Biosystems最新文献

{"title":"Theories of the origin of the genetic code: Strong corroboration for the coevolution theory","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105217","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105217","url":null,"abstract":"<div><p>I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140647576","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":"Unsolved morphogenesis problems and the hidden order","authors":"A.V. Melkikh","doi":"10.1016/j.biosystems.2024.105218","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105218","url":null,"abstract":"<div><p>In this work, the morphogenesis mechanisms are considered from the complexity perspective. It is shown that both morphogenesis and the functioning of organs should be unstable in the case of short-range interaction potentials. The repeatability of forms during evolution is a strong argument for its directionality. The formation of organs during evolution can occur only in the presence of a priori information about the structure of such an organ. The focus of the discussion is not merely on constraining potential possibilities but on the concept of directed evolution itself. A morphogenesis model was constructed based on nontrivial quantum effects. These interaction effects between biologically important molecules ensure the accurate synthesis of cells, tissues, and organs.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140643651","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 emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890–1938) in English translation","authors":"Miklós Müller ,&nbsp;Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2024.105201","DOIUrl":"10.1016/j.biosystems.2024.105201","url":null,"abstract":"<div><p>Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His 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. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper “The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it” published in Naturwissenschaften (1920) and the excerpts from his magnum opus “Theoretical Biology” (1935). These works became a bibliographical rarity. A complete English translation of “Theoretical Biology” is an important task for the future.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724000868/pdfft?md5=ce464ab908e51009e23d0f13e4d325c0&pid=1-s2.0-S0303264724000868-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864014","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":"Bio-analog dissipative structures and principles of biological behavior","authors":"Benjamin De Bari ,&nbsp;Dilip K. Kondepudi ,&nbsp;Ashwin Vaidya ,&nbsp;James A. Dixon","doi":"10.1016/j.biosystems.2024.105214","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105214","url":null,"abstract":"<div><p>The place of living organisms in the natural world is a nearly perennial question in philosophy and the sciences; how can inanimate matter yield animate beings? A dominant answer for several centuries has been to treat organisms as sophisticated machines, studying them with the mechanistic physics and chemistry that have given rise to technology and complex machines. Since the early 20th century, many scholars have sought instead to naturalize biology through thermodynamics, recognizing the precarious far-from-equilibrium state of organisms. Erwin Bauer was an early progenitor of this perspective with ambitions of “general laws for the movement of living matter”. In addition to taking a thermodynamic perspective, Bauer recognized that organisms are fundamentally <em>behaving</em> systems, and that explaining the physics of life requires explaining the origins of intentionality, adaptability, and self-regulation. Bauer, like some later scholars, seems to advocate for a “new physics”, one that extends beyond mechanics and classical thermodynamic, one that would be inclusive of living systems. In this historical review piece, we explore some of Bauer's ideas and explain how similar concepts have been explored in modern non-equilibrium thermodynamics and dissipative structure theory. Non-living dissipative structures display end-directedness, self-maintenance, and adaptability analogous to organisms. These findings also point to an alternative framework for the life sciences, that treats organisms not as machines but as sophisticated dissipative structures. We evaluate the differences between mechanistic and thermodynamic perspectives on life, and what each theory entails for understanding the behavior of organisms.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140621783","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 Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA","authors":"Christos A. Ouzounis","doi":"10.1016/j.biosystems.2024.105199","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105199","url":null,"abstract":"<div><p>Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140641376","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":"Circular code in introns","authors":"Christian J. Michel","doi":"10.1016/j.biosystems.2024.105215","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105215","url":null,"abstract":"<div><p>A massive statistical analysis based on the autocorrelation function of the circular code <span><math><mi>X</mi></math></span> observed in genes is performed on the (eukaryotic) introns. Surprisingly, a circular code periodicity 0 modulo 3 is identified in 5 groups of introns: birds, ascomycetes, basidiomycetes, green algae and land plants. This circular code periodicity, which is a property of retrieving the reading frame in (protein coding) genes, may suggest that these introns have a coding property. In a well-known way, a periodicity 1 modulo 2 is observed in 6 groups of introns: amphibians, fishes, mammals, other animals, reptiles and apicomplexans. A mixed periodicity modulo 2 and 3 is found in the introns of insects. Astonishing, a subperiodicity 3 modulo 6 is a common statistical property in these 3 classes of introns. When the particular trinucleotides <span><math><mrow><msub><mrow><mi>N</mi></mrow><mrow><mn>1</mn></mrow></msub><msub><mrow><mi>N</mi></mrow><mrow><mn>2</mn></mrow></msub><msub><mrow><mi>N</mi></mrow><mrow><mn>1</mn></mrow></msub></mrow></math></span> of the circular code <span><math><mi>X</mi></math></span> are not considered, the circular code periodicity 0 modulo 3, hidden by the periodicity 1 modulo 2, is now retrieved in 5 groups of introns: amphibians, fishes, other animals, reptiles and insects. Thus, 10 groups of introns, taxonomically different, out of 12 have a coding property related to the reading frame retrieval. The trinucleotides <span><math><mrow><msub><mrow><mi>N</mi></mrow><mrow><mn>1</mn></mrow></msub><msub><mrow><mi>N</mi></mrow><mrow><mn>2</mn></mrow></msub><msub><mrow><mi>N</mi></mrow><mrow><mn>1</mn></mrow></msub></mrow></math></span> are analysed in the 216 maximal <span><math><msup><mrow><mi>C</mi></mrow><mrow><mn>3</mn></mrow></msup></math></span> self-complementary trinucleotide circular codes. A hexanucleotide code (words of 6 letters) is proposed to explain the periodicity 3 modulo 6. It could be a trace of more general circular codes at the origin of the circular code <span><math><mi>X</mi></math></span>.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140621782","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 history of Ervin Bauer's publications on the theory of life","authors":"Miklós Müller ,&nbsp;Gábor Elek","doi":"10.1016/j.biosystems.2024.105212","DOIUrl":"10.1016/j.biosystems.2024.105212","url":null,"abstract":"<div><p>Ervin Bauer (1890–1938) made historical contributions to contemporary biology, provided a new definition of life, defined the contents of theoretical biology. He worked in different countries, perturbed by deep historical events. These historical events necessarily impacted his fate and finally led to the violent loss of his life and the life of his wife. His work and with it his theory of life had a no less complicated history than the history of his personal life. Bauer's main work “Theoretical Biology” was published in 1935 in Russian. The author and his wife Stefánia became victims of the Great Purge. They were executed in 1938, all their publications were banned and most copies of “Theoretical Biology” destroyed. Ervin and Stefánia Bauer were rehabilitated in 1956 but renewed publication of Bauer's works was delayed. The first reprint edition of “Theoretical Biology” of 1967 was not in Russian, but was a translation into Hungarian, the native language of Bauer. The first Russian reprint of “Theoretical Biology”, in which the original Russian chapters are followed by short English summaries, was published in Hungary in 1982. This edition was prepared by Hungarian and Russian scientists. The best-known Russian edition of “Theoretical Biology” was published in 2002 in St. Petersburg. A complete English translation of Bauer's main work “Theoretical Biology” is still outstanding.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140856644","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 cluster model of energy transduction in biological systems","authors":"John Grant Watterson","doi":"10.1016/j.biosystems.2024.105213","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105213","url":null,"abstract":"<div><p>The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels – some upwards, to larger assemblies, others downwards into energy rich molecules – before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units – the protein domains – rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called “Newton's cradle” provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724000984/pdfft?md5=7ada24f35a7a9e3cdb318a9aa5d09983&pid=1-s2.0-S0303264724000984-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140843333","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":"Fractional nutrient uptake model of plant roots","authors":"Yue Wang ,&nbsp;Mingfang Lin ,&nbsp;Quanbiao Gong ,&nbsp;Zhonghui Ou","doi":"10.1016/j.biosystems.2024.105210","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105210","url":null,"abstract":"<div><p>Most nutrient uptake problems are modeled by the convection–diffusion equation (CDE) abiding by Fick’s law. Because nutrients needed by plants exist in the soil solution as a form of ions and the soil is a typical fractal structure of heterogeneity, it makes the solute transport appear anomalous diffusion in soil. Taking anomalous diffusion as a transport process, we propose time and space fractional nutrient uptake models based on the classic Nye–Tinker–Barber model. There does not appear apparent sub-diffusion of nitrate in the time fractional model until four months and the time fractional models are appropriate for describing long-term dynamics and slow sorption reaction; the space fractional model can capture super-diffusion in short term and it is suitable for describing nonlocal phenomena and daily variations driven by transpiration and metabolism; the anomalous diffusion more apparently appears near the root surface in the modeling simulation.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140540138","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":"Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation","authors":"Fabio Vittorio De Blasio ,&nbsp;Birgitte Freiesleben De Blasio","doi":"10.1016/j.biosystems.2024.105198","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105198","url":null,"abstract":"<div><p>The coexistence of cladogenesis, i.e., the branching of lineages along an evolutionary tree as observed in the fossil record, and anagenesis, which is the progressive evolution within populations, lacks a clear explanation. In this study, we examine a simple model that simulates the evolutionary changes occurring within populations inhabiting the same environment in sympatry, and driven by ecological competition. Our model characterizes populations through a set of evolving morphological traits represented by mathematical points within a two-dimensional morphospace. Such points may reproduce or die due to overcrowding, implying competition in morphospace as suggested by the ecological phenomenon of character displacement. By focusing on the morphospace rather than physical space, the model effectively captures the simultaneous evolution of coexisting populations.</p><p>Central to the model is the delicate balance between the range of competition and the range of reproduction within the morphospace. Interesting patterns emerge when the ratio between the competition to reproducetion ranges, referred to as CR ratio, changes from values slightly smaller to significantly larger than unity. When competition acts over short distances relative to the reproduction range (low CR), the phylogenetic tree takes on a nearly uniform appearance, gradually transforming into a more bush-like structure for slightly higher CR values. With further increases in CR, evolutionary lineages become more discernible, and the morphogenetic pattern shifts from a bush-like shape to a more tree-like arrangement and few branches for very large CRs.</p><p>At specific time sections, the synthetic phylogenetic tree appears as an assembly of clusters of individuals within the morphospace. These clusters, interpretable as simulated models of species, exhibit distinct separation within the morphospace and are subject to dynamic inter-cluster repulsion. Notably, clusters tend to be resistant to change. They maintain relatively constant abundances while gradually shifting their positions within the morphospace—a phase that aligns with the concept of phyletic gradualism. However, this predictable pattern is occasionally upset by the abrupt divisions into multiple groups, interpreted as cladogenesis events. The intricacies of the splitting process are explored, revealing that in scenarios with large CR values, the splitting can emerge much more rapidly than phyletic changes. This accelerated process of splitting is initiated by one or few individuals at the fringes of a cluster, where competition is minimal. The newly generated cluster then undergoes deformation, swiftly followed by divergence and splitting (seen as branching in the synthetic phylogenetic tree), as if an inherent \"repulsion\" triggered the division between species.</p><p>The simple rules implied in the interacting-particle model may provide insight into the coexistence of gradualism and cladogenesis along lineages,","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724000832/pdfft?md5=3e5d3f242ecf23662c3b936a1ede68ac&pid=1-s2.0-S0303264724000832-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140536217","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}