Biosystems最新文献

{"title":"Impacts of emergent structural topologies on the stability of an adaptive plant-animal network","authors":"Min Su,&nbsp;Zhongyi Wang,&nbsp;Qi Ma","doi":"10.1016/j.biosystems.2025.105522","DOIUrl":"10.1016/j.biosystems.2025.105522","url":null,"abstract":"<div><div>Plant species, interacting with both pollinators and herbivores, form a 3-guild ecological network that encompasses mutualistic and antagonistic subnetworks. These plant-animal interactions typically evolve through adaptive interaction switching, which tends to promote species abundance. In this study, we constructed an adaptive plant-animal network and explored how interaction rewiring among species from different guilds influences the structure and stability of this 3-guild network. Our findings reveal that interaction rewiring dynamically reshapes network architecture, with plant degree centrality correlations between mutualistic and antagonistic subnetworks emerging as a critical determinant of community stability. Notably, extreme centrality correlations, driven by interaction switching, can undermine network stability. In contrast, moderate correlations enhance resilience, rendering optimized networks more robust than their randomly assigned counterparts. These results underscore the importance of interaction switching in shaping the structure and stability of 3-guild ecological networks. Moreover, these findings provide mechanistic evidence that plant generalism fundamentally influences resilience in optimized networks, mediated through the evolutionary trade-off between herbivore defense and pollinator attraction.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105522"},"PeriodicalIF":2.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144331084","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":"Roland Cazalis","doi":"10.1016/j.biosystems.2025.105521","DOIUrl":"10.1016/j.biosystems.2025.105521","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105521"},"PeriodicalIF":2.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144331085","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":"Animal and human behavior to maximize energy income and to minimize its expenditure","authors":"Alexander V. Sirotkin","doi":"10.1016/j.biosystems.2025.105523","DOIUrl":"10.1016/j.biosystems.2025.105523","url":null,"abstract":"<div><div>The viability and competitiveness of any living organism depend on its ability (1) to get the maximum of energy/resources and (2) to save maximum of obtained energy and to reduce its expenditure. Behavioral traits to achieve these goals listed above include different forms of territorial and social behavior, overconsumption of resources, temporal suppression of energy-demanding activity, as well as some kinds of individual protective behavior towards minimization of energy expenditure for manual and intellectual labor. In addition to these measures, in modern humans the increase in energy consumption: energy expenditure rate can be achieved not only by cooperation in increase of the efficiency of biological processes, but also in the application of instruments. The technical progress aims to unleash the people from energy-demanding labor, to get as much energy for covering their biological needs by investment of minimum of their own bioenergy. The present interdisciplinary approach enables a better understanding of the behavioral strategies to maximize efficiency of energy metabolism and their good and bad consequences for individuals and the society as a whole.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105523"},"PeriodicalIF":2.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144331083","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 never-ending prediction: meta-prediction, counter-oscillatory system and traumatic affordance","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2025.105508","DOIUrl":"10.1016/j.biosystems.2025.105508","url":null,"abstract":"<div><div>This article comes back on the hypothesis developed by the evolutionary theory of the sensorimotor paradox that our capacity to produce mental representation could be derived from a dissociation of sensory prediction systems from motor action. As they should be then coordinated together, we are drawing further possible leads regarding the intermediary space between linear mental projections that are not bound and stopped by sensory feedback, and ongoing sensory perception whether large or discrete. Dissociated prediction would be eventually interrupted by sensory input, getting lost, reinitiated and derived onto another prediction. In that sense, we connect this inspection with studies on attentional capture and the interference caused by sensory perception of cyclical and discrete body events such as breathing, blinking and swallowing. A global state of balance and expectation to dissociative activity, called meta-prediction, could compensate on the other hand for the lack of sensory feedback. As a representational infrastructure, its model is to be detailled, as would be the role of a system's avoidance of memories of pain, defined here by the concept of traumatic affordance, or the stabilising role of gravity. If the stochastic approach of this hypothesis is yet mostly speculative, interrogating mental imagery and language's structure, this article suggests several ways of testing the theory based on upcoming EEG recordings.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105508"},"PeriodicalIF":2.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144312898","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 repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation","authors":"Raúl Arias-Carrasco ,&nbsp;Victor Aliaga-Tobar ,&nbsp;Sebastian Abades ,&nbsp;Vinicius Maracaja-Coutinho","doi":"10.1016/j.biosystems.2025.105519","DOIUrl":"10.1016/j.biosystems.2025.105519","url":null,"abstract":"<div><div>Noncoding RNAs (ncRNAs) play a crucial role in the fine-tuning regulation of cells in all domains of life. In archaea, ncRNAs remain poorly studied, with only a few ncRNA classes well characterised. Archaea are renowned for their ability to survive in harsh environments, though they have been discovered in a variety of other habitats as well. We have determined the ncRNA candidate repertoire across 270 archaeal genomes using secondary structure inferences and sequence similarity searches. Here, 33 non-coding RNA classes were identified in these genomes. The correlation between all ncRNA classes and optimal growth temperature (OGT) was R² 0.65. Phylogenetic analysis based on multiple alignments of a set of highly conserved proteins revealed preferences for ncRNA classes at the phylum and genus levels. All of the ncRNA data generated by this study reveals a correlation between the genomic abundance of specific ncRNA classes and the optimal growth temperature, especially for the sRNA C/D box type. All the genomic and ncRNA archaeal data generated is a valuable resource that will stimulate experimentalists to investigate whether or not their predicted ncRNAs are correct and biologically meaningful, boosting further associative studies using the unique features of this domain.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105519"},"PeriodicalIF":2.0,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271659","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":"From code to archetype: Toward a unified theory of biological, neural, and artificial artifacts","authors":"João Carlos Major","doi":"10.1016/j.biosystems.2025.105516","DOIUrl":"10.1016/j.biosystems.2025.105516","url":null,"abstract":"<div><div>Carl Jung's concept of archetypes as innate, universal structures of the human psyche finds surprising resonance with contemporary theories in Code Biology, neuroscience, and artificial intelligence. Archetypes, far from being metaphysical abstractions, can be reframed as codified artifacts of the mind, shaped by phylogenetic inheritance, stabilized by neural coding, and expressed through cognitive and cultural configurations.</div><div>Marcello Barbieri's Code Biology demonstrates that life is driven not only by biochemical causality but also by natural conventions — systems of natural correspondence that create functional structures, or bio-artifacts, through processes of translation carried out by molecular mediators. Similarly, research in neuroscience identifies neural codes as dynamic patterns of brain activity that organize perception, emotion, and cognition.</div><div>Building on this, this paper advances the hypothesis that archetypes operate as neurofunctional artifacts — internal configurations that stabilize recurring experiences across individuals and cultures, leading to expressive forms such as myths, dreams, and emotional constellations that shape human meaning-making. These artifacts are not limited to biology or psyche alone; they now appear in the digital realm. The rise of generative AI systems, such as large language models (LLMs), introduces a new category of algorithmic artifacts that replicate archetypes. These systems simulate meaning without subjective intentionality.</div><div>This interdisciplinary framework brings together biology, psychology, and AI under a unified theory of codified form. Archetypes, in this perspective, are artifacts instantiated by lower-level codes that serve as mediators in higher-level interpretative processes — acting as a bridge between gene and glyph, neuron and narrative, matter and symbol … and silicon.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105516"},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276532","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":"Metschnikowia bicuspidata in aquaculture: Pathogenesis, characteristics, and biocontrol approaches","authors":"Vinh Hong Thinh Le ,&nbsp;Baoying Lu ,&nbsp;Yunxia Hu,&nbsp;Qinghua Wang","doi":"10.1016/j.biosystems.2025.105518","DOIUrl":"10.1016/j.biosystems.2025.105518","url":null,"abstract":"<div><div><em>Metschnikowia bicuspidata</em>, a pathogenic yeast species, is responsible for significant disease outbreaks, including the devastating milky disease in aquaculture systems. This review consolidates current knowledge of its pathogenesis, genomic characteristics, histopathology, and treatments. The yeast's psychrotolerant nature and ability to exploit aquatic hosts even under adverse conditions have heightened its impact, particularly in high-density farming environments. Potential treatments, such as antibiotics, killer toxins, and Massoia lactone, show promising antifungal activity, yet each presents challenges regarding environmental impact, resistance development, and application efficiency. Advancements in genomic research and innovative biocontrol methods, including nanotechnology-enhanced delivery systems, provide new opportunities for disease management. This review emphasizes the urgent need for effective and eco-friendly strategies to combat <em>M. bicuspidata</em> in aquaculture while identifying critical areas for future investigation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"254 ","pages":"Article 105518"},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276534","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":"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}