Uzoigwe","doi":"10.1016/j.biosystems.2025.105407","DOIUrl":"10.1016/j.biosystems.2025.105407","url":null,"abstract":"<div><div>ATP is a universal bio-currency, with chemiosmosis the metabolic mint by which currency is printed. Chemiosmosis leverages a membrane potential and ion gradient, typically a proton gradient, to generate ATP. The current chemiosmotic hypothesis is both cannon and dogma. However, there are obstacles to the unqualified and uncritical acceptance of this model. Intriguingly the proton is sufficiently small to exhibit quantum phenomena of wave-particle duality, often thought the exclusive prerogative of smaller subcellular particles. Evidence shows that chemiosmosis is by necessity critically dependent upon these nuclear quantum effects (NQE) of hydrogen, most notably as a proton. It is well established scientific orthodoxy that protons in water and hydrogen atoms of water molecules exhibit quantum phenomena. The effect is amplified by the hydrogen bonding and juxta-membrane location of protons in mitochondria and chloroplasts. NQE explains the otherwise inexplicable features of chemiosmosis, including the paucity of protons, the rate of proton movement and ATP genesis in otherwise subliminal proton motive forces and thus functionality of alkaliphiles. It also accounts for the efficiencies of chemiosmosis reported at greater than 100% in certain contexts, which violates the second law of thermodynamics under the paradigm of classical physics.</div><div>Mitochondria may have evolved to exploit quantum biology with notable features such as dimeric ATP synthases adumbrating the first double-slip experiment with the protons. The dramatic global deceleration of mitochondrial chemiosmosis and all cellular function following proton substitution with its heavier isotopes, deuterium and tritium: “deuteruction”, is testimony to the primacy of nuclear quantum effects in this Quantum Chemiosmosis. Indeed the speed of evolution itself and its inexorable route to homeothermy may be due to the power of nuclear quantum effects of the smallest nucleus, the proton. The atom that is almost nothing was selected to bring about the most important processes and complex manifestations of life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105407"},"PeriodicalIF":2.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From reactions to reflection: A recursive framework for the evolution of cognition and complexity","authors":"Joseph J. Trukovich","doi":"10.1016/j.biosystems.2025.105408","DOIUrl":"10.1016/j.biosystems.2025.105408","url":null,"abstract":"<div><div>This paper presents a comprehensive framework that traces the evolution of consciousness through a continuum of recursive processes spanning reaction, temporogenesis, symbiogenesis, and cognogenesis. By integrating biological cooperation, temporal structuring, and self-referential processing, our model provides a novel perspective on how complexity emerges and scales across evolutionary time. Reaction is established as the foundational mechanism that enables adaptive responses to environmental stimuli, which, through recursive refinement, transitions into temporogenesis—the synchronization of internal processes with external temporal rhythms. Symbiogenesis further enhances this process by fostering cooperative interactions at multiple biological levels, facilitating the emergence of higher-order cognitive functions. Cognogenesis represents the culmination of these recursive processes, where self-awareness and intentionality arise through iterative feedback loops. Our framework offers a biologically grounded pathway to addressing the \"hard problem\" of consciousness by proposing that subjective experience emerges as a result of progressively complex recursive interactions rather than as a static or isolated phenomenon. In comparing our approach with established theories such as Integrated Information Theory, Global Workspace Theory, and enactive cognition, we highlight its unique contributions in situating consciousness within a broader evolutionary and biological context. This work aims to provide a foundational model that bridges the gap between reaction and reflection, offering empirical avenues for further exploration in neuroscience, evolutionary biology, and artificial intelligence.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"250 ","pages":"Article 105408"},"PeriodicalIF":2.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic ecology in aquatic ecosystems: Viewed from trophic compartments and communities in food webs","authors":"Ichiro Aoki","doi":"10.1016/j.biosystems.2025.105401","DOIUrl":"10.1016/j.biosystems.2025.105401","url":null,"abstract":"<div><div>A different perspective in metabolic ecology is presented using food web data, based on trophic compartments and communities in aquatic ecosystems (coastal areas, shelves and estuaries in marine ecosystems, and lake ecosystems), including primary producers (phytoplankton and aquatic plants). The relationships among the metabolic traits (biomass, respiration and production) in aquatic communities are expressed through power laws, hence, the value of one of the three metabolic traits provides the values of the other two. Noteworthily, these metabolic traits (biomass, respiration, production) are related to those of primary producers according to various power laws. That is: the metabolic traits of communities can be estimated from those of primary producers alone. These power laws appear to be universal in marine ecosystems but vary among different lake ecosystems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"249 ","pages":"Article 105401"},"PeriodicalIF":2.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Constructal thermodynamics and its semantic ontology in autopoietic, digital, and computational architectural and urban space open systems","authors":"Lazaros Mavromatidis","doi":"10.1016/j.biosystems.2025.105404","DOIUrl":"10.1016/j.biosystems.2025.105404","url":null,"abstract":"<div><div>This paper explores the intersections of constructal thermodynamics, and its semantic ontology within the context of autopoietic, digital and computational design in protocell inspired numerical architectural and urban narratives that are examined here as open systems. Constructal law is the thermodynamic theory based on the analysis of fluxes across the boundaries of an open system. Protocells, as dynamic, autopoietic and adaptive open finite size systems, serve in this paper as a compelling metaphor and design model for responsive and sustainable manmade architectural and urban environments. The ability of protocells to harness energy, minimize entropy, and adapt to environmental changes mirrors the principles of constructal thermodynamics, which govern the flow and distribution of resources in complex self-organizing information open systems in nature. By applying these principles to digital architecture, this study investigates how relational dynamics between spaces, materials, and functions can create adaptive designs that “<em>go with the flow</em>” of ecological and cultural systems. The research demonstrates using the Gouy-Stodola theorem as a variational principle, how protocell-inspired processes facilitate exergy-efficient designs, minimizing waste while maximizing resilience and flexibility. The present paper argues -through an applied case study- for a paradigm where protocell digital architecture serves not only as an ecological and material model but mainly as a spatial narrative driver, blending constructal and digital tools with cultural mythos. Finally, this paper exploring simultaneously the semantic complexity and ontology of such systems, in turn, connects these constructal driven digital designs to broader poly-narratives, embedding cultural, symbolic, philosophical and functional predicates into architectural forms.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"249 ","pages":"Article 105404"},"PeriodicalIF":2.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological mechanisms contradict AI consciousness: The spaces between the notes","authors":"William B. Miller Jr. ,&nbsp;František Baluška ,&nbsp;Arthur S. Reber ,&nbsp;Predrag Slijepčević","doi":"10.1016/j.biosystems.2024.105387","DOIUrl":"10.1016/j.biosystems.2024.105387","url":null,"abstract":"<div><div>The presumption that experiential consciousness requires a nervous system and brain has been central to the debate on the possibility of developing a conscious form of artificial intelligence (AI). The likelihood of future AI consciousness or devising tools to assess its presence has focused on how AI might mimic brain-centered activities. Currently, dual general assumptions prevail: AI consciousness is primarily an issue of functional information density and integration, and no substantive technical barriers exist to prevent its achievement. When the cognitive process that underpins consciousness is stipulated as a cellular attribute, these premises are directly contradicted. The innate characteristics of biological information and how that information is managed by individual cells have no parallels within machine-based AI systems. Any assertion of computer-based AI consciousness represents a fundamental misapprehension of these crucial differences.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105387"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Hans Liljenström","doi":"10.1016/j.biosystems.2024.105377","DOIUrl":"10.1016/j.biosystems.2024.105377","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105377"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143103220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling the origin, evolution, and functioning of the genetic code","authors":"Branko Dragovich,&nbsp;Elena Fimmel,&nbsp;Andrei Khrennikov,&nbsp;Nataša Ž. Mišić","doi":"10.1016/j.biosystems.2024.105373","DOIUrl":"10.1016/j.biosystems.2024.105373","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105373"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An irreversible thermodynamic model of prebiological dissipative molecular structures inside vacuoles at the surface of the Archean Ocean","authors":"Jorge A. Montemayor-Aldrete ,&nbsp;José Manuel Nieto-Villar ,&nbsp;Carlos J. Villagómez ,&nbsp;Rafael F. Márquez-Caballé","doi":"10.1016/j.biosystems.2024.105379","DOIUrl":"10.1016/j.biosystems.2024.105379","url":null,"abstract":"<div><div>A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms is developed to describe the maximum possible concentration of solar power to be dissipated on topological circular molecules structures encapsulated in lipid-walled vacuoles, which floated in the Archean oceans. By considering previously, the analysis of 71 species examined by covering 18 orders of mass magnitude from the <em>Megapteranovaeangliae</em> to <em>Saccharomyces cerevisiae</em> suggest that in molecular structures of smaller masses than any living being known nowadays, the power dissipation must be directly proportional to the power of the photons of solar origin that impinge them to give rise to the formation of more complex self-assembled molecular structures at the prebiotic stage by a quantum mechanics model of resonant photon wavelength excitation. The analysis of 12 circular molecules (encapsulated in lipid-walled vacuoles) relevant to the evolution of life on planet Earth such as the five nucleobases, and some aromatic molecules as pyrimidine, porphyrin, chlorin, coumarin, xanthine, etc., were carried out. Considering one vacuole of each type of molecule per square meter of the ocean's surface of planet Earth (<span><math><mrow><mn>1.8</mn><mo>∗</mo><msup><mn>10</mn><mn>15</mn></msup></mrow></math></span> vacuoles), their dissipative operation would require only <span><math><mrow><msup><mn>10</mn><mrow><mo>−</mo><mn>10</mn></mrow></msup></mrow></math></span> times the matter used by the biomass currently existing on Earth. Relevant numbers <span><math><mrow><mo>(</mo><mrow><msup><mn>10</mn><mn>20</mn></msup><msup><mrow><mo>−</mo><mn>10</mn></mrow><mn>21</mn></msup></mrow><mo>)</mo></mrow></math></span> for the annual dissipative cycles corresponding to high energy photo chemical events, which in principle allow the assembling of more complex polymers, were obtained. The previous figures are compatible with some results obtained by followers of the primordial soup theory where under certain suppositions about the Archean chemical kinetical changes on the precursors of RNA and DNA try to justify the formation rate of RNA and DNA components and the emergence of life within a 10-million-year window, 3.5 billion years ago. The physical foundation perspective and the simplicity of the proposed approach suggests that it can serve as a possible template for both, the development of new kind of experiments, and for prebiotic theories that address self-organization occurring inside such vacuoles. Our model provides a new way to conceptualize the self-production of simple cyclic dissipative molecular structures in the Archean period of planet Earth.</div><div>© 2017 ElsevierInc.Allrightsreserved.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105379"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A possible origin of life in nonpolar environments","authors":"Marko Vitas ,&nbsp;Andrej Dobovišek","doi":"10.1016/j.biosystems.2024.105384","DOIUrl":"10.1016/j.biosystems.2024.105384","url":null,"abstract":"<div><div>Explaining the emergence of life is perhaps the central and most challenging question in modern science. We are proposing a new hypothesis concerning the origins of life. The new hypothesis is based on the assumption that during the emergence of life, evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity. Additionally, the key abiotic and early biotic molecules required in the formation of early life, like cofactors, coenzymes, nucleic bases, prosthetic groups, polycyclic aromatic hydrocarbons (PAHs), some pigments, etc. are poorly soluble in aqueous media. To avoid the latter concentration problem, the new hypothesis assumes that life could have emerged in the nonpolar environments or low water systems, or at the interphase of the nonpolar and polar water phase, from where it was subsequently transferred to the aqueous environment. To support our hypothesis, we assume that hydrocarbons and oil on the Earth have abiotic origins.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105384"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}