Theory in Biosciences最新文献_第2页

Dynamics of neural fields with exponential temporal kernel. 具有指数时间核的神经场动力学。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-06-01 Epub Date: 2024-03-09 DOI: 10.1007/s12064-024-00414-7

Elham Shamsara, Marius E Yamakou, Fatihcan M Atay, Jürgen Jost

引用次数: 0

Behavioral selection in structured populations. 结构化种群中的行为选择。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-06-01 Epub Date: 2024-03-05 DOI: 10.1007/s12064-024-00413-8

Matthias Borgstede

{"title":"Behavioral selection in structured populations.","authors":"Matthias Borgstede","doi":"10.1007/s12064-024-00413-8","DOIUrl":"10.1007/s12064-024-00413-8","url":null,"abstract":"The multilevel model of behavioral selection (MLBS) by Borgstede and Eggert (Behav Process 186:104370. 10.1016/j.beproc.2021.104370 , 2021) provides a formal framework that integrates reinforcement learning with natural selection using an extended Price equation. However, the MLBS is so far only formulated for homogeneous populations, thereby excluding all sources of variation between individuals. This limitation is of primary theoretical concern because any application of the MLBS to real data requires to account for variation between individuals. In this paper, I extend the MLBS to account for inter-individual variation by dividing the population into homogeneous sub-populations and including class-specific reproductive values as weighting factors for an individual's evolutionary fitness. The resulting formalism closes the gap between the theoretical underpinnings of behavioral selection and the application of the theory to empirical data, which naturally includes inter-individual variation. Furthermore, the extended MLBS is used to establish an explicit connection between the dynamics of learning and the maximization of individual fitness. These results expand the scope of the MLBS as a general theoretical framework for the quantitative analysis of learning and evolution.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11127832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029545","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}

引用次数: 0

The bubble theory: exploring the transition from first replicators to cells and viruses in a landscape-based scenario. 气泡理论：在基于景观的情景中探索从最初的复制者到细胞和病毒的过渡。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-06-01 Epub Date: 2024-05-09 DOI: 10.1007/s12064-024-00417-4

Radoslaw W Piast

{"title":"The bubble theory: exploring the transition from first replicators to cells and viruses in a landscape-based scenario.","authors":"Radoslaw W Piast","doi":"10.1007/s12064-024-00417-4","DOIUrl":"10.1007/s12064-024-00417-4","url":null,"abstract":"This study proposes a landscape-based scenario for the origin of viruses and cells, focusing on the adaptability of preexisting replicons from the RNP (ribonucleoprotein) world. The scenario postulates that life emerged in a subterranean \"warm little pond\" where organic matter accumulated, resulting in a prebiotic soup rich in nucleotides, amino acids, and lipids, which served as nutrients for the first self-replicating entities. Over time, the RNA world, followed by the RNP world, came into existence. Replicators/replicons, along with the nutritious soup from the pond, were washed out into the river and diluted. Lipid bubbles, enclosing organic matter, provided the last suitable environment for replicons to replicate. Two survival strategies emerged under these conditions: cell-like structures that obtained nutrients by merging with new bubbles, and virus-like entities that developed various techniques to transmit themselves to fresh bubbles. The presented hypothesis provides the possibility for the common origin of cells and viruses on rocky worlds hosting liquid water, like Earth.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11127830/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900091","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}

引用次数: 0

Rethinking some roots of ecosystem approach in aquatic ecology: between the food cycle and lake metabolism 重新思考水生生态学中生态系统方法的某些根源：食物循环与湖泊新陈代谢之间的关系

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-04-26 DOI: 10.1007/s12064-024-00416-5

Alexandra L. Rizhinashvili

{"title":"Rethinking some roots of ecosystem approach in aquatic ecology: between the food cycle and lake metabolism","authors":"Alexandra L. Rizhinashvili","doi":"10.1007/s12064-024-00416-5","DOIUrl":"https://doi.org/10.1007/s12064-024-00416-5","url":null,"abstract":"The present study provides new insight into the key aspects of the early formative period of the ecosystem concept in aquatic ecology. Raymond Lindeman’s trophodynamics is known to be a starting point for the development of the modern concept of ecosystem. The trophodynamic approach in ecology was proposed by Lindeman in his widely cited paper of 1942. Lindeman’s views are analyzed in comparison with the contemporary production studies in aquatic ecology. It is shown that a similar theoretical system has been proposed in the USSR at the end of the 1930s by Georgiy G. Vinberg. He introduced the concept of biotic balance based on the wide appraisal of the dark and light bottles method. The study shows that both Lindeman’s trophodynamics and Vinberg’s concept of biotic balance relied on an energy-based approach in considering the wholeness of a water body. The two scientists, however, differed in several important aspects concerning the interpretation of the role of living organisms. The holistic interpretation of ecosystem by Lindeman and Vinberg can be seen as part of the dilemma between physicalism and organicism. At the same time, the main emphasis in the concepts of both Vinberg and Lindemann was on the primary production component, a feature that was common to the first holistic systems in production hydrobiology (e.g., E. Naumann’s regional limnology). It is clear that modern problems of aquatic ecology should be addressed from the perspective of the organismocentric understanding of the ecosystem, but undoubtedly at the new level of development of this view.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140809912","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}

引用次数: 0

Mathematical analysis of a modified Volterra-Leslie chemostat Model 修正的 Volterra-Leslie 化合模型的数学分析

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-04-09 DOI: 10.1007/s12064-024-00415-6

Mohammed Amine Hamra

引用次数: 0

Normalizing need not be the norm: count-based math for analyzing single-cell data. 规范化不一定是常态：用于分析单单元格数据的基于计数的数学。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2023-11-10 DOI: 10.1007/s12064-023-00408-x

Samuel H Church, Jasmine L Mah, Günter Wagner, Casey W Dunn

{"title":"Normalizing need not be the norm: count-based math for analyzing single-cell data.","authors":"Samuel H Church, Jasmine L Mah, Günter Wagner, Casey W Dunn","doi":"10.1007/s12064-023-00408-x","DOIUrl":"10.1007/s12064-023-00408-x","url":null,"abstract":"Counting transcripts of mRNA are a key method of observation in modern biology. With advances in counting transcripts in single cells (single-cell RNA sequencing or scRNA-seq), these data are routinely used to identify cells by their transcriptional profile, and to identify genes with differential cellular expression. Because the total number of transcripts counted per cell can vary for technical reasons, the first step of many commonly used scRNA-seq workflows is to normalize by sequencing depth, transforming counts into proportional abundances. The primary objective of this step is to reshape the data such that cells with similar biological proportions of transcripts end up with similar transformed measurements. But there is growing concern that normalization and other transformations result in unintended distortions that hinder both analyses and the interpretation of results. This has led to an intense focus on optimizing methods for normalization and transformation of scRNA-seq data. Here, we take an alternative approach, by avoiding normalization and transformation altogether. We abandon the use of distances to compare cells, and instead use a restricted algebra, motivated by measurement theory and abstract algebra, that preserves the count nature of the data. We demonstrate that this restricted algebra is sufficient to draw meaningful and practical comparisons of gene expression through the use of the dot product and other elementary operations. This approach sidesteps many of the problems with common transformations, and has the added benefit of being simpler and more intuitive. We implement our approach in the package countland, available in python and R.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016176","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}

引用次数: 0

Optimal dispersal and diffusion-enhanced robustness in two-patch metapopulations: origin's saddle-source nature matters. 双补丁元种群中的最佳扩散和扩散增强的稳健性：起源的鞍源性质很重要。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-02-21 DOI: 10.1007/s12064-023-00411-2

Marc Jorba-Cuscó, Ruth I Oliva-Zúniga, Josep Sardanyés, Daniel Pérez-Palau

{"title":"Optimal dispersal and diffusion-enhanced robustness in two-patch metapopulations: origin's saddle-source nature matters.","authors":"Marc Jorba-Cuscó, Ruth I Oliva-Zúniga, Josep Sardanyés, Daniel Pérez-Palau","doi":"10.1007/s12064-023-00411-2","DOIUrl":"10.1007/s12064-023-00411-2","url":null,"abstract":"A two-patch logistic metapopulation model is investigated both analytically and numerically focusing on the impact of dispersal on population dynamics. First, the dependence of the global dynamics on the stability type of the full extinction equilibrium point is tackled. Then, the behaviour of the total population with respect to the dispersal is studied analytically. Our findings demonstrate that diffusion plays a crucial role in the preservation of both subpopulations and the full metapopulation under the presence of stochastic perturbations. At low diffusion, the origin is a repulsor, causing the orbits to flow nearly parallel to the axes, risking stochastic extinctions. Higher diffusion turns the repeller into a saddle point. Orbits then quickly converge to the saddle's unstable manifold, reducing extinction chances. This change in the vector field enhances metapopulation robustness. On the other hand, the well-known fact that asymmetric conditions on the patches is beneficial for the total population is further investigated. This phenomenon has been studied in previous works for large enough or small enough values of the dispersal. In this work, we complete the theory for all values of the dispersal. In particular, we derive analytically a formula for the optimal value of the dispersal that maximizes the total population.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10904506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139934268","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}

引用次数: 0

Speciation, natural selection, and networks: three historians versus theoretical population geneticists. 物种、自然选择和网络：三位历史学家与理论人口遗传学家的比较。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-01-29 DOI: 10.1007/s12064-024-00412-9

Donald R Forsdyke

{"title":"Speciation, natural selection, and networks: three historians versus theoretical population geneticists.","authors":"Donald R Forsdyke","doi":"10.1007/s12064-024-00412-9","DOIUrl":"10.1007/s12064-024-00412-9","url":null,"abstract":"In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a \"modern synthesis\" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional \"just-so-stories.\" They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a \"collective variation\" postulated by Darwin's young research associate, George Romanes, and a mysterious \"residue\" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139572208","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}

引用次数: 0

Modeling stress-induced responses: plasticity in continuous state space and gradual clonal evolution. 压力诱导反应建模：连续状态空间中的可塑性和渐进克隆进化

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-01-30 DOI: 10.1007/s12064-023-00410-3

Anuraag Bukkuri

引用次数: 0

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis. 托马斯·库恩:更好地理解扩展进化综合的关键。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2023-11-17 DOI: 10.1007/s12064-023-00409-w

Koen B Tanghe

{"title":"Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis.","authors":"Koen B Tanghe","doi":"10.1007/s12064-023-00409-w","DOIUrl":"10.1007/s12064-023-00409-w","url":null,"abstract":"In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and \"old-fashioned\" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136400311","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}

引用次数: 0