Biosystems最新文献

{"title":"Stages and causes of the evolution of language and consciousness: A theoretical reconstruction","authors":"Nikolai S. Rozov","doi":"10.1016/j.biosystems.2024.105389","DOIUrl":"10.1016/j.biosystems.2024.105389","url":null,"abstract":"<div><div>This article presents a refinement of theoretical explanations of the main stages of linguistic and cognitive evolution in anthropogenesis. The concepts of language, consciousness, self-consciousness, the self, the unconscious, the subconscious, and the relation between free will and determinism remain at the center of active and complex debates in philosophy and neuroscience. A basic theoretical apparatus comprising the central concepts of \"concern\" and \"providing structure\" (an extension of the biological concept of \"adaptation\") develops the paradigm of the extended evolutionary synthesis. Challenge-threats and challenge-opportunities are invariably associated with concerns pertaining to sustenance, safety, sexuality, parenthood, status, and emotional support. The consolidation of successful behavioral tries (tries), in response to these challenges occurs through the formation of a variety of providing structures including practices, abilities, and attitudes. These structures are formed through mechanisms of interactive rituals and internalization. These novel practices facilitate the transformation of both techno-natural environmental niches and group niches. The emergence of new structures gives rise to new challenges and concerns, which in turn necessitate undertaking of new tries. In the context of African multiregionalism, hominin groups and populations that experienced favorable periods of demographic growth, active migration, genetic, technological, and skill exchange also underwent significant demographic disasters. During the most unfavorable bottleneck periods only the most advanced groups, populations and species survived. The achieved potential for these abilities was consolidated as complexes of innate assignments in gene pools through the Baldwin effect and the multilevel selection. This logic provides an explanation for the main stages of language and speech complication (from holophrases and articulation to complex syntax), as well as the emergence of new abilities of consciousness (from the expansion of attention field to self-consciousness and the \"I\"-structure).</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105389"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923801","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":"Neural networks through the lens of evolutionary dynamics","authors":"Dan C. Baciu","doi":"10.1016/j.biosystems.2024.105386","DOIUrl":"10.1016/j.biosystems.2024.105386","url":null,"abstract":"<div><div>This article revisits Artificial Neural Networks (NNs) through the lens of Evolutionary Dynamics. The two most important features of NNs are shown to reflect the two most general processes of Evolutionary Dynamics. This overlap may serve as a new and powerful connection between NNs and Evolutionary Dynamics, which encompasses a body of knowledge that has been built over multiple centuries and has been expanded to inspire applications across a vast range of disciplines. Consequently, NNs should also be applicable across the same range of disciplines—that is, much more broadly than initially envisioned. The article concludes by opening questions about NN dynamics, based on the new connection to Evolutionary Dynamics.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105386"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928752","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":"Corrigendum to “The concepts of code biology” [Biosyst. 248 (2025) 105400 1–6]","authors":"Marcello Barbieri","doi":"10.1016/j.biosystems.2025.105403","DOIUrl":"10.1016/j.biosystems.2025.105403","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105403"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076469","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":"The non-canonical nucleotides and prebiotic evolution","authors":"Alexey S. Ruzov ,&nbsp;Alexander S. Ermakov","doi":"10.1016/j.biosystems.2025.105411","DOIUrl":"10.1016/j.biosystems.2025.105411","url":null,"abstract":"<div><div>The mystery of the origin of life has been puzzling mankind for several millenia. Starting from the second half of the 20^th century, when the crucial role of nucleic acids in biological heredity became apparent, the emphasis in the field has shifted to the explanation of the origin of nucleic acids and the mechanisms of copying of macromolecules. In the 1960s, the hypothesis of the RNA World was proposed, according to which the first stages of the origin of life on Earth were associated with the appearance of self-replicating complexes based on RNA, that were akin to RNA-enzymes that catalyze critical for life chemical reactions. Currently, it has been shown that different forms of RNA include not only canonical (adenine, uracil, guanine, cytosine), but also about 170 non-canonical nucleotides. In this review, we discuss potential roles of these non-canonical nucleotides in the processes of molecular prebiotic evolution, such as the emergence of canonical RNA nucleotides and catalytic RNAs, as well as the origin of template synthesis of RNA and proteins.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105411"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123994","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":"Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation","authors":"Olga S. Knyazeva ,&nbsp;Anton A. Oreshkin ,&nbsp;Sofia I. Kisil ,&nbsp;Ekaterina A. Samarina ,&nbsp;Kristina N. Mikheeva ,&nbsp;Alexey A. Tsukanov ,&nbsp;Irina V. Gosteva ,&nbsp;Eugene A. Grachev","doi":"10.1016/j.biosystems.2024.105390","DOIUrl":"10.1016/j.biosystems.2024.105390","url":null,"abstract":"<div><div>As an important part of lipid metabolism the liver produces large particles called very low density lipoproteins, filled mostly with triglyceride and cholesterol esters mixture. A large percentage of the mixture composition components has a melting point above physiological temperature. Thus solid cluster formation or phase transition could be expected. Though various single-component triglyceride systems are well researched both experimentally and by various simulation techniques, to our best knowledge, tripalmitin/cholesteryl-palmitate binary mixture was not yet studied. We study tripalmitin single component system, as well as 20%–80% and 50%–50% binary mixtures of cholesteryl-palmitate and tripalmitin using molecular dynamics approach. All systems are studied at the pressure of 1 atm and the physiological temperature of 310 K, which is below the melting points of both tripalmitin and cholesteryl-palmitate. Our results show that at the time of 1000 ns, there is still no phase transition, but there is a noticeable tendency to intermolecular organizing and early signs of clustering. We check fatty acid arrangements of tripalmitin molecules in both single component system and binary mixtures with two different percentages of cholesteryl-palmitate mixed in. Our results show that the more cholesteryl-palmitate molecules are in the mixture the smaller number of tripalmitin molecules transitions to ’a fork/chair’ configuration during the same calculation time. Calculated angle distributions between fatty acid chains of tripalmitin molecules confirm that. Thus, our simulation results suggest slowing down or interfering effect of cholesteryl-palmitate on the crystallizing process of the binary mixture.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"248 ","pages":"Article 105390"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142957153","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":"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}