Biosystems最新文献

{"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":"244 ","pages":"Article 105297"},"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":"244 ","pages":"Article 105310"},"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":"245 ","pages":"Article 105298"},"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":"244 ","pages":"Article 105308"},"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":"245 ","pages":"Article 105296"},"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":"244 ","pages":"Article 105285"},"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}

{"title":"Evolutionary stability of developmental commitment","authors":"Yuka Shirokawa","doi":"10.1016/j.biosystems.2024.105309","DOIUrl":"10.1016/j.biosystems.2024.105309","url":null,"abstract":"<div><p>Evolution of unicellular to multicellular organisms must resolve conflicts in reproductive interests between individual cells and the group. The social amoeba <em>Dictyostelium discoideum</em> is a soil-living eukaryote with facultative sociality. While cells grow in the presence of nutrients, cells aggregate under starvation to form fruiting bodies containing spores and altruistic stalk cells. Once cells socially committed, they complete formation of fruiting bodies, even if a new source of nutrients becomes available. The persistence of this social commitment raises questions as it inhibits individual cells from swiftly returning to solitary growth. I hypothesize that traits enabling premature de-commitment are hindered from being selected. Recent work has revealed outcomes of the premature de-commitment through forced refeeding; The de-committed cells take an altruistic prestalk-like position due to their reduced cohesiveness through interactions with socially committed cells. I constructed an evolutionary model assuming their division of labor. The results revealed a valley in the fitness landscape that prevented invasion of de-committing mutants, indicating evolutionary stability of the social commitment. The findings provide a general scheme that maintains multicellularity by evolving a specific division of labor, in which less cohesive individuals become altruists.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105309"},"PeriodicalIF":2.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996893","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":"Evolutionary dynamics of cooperation coupled with ecological feedback compensation","authors":"Zi-Xuan Guo ,&nbsp;Tian-Jiao Feng ,&nbsp;Yi Tao ,&nbsp;Rui-Wu Wang ,&nbsp;Xiu-Deng Zheng","doi":"10.1016/j.biosystems.2024.105282","DOIUrl":"10.1016/j.biosystems.2024.105282","url":null,"abstract":"<div><p>A simple theoretical model (or a demonstrative example) was developed to illustrate how the evolution of cooperation can be affected by the density-dependent survival competition, in which we assume that the fertility of an individual depends only on the pairwise interaction between him and other individuals based on Prisoner’s Dilemma game, while its viability is only related to the density-dependent survival competitiveness. Our results show that not only cooperation could be evolutionarily stable if the advantage of cooperators in viability can compensate for the cost they pay for their fertility, but also the long-term stable coexistence of cooperation and defection is possible if none of cooperation and defection is evolutionarily stable. Moreover, for the stochastic evolutionary dynamics in a finite population, our analysis shows that the increase (or decrease) of the survival competitiveness of cooperators (or defectors) should be conductive to the evolutionary emergence of cooperation.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105282"},"PeriodicalIF":2.0,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989441","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 evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain","authors":"Miklós Péter Kalapos ,&nbsp;Lidia de Bari","doi":"10.1016/j.biosystems.2024.105288","DOIUrl":"10.1016/j.biosystems.2024.105288","url":null,"abstract":"<div><p>This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105288"},"PeriodicalIF":2.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917987","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 polyphyletic origins of glycyl-tRNA synthetase and lysyl-tRNA synthetase and their implications","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105287","DOIUrl":"10.1016/j.biosystems.2024.105287","url":null,"abstract":"<div><p>I analyzed the polyphyletic origin of glycyl-tRNA synthetase (GlyRS) and lysyl-tRNA synthetase (LysRS), making plausible the following implications. The fact that the genetic code needed to evolve aminoacyl-tRNA synthetases (ARSs) only very late would be in perfect agreement with a late origin, in the main phyletic lineages, of both GlyRS and LysRS. Indeed, as suggested by the coevolution theory, since the genetic code was structured by biosynthetic relationships between amino acids and as these occurred on tRNA-like molecules which were evidently already loaded with amino acids during its structuring, this made possible a late origin of ARSs. All this corroborates the coevolution theory of the origin of the genetic code to the detriment of theories which would instead predict an early intervention of the action of ARSs in organizing the genetic code. Furthermore, the assembly of the GlyRS and LysRS protein domains in main phyletic lineages is itself at least evidence of the possibility that ancestral genes were assembled using pieces of genetic material that coded these protein domains. This is in accordance with the exon theory of genes which postulates that ancestral exons coded for protein domains or modules that were assembled to form the first genes. This theory is exemplified precisely in the evolution of both GlyRS and LysRS which occurred through the assembly of protein domains in the main phyletic lineages, as analyzed here. Furthermore, this late assembly of protein domains of these proteins into the two main phyletic lineages, i.e. a polyphyletic origin of both GlyRS and LysRS, appears to corroborate the progenote evolutionary stage for both LUCA and at least the first part of the evolutionary stages of the ancestor of bacteria and that of archaea. Indeed, this polyphyletic origin would imply that the genetic code was still evolving because at least two ARSs, i.e. proteins that make the genetic code possible today, were still evolving. This would imply that the evolutionary stages involved were characterized not by cells but by protocells, that is, by progenotes because this is precisely the definition of a progenote. This conclusion would be strengthened by the observation that both GlyRS and LysRS originating in the phyletic lineages leading to bacteria and archaea, would demonstrate that, more generally, proteins were most likely still in rapid and progressive evolution. Namely, a polyphyletic origin of proteins which would qualify at least the initial phase of the evolutionary stage of the ancestor of bacteria and that of archaea as stages belonging to the progenote.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"244 ","pages":"Article 105287"},"PeriodicalIF":2.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914468","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}