Biosystems最新文献

{"title":"Major transitions in the physiological machinery of cognition","authors":"Breno B. Just ,&nbsp;Sávio Torres de Farias","doi":"10.1016/j.biosystems.2025.105517","DOIUrl":"10.1016/j.biosystems.2025.105517","url":null,"abstract":"<div><div>Cognition refers to the processes organisms use to interact with and understand their world, a fundamental biological function present in all cellular life. As with any biological process, cognitive capacity and its underlying mechanisms vary widely across species. Evolution has shaped cognition, leading to increasingly complex forms in certain lineages. The concept of evolutionary transitions, introduced by Maynard-Smith and Szathmary, describes major shifts in biological organization. In 2021, Ginsburg &amp; Jablonka, and in 2023, Barron and collaborators explored cognitive transitions within neural systems, the evolution of cognition in aneural organisms remains understudied. Building on prior frameworks, we analyze cognitive transitions in the aneural realm, focusing on the physiological machinery responsible for cognition. The first transition is the emergence of cognitive machinery in prokaryotic cells (cellular cognition), followed by its complexification in eukaryotes (complex cellular cognition). The third transition marks cognition based on multiple cells (multicellular-based cognition). The fourth is the development of neurons and a diffuse nervous system (decentralized neural cognition), followed by its centralization (brain cognition). The sixth transition involves advanced brain architectures enabling complex cognition (complex brain cognition). The final transition is the emergence of human cognition, supported by symbols and culture (cultural-linguistic cognition). This hierarchical framework captures the increasing complexity of cognitive machinery across evolutionary transitions. By incorporating aneural cognition, we provide a more comprehensive view of the diversity of cognitive systems in nature.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105517"},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276533","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":"Codes across (life)sciences","authors":"Robert Prinz ,&nbsp;Philipp Bucher ,&nbsp;Ádám Kun ,&nbsp;Omar Paredes ,&nbsp;Anna Aragno ,&nbsp;Candice Shelby ,&nbsp;Markus Gumbel ,&nbsp;Elena Fimmel ,&nbsp;Lutz Strüngmann","doi":"10.1016/j.biosystems.2025.105515","DOIUrl":"10.1016/j.biosystems.2025.105515","url":null,"abstract":"<div><div>The concept of “<em>code</em>” connotes different meanings, intentions, and formalizations. From <em>mathematics</em> and <em>computer sciences</em> to <em>psychology</em> and <em>culture</em>, the term becomes less formal, more diverse, and sometimes appears ambiguous. In <em>biology</em> a growing number of codes ignite a debate about their role in evolution, biocomplexity, and agency, to name just a few. Here, a transdisciplinary group of code scientists attempts to capture the <em>big picture</em> of code research across their fields of interest. In this cross-sectional overview commonalities emerge that may pave the way towards a unified theory of <em>life-based-on-codes</em>. Codes underly cellular processes, perception, cognition, and communication. From <em>ecosystems</em> to <em>human language</em>, codes influence how individuals behave in groups, memorize, learn, and take part in <em>cultural practices</em>. Emotions like aggression, fear, anger, frustration, are important motivators of behaviour modulating mutual communication and sculpting individual experience. The inheritance of experience in form of innate release mechanisms, stereotyped behaviour, or archetypes may have phylogenetic and ontogenetic roots that rely on codes and impact our conscious decision making. Unconsciously, even our <em>dreams draw on codes</em>. In the future, conflation of different coding systems, e.g., from synthetic biology and generative artificial intelligence, will merge biological codes with machine <em>logic</em> and <em>computer language</em> to promote next-level <em>transhumanism</em>. Codes emerge as a currency converter between systems of life and between different scientific disciplines.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105515"},"PeriodicalIF":2.0,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259292","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":"Thermal diodes, transistors and logic: Review of unconventional computing methods","authors":"Philip Tabor,&nbsp;Matei C. Ignuta-Ciuncanu,&nbsp;Ricardo F. Martinez-Botas","doi":"10.1016/j.biosystems.2025.105491","DOIUrl":"10.1016/j.biosystems.2025.105491","url":null,"abstract":"<div><div>In the evolving landscape of unconventional computing, this review explores the nascent field of thermal computing. Thermal computers, which use heat as a computational element, present a significant shift from traditional computing paradigms. This review focuses on memory devices and logic gates that function via heat transfer mechanisms, exploring thermal computing’s potential to harness heat for computational purposes and expand the horizons of computing beyond conventional electronic paradigms. The motivation for this work stems from the need to expand the horizons of computing beyond conventional electronic systems-which have overshadowed all other forms of computing since the 20th century-leveraging the 72% of global primary energy lost in conversion processes. By harnessing the world’s ample amounts of waste thermal energy, one can envisage computational advancements in diverse areas such as self-powered systems, extreme environmental applications, and server farms, wherein thermal computing devices could synergistically interact with electronic systems. To address the gap in comprehensive studies on thermal computing’s engineering applicability and real-world integration, this review includes a detailed analysis of thermal memory devices and logic gates, evaluating their data retention, distinct states, and read/write speeds, alongside their scalability and potential real-world applications. A comprehensive technology readiness assessment for these devices underscores their potential and the challenges ahead in transitioning from theoretical constructs to practical tools. The outcomes of this assessment found that the Radiative Thermal Transistor score outperformed all other memory devices by 9.4% and the NanoThermoMechanical logic gates score outperformed other logic devices by 27%. To conclude, this review highlights the need for further advancement in thermal computing, underlining its potential to revolutionize computational models and expand the frontiers of information science. By integrating hysteresis and bistability with effective thresholding, thermal computing devices could provide stable, reliable, and efficient alternatives to electronic counterparts, leading to a seismic shift in computational technologies.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105491"},"PeriodicalIF":2.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144242720","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":"Ervin Bauer and the foundations of theoretical biology","authors":"Abir U. Igamberdiev ,&nbsp;Miklós Müller ,&nbsp;Gábor Elek ,&nbsp;George E. Mikhailovsky","doi":"10.1016/j.biosystems.2025.105424","DOIUrl":"10.1016/j.biosystems.2025.105424","url":null,"abstract":"<div><div>Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology in his monograph “Fundamental Principles of Biology as Pure Natural Science and their Applications in Physiology and Pathology” (1920) and further developed these ideas in his book “Theoretical Biology” (1935). In these works, he defined the foundations of theoretical biology from the perspective of biophysics and bioenergetics, formulated the principle of a sustainable non-equilibrium state, which is continuously maintained by all biological systems throughout their life, and developed original views on cell differentiation, adaptation, and evolution. In 1938, Ervin Bauer and his wife Stefánia became the victims of Stalin's Great Terror. The book of 1920 was published in German. It outlines the main principles of Bauer's concept. Bauer's <em>magnum opus</em> “Theoretical Biology” (1935) was published in Russian and republished in 1967 in Hungarian (together with the monograph of 1920) and several times in Russian. Immediately after the Russian edition appeared, two chapters were also published in German translation. Only small excerpts of the book were published in English translation. Here we present a complete English translation of both books. The books contain many important ideas that remain actual today and have great potential for further development in modern concepts of the foundations of life, the structure of living matter, and evolution.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105424"},"PeriodicalIF":2.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426571","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":"Theoretical biology","authors":"Ervin Bauer","doi":"10.1016/j.biosystems.2025.105426","DOIUrl":"10.1016/j.biosystems.2025.105426","url":null,"abstract":"<div><div>This is a complete English translation of the magnum opus of Ervin Bauer (1890-1938), published in Russian in 1935. The book develops the first fundamental concept of theoretical biology, which is grounded in biophysics and bioenergetics. Bauer’s molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Bauer’s ideas remain actual for the development of modern concepts of the foundations of life, the structure of living matter, and biological evolution.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105426"},"PeriodicalIF":2.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484572","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":"Fundamental principles of biology as pure natural science and their applications in physiology and pathology","authors":"Ervin Bauer","doi":"10.1016/j.biosystems.2025.105425","DOIUrl":"10.1016/j.biosystems.2025.105425","url":null,"abstract":"<div><div>This is a complete English translation of the first book of Ervin Bauer (1890-1938), published in German in 1920. The book outlines the main principles of Bauer’s thermodynamic concept of theoretical biology and their applications in physiology and pathology. It contains the fundamental ideas that remain actual and have the potential for further development in modern concepts of the foundations of life and the structure of living matter.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105425"},"PeriodicalIF":2.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469962","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":"Thermodynamics of Nath’s 2-ion model for ATP synthesis","authors":"Lee D. Hansen ,&nbsp;Sunil Nath","doi":"10.1016/j.biosystems.2025.105505","DOIUrl":"10.1016/j.biosystems.2025.105505","url":null,"abstract":"<div><div>A major finding of studies of organic acid ionization was that substituents on an aliphatic chain attached to a carboxyl group have large effects on the equilibrium constant but very little effect on Δ_ionizH which is in the range 0 ± 4 kJ/mol for all carboxylic acids of this type. According to Nath’s 2-ion mechanism for ATP synthesis, succinic acid was selected by biological evolution because an acid that could be ionized with no energy input was required, i.e., with Δ_ionizH near zero. In support of this, ATP synthesis evolved in prokaryotes in a world without oxygen in the atmosphere and consequently catabolic reactions in prokaryotes that are coupled to ATP synthesis generally have small enthalpy changes. ATP synthesis in anaerobes is thus driven by the potential energy in concentration gradients. This potential energy is associated with a probability field quantified by the change in the number of microstates of particle distributions. ATP synthesis is thus powered by a probability field associated with a concentration gradient of ions consistent with Nath’s 2-ion mechanism.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105505"},"PeriodicalIF":2.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200747","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":"Formation flight design via Constructal Law","authors":"Samuel A. Savitt","doi":"10.1016/j.biosystems.2025.105482","DOIUrl":"10.1016/j.biosystems.2025.105482","url":null,"abstract":"<div><div>Formation fliers utilize varying designs to save energy by flying in the wake of preceding fliers, reducing induced drag and boosting lift. The Constructal Law is applied to this formation flight problem to analyze how the distribution of drag among fliers in a V-formation design is related to the optimal formation flight configuration. An analytical model that predicts this optimal configuration is developed and expressed in terms of the fundamental formation parameters (velocity, number of fliers, wingspan, weight, and air density). Results show that there is not a fixed optimal V-formation design for all formation systems. Rather, the optimal configuration is evolutionary: it constantly adapts as parameters change to maximize access to energy savings. Trends predicted by the model are substantiated by observations from nature. In line with Constructal Law predictions, induced drag along the optimal V-formation configuration is distributed as uniformly as possible among fliers.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105482"},"PeriodicalIF":2.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182757","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":"Mechanism and biological significance of erythrocyte homoaggregation (rouleaux formation): temperature-dependent entropic liberation of water from cells and macromolecules","authors":"Donald R. Forsdyke","doi":"10.1016/j.biosystems.2025.105504","DOIUrl":"10.1016/j.biosystems.2025.105504","url":null,"abstract":"<div><div>In the pre-antibiotic era, infections were usually more frequent and serious than today. Robin Fåhraeus (1888–1958) examined the erythrocyte sedimentation rate (ESR) test for infections, which was normally carried out in vitro with freshly drawn blood. His extensive studies on the mechanism and physiological significance of the enhanced sedimentation of erythrocyte aggregates (rouleaux) in disease included in vivo simulation. This led him to propose an explanation for the finding of long white strips (“fibrin coagula”) within the blood vessels of those who had died from infections. The surge of serious infections in pandemic times has likely kindled a reemergence. He further speculated that (i) the weak aggregation of red blood cells (RBCs) followed the liberation of water molecules from their surfaces, and (ii) the importance of their aggregation, which was induced by changes in serum proteins (not necessarily antibodies), extended beyond the clinic. In modern times these changes have led to immunologically significant entropic interpretations of infection-associated aggregations, whether cellular (e.g., RBC) or molecular (i.e., macromolecular polymerizations). Thus, rouleaux formation displays a process at the cellular level that can proceed in parallel at a less visible macromolecular level. It has been proposed that, when intracellular, aggregations would discriminate between self and not-self proteins in the crowded cytosol. Favoured by an associated pyrexia, this could lead, by mechanisms to be determined, to the preferential loading of peptides from proteins deemed “foreign” for presentation as major histocompatibility complexes (MHCs) to specific clones of immune cells.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105504"},"PeriodicalIF":2.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166201","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 Bayesian approach to investigating presumed retinal micro(nano)plastics","authors":"Tan Aik Kah","doi":"10.1016/j.biosystems.2025.105502","DOIUrl":"10.1016/j.biosystems.2025.105502","url":null,"abstract":"<div><div>The human retina, a highly vascularized, metabolically active, and immunologically privileged neural tissue, stands in contrast to the ubiquity of micro(nano)plastics (MNPs), which have been reported in every other organ system. Despite this, the presence of MNPs in the retina remains undocumented, a critical gap given their potential to contribute to local inflammation, microvascular occlusion, or act as cofactors in diseases such as diabetic retinopathy, age-related macular degeneration, or uveitis. Furthermore, the diverse physicochemical properties of MNPs – including their varying sizes, shapes, colors, and optical characteristics – raise the intriguing possibility that their presence within the retina could mimic commonly observed ophthalmic features. I hypothesize that certain features—previously attributed to other causes—such as tiny discrete foci in fundus photography and hyperreflective retinal foci in optical coherence tomography, may actually contain MNPs. This hypothesis carries significant biological implications not only for ophthalmology but also for environmental toxicology and public health. To formally evaluate its plausibility, I constructed a Bayesian model incorporating initial skepticism and considering varying likelihoods of observed evidence under both null and alternative assumptions. The model demonstrates that even with an extremely low prior probability, the reproducibility and discernible patterns of certain imaging findings can justify a significantly increased posterior belief, thus warranting further scientific inquiry. This work offers a probabilistic framework to re-evaluate retinal anomalies and encourages empirical investigation in environmental ophthalmology, without definitively proving MNP presence. The development of retinal imaging techniques for the specific detection of MNPs could provide a valuable tool for environmental toxicology, preventive medicine, and public health by offering a non-invasive biomarker for systemic MNPs exposure.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"253 ","pages":"Article 105502"},"PeriodicalIF":2.0,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155181","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}