Biosystems最新文献

{"title":"On the possibility of implementing a quantum entanglement distribution in a biosystem: Microtubules","authors":"Sergey E. Shirmovsky","doi":"10.1016/j.biosystems.2024.105320","DOIUrl":"10.1016/j.biosystems.2024.105320","url":null,"abstract":"<div><p>The paper considers the possibility of implementing a quantum entanglement distribution in the cell microtubule. It has been shown that a quantum entanglement distribution proposed in the paper determines the process of quantum state teleportation through microtubule tryptophan chain. The work shows that the system of tryptophans in a microtubule essentially is a quantum network that consists of: spatially spaced nodes — tryptophans, quantum communication channels connecting tryptophans and qubits transmitted through these communication channels. The connection between the process of quantum teleportation in living nature and its classical analogue is discussed. The quantum protocol established in the work determines the possible principle of quantum information transmission in biosystems and also in the similar nanostructures.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094660","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":"Advanced technologies and mathematical metacognition: The present and future orientation","authors":"Alexios Kouzalis ,&nbsp;Antonios Antoniou ,&nbsp;Nicos Rossides ,&nbsp;Rita Panaoura ,&nbsp;Priyanka Yadav","doi":"10.1016/j.biosystems.2024.105312","DOIUrl":"10.1016/j.biosystems.2024.105312","url":null,"abstract":"<div><p>The intersection of mathematical cognition, metacognition, and advanced technologies presents a frontier with profound implications for human learning and artificial intelligence. This paper traces the historical roots of these concepts from the Pythagoreans and Aristotle to modern cognitive science and explores their relevance to contemporary technological applications. We examine how the Pythagoreans' view of mathematics as fundamental to understanding the universe and Aristotle's contributions to logic and categorization have shaped our current understanding of mathematical cognition and metacognition. The paper investigates the role of Boolean logic in computational processes and its relationship to human logical reasoning, as well as the significance of Bayesian inference and fuzzy logic in modelling uncertainty in human cognition and decision-making. We also explore the emerging field of Chemical Artificial Intelligence and its potential applications. We argue for unifying mathematical metacognition with advanced technologies, including artificial intelligence and robotics, while identifying the multifaceted benefits and challenges of such unification. The present paper examines essential research directions for integrating cognitive sciences and advanced technologies, discussing applications in education, healthcare, and business management. We provide suggestions for developing cognitive robots using specific cognitive tasks and explore the ethical implications of these advancements. Our analysis underscores the need for interdisciplinary collaboration to realize the full potential of this integration while mitigating potential risks.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057199","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 “An efficient approach for identifying important biomarkers for biomedical diagnosis” [Biosystems 237 (2024) 105163]","authors":"Jing-Wen Huang ,&nbsp;Yan-Hong Chen ,&nbsp;Frederick Kin Hing Phoa ,&nbsp;Yan-Han Lin ,&nbsp;Shau-Ping Lin","doi":"10.1016/j.biosystems.2024.105286","DOIUrl":"10.1016/j.biosystems.2024.105286","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001710/pdfft?md5=99936dead43c78edec8d85e4c0f80013&pid=1-s2.0-S0303264724001710-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019472","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":"Why does a cell function? New arguments in favor of quantum effects","authors":"A.V. Melkikh","doi":"10.1016/j.biosystems.2024.105311","DOIUrl":"10.1016/j.biosystems.2024.105311","url":null,"abstract":"<div><p>In this study, the complexities of intracellular processes have been analyzed, including DNA folding, alternative splicing, mitochondrial function, and enzyme transport in lysosomes. Based on a previously proposed hypothesis (Levinthal's generalized paradox), a conclusion is made that all abovementioned processes cannot be realized with sufficient accuracy and in a realistic timeframe within the framework of classical physics. It is unclear why the cell functions at all. For the cell to function, its internal environment must be highly structured. In this regard, the cell shares similarities with computational devices (computers). In this study, quantum models of interactions between biologically important molecules were constructed, taking into account the long-range effects. One significant aspect of these models is the special role of the phase of the wavefunction, which serves as a controlling parameter. Experiments have been proposed that may confirm or refute these models.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037641","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":"Comparing the complexity of written and molecular symbolic systems","authors":"Julia Esposito ,&nbsp;Jyotika Kakar ,&nbsp;Tasneem Khokhar ,&nbsp;Tiana Noll-Walker ,&nbsp;Fatima Omar ,&nbsp;Anna Christen ,&nbsp;H. James Cleaves II ,&nbsp;McCullen Sandora","doi":"10.1016/j.biosystems.2024.105297","DOIUrl":"10.1016/j.biosystems.2024.105297","url":null,"abstract":"<div><p>Symbolic systems (SSs) are uniquely products of living systems, such that symbolism and life may be inextricably intertwined phenomena. Within a given SS, there is a range of symbol complexity over which signaling is functionally optimized. This range exists relative to a complex and potentially infinitely large background of latent, unused symbol space. Understanding how symbol sets sample this latent space is relevant to diverse fields including biochemistry and linguistics.</p><p>We quantitatively explored the graphic complexity of two biosemiotic systems: genetically encoded amino acids (GEAAs) and written language. Molecular and graphical notions of complexity are highly correlated for GEAAs and written language. Symbol sets are generally neither minimally nor maximally complex relative to their latent spaces, but exist across an objectively definable distribution, with the GEAAs having especially low complexity. The selection pressures guiding these disparate systems are explicable by symbol production and disambiguation efficiency. These selection pressures may be universal, offer a quantifiable metric for comparison, and suggest that all life in the Universe may discover optimal symbol set complexity distributions with respect to their latent spaces. If so, the “complexity” of individual components of SSs may not be as strong a biomarker as symbol set complexity distribution.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001261","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":"Developmental noise, entropy, and biological system condition","authors":"Vladimir M. Zakharov,&nbsp;Ilya E. Trofimov","doi":"10.1016/j.biosystems.2024.105310","DOIUrl":"10.1016/j.biosystems.2024.105310","url":null,"abstract":"<div><p>Developmental noise is considered as a permissible level of entropy, as a compromise between the cost and needed precision of the realization of genetic information. In terms of entropy, noise is a measure of acceptable level of disorder to ensure a reliable system operation. Developmental noise plays a role in the observed phenotypic diversity and is associated with other indicators of the biological system condition. The thermodynamic characteristic of entropy by the energy metabolism also turns out to be related to the developmental noise. Phenotypic variability is largely determined by developmental homeostasis, including both canalization (an ability to form a similar phenotype under different conditions) and developmental stability (a capability for perfect development measured by noise level). It is shown that the change in the noise level, as an expression of the certain entropy level, unlike other forms of phenotypic variability, is a reflection of a change in the system condition. Although the entropy indices of ontogeny and community under certain conditions can change simultaneously, the entropy index at the level of developmental noise proves to be a more unambiguous and universal measure of the disorder of a biological system, compared to biodiversity indices at the community level.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001262","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":"Micro-electrode array recording of extracellular electrical potentials of liquid static surface fermented Hericium erinaceus","authors":"Davin Browner,&nbsp;Andrew Adamatzky","doi":"10.1016/j.biosystems.2024.105298","DOIUrl":"10.1016/j.biosystems.2024.105298","url":null,"abstract":"<div><p><em>Hericium erinaceus</em> is a basidiomycetes fungus with previously uncharacterised extracellular electrophysiology. Here, we present results of recordings of the electrical potentials of fungal biofilms of this species using microelectrode arrays (MEAs). In particular, we focused on modelling the temporal and spatial progression of the low frequency (<span><math><mo>≤</mo></math></span> 1 Hz) potentials. Culture media control studies showed that the electrical potential activity results from the growth and subsequent spiking behaviours of the mycelium extracellular matrices. An antifungal assay using nystatin suspension, 10,000 unit/mL in DPBS, provided evidence for the biological origin of electrical potentials due to targeting of the selective permeability of the cell membrane and subsequent cessation of electrical activity. Conversely, injection of L-glutamic acid increased the combined multi-channel mean firing rate from 0.04 Hz to 0.1 Hz. Analysis of bursting and spatial propagation of the extracellular signals are also presented.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001837/pdfft?md5=2dbd9b09c85e85104e02db231527f890&pid=1-s2.0-S0303264724001837-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005742","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":"Circular code identified by the codon usage","authors":"Christian J. Michel","doi":"10.1016/j.biosystems.2024.105308","DOIUrl":"10.1016/j.biosystems.2024.105308","url":null,"abstract":"<div><p>Since 1996, circular codes in genes have been identified thanks to the development of 6 statistical approaches: trinucleotide frequencies per frame (Arquès and Michel, 1996), correlation functions per frame (Arquès and Michel, 1997), frame permuted trinucleotide frequencies (Frey and Michel, 2003, 2006), advanced statistical functions at the gene population level (Michel, 2015) and at the gene level (Michel, 2017). All these 3-frame statistical methods analyse the trinucleotide information in the 3 frames of genes: the reading frame and the 2 shifted frames. Notably, codon usage does not allow for the identification of circular codes (Michel, 2020). This has been a long-standing problem since 1996, hindering biologists’ access to circular code theory.</p><p>By considering circular code conditions resulting from code theory, particularly the concept of permutation class, and building upon previous statistical work, a new statistical approach based solely on the codon usage, i.e. a 1-frame statistical method, surprisingly reveals the maximal <span><math><msup><mrow><mi>C</mi></mrow><mrow><mn>3</mn></mrow></msup></math></span> self-complementary trinucleotide circular code <span><math><mi>X</mi></math></span> in bacterial genes and in average (bacterial, archaeal, eukaryotic) genes, and almost in archaeal genes. Additionally, a new parameter definition indicates that bacterial and archaeal genes exhibit codon usage dispersion of the same order of magnitude, but significantly higher than that observed in eukaryotic genes. This statistical finding may explain the greater variability of codes in eukaryotic genes compared to bacterial and archaeal genes, an issue that has been open for many years. Finally, biologists can now search for new (variant) circular codes at both the genome level (across all genes in a given genome) and the gene level using only codon usage, without the need for analysing the shifted frames.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005741","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 exploration of ecoacoustics and its applications in conservation ecology","authors":"A. Farina ,&nbsp;B. Krause ,&nbsp;T.C. Mullet","doi":"10.1016/j.biosystems.2024.105296","DOIUrl":"10.1016/j.biosystems.2024.105296","url":null,"abstract":"<div><p>Our planet is facing unprecedented adversity due to the global impacts of climate change and an emerging sixth mass extinction. These impacts are exacerbated by population and industrial growth, where increased resource extraction is required to meet our insatiable demands. Yet, the tangible elements of our lone inhabited planet in the solar system are not the only things disappearing or being modified. The sounds of Earth are being altered in ways that may never be recovered. Indeed, we occupy a noisier world in this age of machines that comes at a great expense in the form of sonic extinctions. It is profoundly apparent, yet not widely recognized, that conservation efforts must consider the importance of the sonic environment (i.e., sonosphere). Although sound has been integral to life for millions of years, our understanding of its ecological role has only just begun. Sounds are one of the most important extensions of the organismic inner world, becoming testimonials of environmental complexity, integration, and relationships between apparently separated parts. From a semiotic perspective, sounds are signals utilized by many organisms to save energy in patrolling, defending, exploring, and navigating their surroundings. Sounds are tools that establish dynamic biological and ecological competencies through refined partitioning in the natural selection process of evolution. Ecoacoustics is a recent scientific discipline that aims to investigate the role of sound in ecological processes. Despite its youth, Ecoacoustics has had rapid theoretical and applied growth, consolidating a diverse array of research on the ecology of sounds across many disciplines. Here, we present how Ecoacoustics plays a significant role in conservation ecology by exploring the discipline's theoretical framework, new descriptors of sonic complexity, and innovative methods for supporting conservation efforts from singular species to entire landscapes across local and global scales. The combination of automated recording units and ecoacoustic indices present a very promising approach to the study of remote areas, rare species, and data rich analyses. While Ecoacoustics scientists continue to explore this new scientific horizon, we encourage others to consider Ecoacoustics in their conservation agendas because of its application to the study and management of terrestrial, marine, and freshwater habitats.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996880","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 innate story code","authors":"Erik Goodwyn","doi":"10.1016/j.biosystems.2024.105285","DOIUrl":"10.1016/j.biosystems.2024.105285","url":null,"abstract":"<div><p>Code biology reveals a great many codes beyond the genetic code as integral to biological functioning. Recent scholars have linked the growing field of code biology to analytical psychology, confirming that the encoded information inherited by the human organism is indeed massive and capable of great sophistication. In this discussion, I will expand on this project by showing how developments in embodied cognition reveal a code that links the world of universal emotional responses to common experiences to the world of embodied visuospatial narratives--i.e., the “archetypes” of analytical psychology. Viewed in this manner, archetypes become spontaneous symbolic narratives that symbolize universal emotional responses to typical human environments. Such symbolic narratives aim toward adaptation, and use a universal code that maps such situations to visuospatial narratives, with the adaptor being the human body itself.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917988","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}