Theory in Biosciences最新文献

{"title":"The shadow of \"the Eclipse of Darwinism\": the problem of evolutionary mechanisms in Republican China, 1910s-1930s.","authors":"Zhixiang Cheng","doi":"10.1007/s12064-022-00378-6","DOIUrl":"https://doi.org/10.1007/s12064-022-00378-6","url":null,"abstract":"<p><p>How did Chinese scientific intellectuals react to the dispute over evolutionary mechanisms during the period of the \"eclipse of Darwinism\"? This is my focal question. To answer it, I survey the attitudes of three groups of people toward the debate in the early decades of the twentieth century: Chinese paleontologists and their general embrace of the anti-Darwinian position, a group of non-specialists (or semi-specialists) and their assertion of a \"revival of Lamarckism,\" and the American-trained Chinese biologists and their typical agnostic stance toward the antagonism between Darwinism and the mutation theory. Different concerns or motivations underlay these three different stances. There were also interesting attempts by biologists like Chen Zhen to exploit some recreational breeding traditions like goldfish breeding peculiar to China to participate in the dispute more directly.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40331950","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":"Thermodynamic principles for system biology and the patterns of flower pigmentation.","authors":"Qinyi Zhao","doi":"10.1007/s12064-022-00372-y","DOIUrl":"https://doi.org/10.1007/s12064-022-00372-y","url":null,"abstract":"<p><p>The thermodynamic principles for system biology are reviewed and formulated, and then basic patterns of flower pigmentation are interpreted. Main thoughts: (1) any biological trait (color or function of a cell) is logically related to a thermodynamic system (or physiological system, signaling network of the cell), (2) the striped, speckled and circle are three basic patterns of flower pigmentation, the development of flowers is an irreversible process, (3) the patterns of flower pigmentation are formed in flower development, (4) the flower cells can change its color in a period of development and this process is controlled thermodynamically, (5) there is giant space of physiology within an organism and within its numerous thermal states can appear under different conditions. In this theory, the dominant inheritance means that a gene contributes great to the thermodynamic stability of a trait related system; different genes can be interacted or integrated thermodynamically according to their contribution to the stability of its related system. By combination of Turing theory and our views, complex patterns of pigmentation could be explained theoretically.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40522132","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":"Phenotypic plasticity in plasmodial slime molds and molecular phylogeny of terrestrial vs. aquatic species.","authors":"T Hoppe,&nbsp;U Kutschera","doi":"10.1007/s12064-022-00375-9","DOIUrl":"https://doi.org/10.1007/s12064-022-00375-9","url":null,"abstract":"<p><p>Fifty years ago, the enigmatic Brazilian myxomycete-species Didymium aquatile was described and analyzed with respect to the structure of the plasmodium and its spores. In this study, we compare this rare plasmodial slime mold with another, temporarily aquatic taxon from Europe, Didymium nigripes. Phenotypic plasticity of D. nigripes was investigated under various environmental conditions. Large changes in the morphology of the plasmodia were observed. For species identification, characteristics of the fruiting bodies are key features. However, Didymium aquatile was only characterized by its \"abnormal\" plasmodia, but no molecular data were available. Here, we analyzed DNA-sequences of 22 species of the genera Didymium and Diderma with a focus on this South American taxon via molecular genetics. A comparison of 18S-rDNA-sequences from D. aquatile and 21 other Didymium (and Diderma)-species indicates that D. aquatile is a reproductively isolated morpho-species. Phenotypic plasticity of D. nigripes is documented with respect to plasmodium morphology and the formation of fruiting bodies, as an example of an adaptation of a terrestrial species to aquatic environments.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9474427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40432301","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":"Goethe and Candolle: National forms of scientific writing?","authors":"Agatha Seo-Hyun Kim,&nbsp;Andrew McNutt","doi":"10.1007/s12064-022-00376-8","DOIUrl":"https://doi.org/10.1007/s12064-022-00376-8","url":null,"abstract":"<p><p>What role does nationality-or the image of a nation-play in how one thinks and receives scientific ideas? This paper investigates the commonly held ideas about \"German science\" and \"French science\" in early nineteenth-century France. During the politically turbulent time, the seemingly independent scientific community found itself in a difficult position: first, between the cosmopolitan ideals of scientific community and the invasive political reality, and second, between the popularized image of national differences and the actual comparisons of international scientific ideas. The tension between multiple sets of fictions and realities underscores the fragility of the concept of nationality as a scientific measure. A case study comparing morphological ideas, receptions in France, and the actual scientific texts of J. W. von Goethe and A. P. de Candolle further illustrates this fragility. Goethe and Candolle make an ideal comparative case because they were received in very different lights despite their similar concept of the plant type. Our sentence-classification and visualization methods are applied to their scientific texts, to compare the actual compositions and forms of the texts that purportedly represented German and French sciences. This paper concludes that there was a gap between what French readers assumed they read and what they really read, when it came to foreign scientific texts. The differences between Goethe's and Candolle's texts transcended the perceived national differences between German Romanticism and French Classicism.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40711562","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":"Growth dynamics of breast cancer stem cells: effects of self-feedback and EMT mechanisms.","authors":"Liuyong Pang,&nbsp;Sanhong Liu,&nbsp;Zhong Zhao,&nbsp;Tianhai Tian,&nbsp;Xinan Zhang,&nbsp;Qiuying Li","doi":"10.1007/s12064-022-00374-w","DOIUrl":"https://doi.org/10.1007/s12064-022-00374-w","url":null,"abstract":"<p><p>Breast cancer stem cells (BCSCs) with the ability to self-renew and differentiate have been identified in primary breast cancer tissues and cell lines. The BCSCs are often resistant to traditional radiation and/or chemotherapies. Previous studies have also shown that successful therapy must eradicate cancer stem cells. The purpose of this paper is to develop a mathematical model with self-feedback mechanism to illustrate the issues regarding the difficulties of absolutely eliminating a breast cancer. In addition, we introduce the mechanism of the epithelial-mesenchymal transition (EMT) to investigate the influence of EMT on the effects of breast cancer growth and treatment. Results indicate that the EMT mechanism facilitates the growth of breast cancer and makes breast cancer more difficult to be cured. Therefore, targeting the signals involved in EMT can halt tumor progression in breast cancer. Finally, we apply the experimental data to carry out numerical simulations and validate our theoretical conclusions.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40688426","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":"First principles of terrestrial life: exemplars for potential extra-terrestrial biology.","authors":"Ian von Hegner","doi":"10.1007/s12064-022-00373-x","DOIUrl":"https://doi.org/10.1007/s12064-022-00373-x","url":null,"abstract":"<p><p>The search for life elsewhere in the universe represents not only a potential expansion of our knowledge regarding life, but also a clarification of the first principles applicable to terrestrial life, which thus restrict the very search for extra-terrestrial life. Although there are no exact figures for how many species have existed throughout Earth's total history, we can still make inferences about how the distribution of this life has proceeded through a bell curve. This graph shows the totality of life, from its origin to its end. The system enclosing life contains a number of first principles designated the walls of minimal complexity and adaptive possibility, the fence of adaptation, and right-skewed extension. In this discussion of life, a framework will be formulated that, based on the dynamic relationship between mesophiles and extremophiles, will be imposed on exoworlds in order to utilize the graph's predictive power to analyze how extra-terrestrial life could unfold. In this framework the evolutionary variation does not depend on the specific biochemistry involved. Once life is 'up and running,' the various biochemical systems that can constitute terrestrial and extra-terrestrial life will have secondary significance. The extremophilic tail represents a range expansion in which all habitat possibilities are tested and occupied. This tail moves to the right not because of the biochemistry constitutions of organisms, but because it can do nothing else. Thus, it can be predicted that graphs of terrestrial and extra-terrestrial life will be similar overall. A number of other predictions can be made; for example, for worlds in which the atmospheric disequilibrium is approaching equilibrium, it is predicted that life may still be present because the extremophilic range expansion is stretched increasingly farther to the right. Because life necessarily arises at a left wall of minimal complexity, it is predicted that any origin of cellular life will have a close structural resemblance to that of the first terrestrial life. Thus, in principle, life may have originated more than once on Earth, and still exist. It is also predicted that there may be an entire subset of life existing among other domains that we do not see because, in an abstract sense, we are inside the graph. If we view the graph in its entirety, this subset appears very much like a vast supra-domain of life.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40662788","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":"Mathematical modeling for mutator phenotype and clonal selection advantage in the risk analysis of lung cancer","authors":"Lingling Li, Ting Zhao, Xingshi He, Xinshe S. Yang, Tianhai Tian, Xinan Zhang","doi":"10.1007/s12064-022-00371-z","DOIUrl":"https://doi.org/10.1007/s12064-022-00371-z","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44037508","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":"Consciousness, decision making, and volition: freedom beyond chance and necessity.","authors":"Hans Liljenström","doi":"10.1007/s12064-021-00346-6","DOIUrl":"10.1007/s12064-021-00346-6","url":null,"abstract":"<p><p>What is the role of consciousness in volition and decision-making? Are our actions fully determined by brain activity preceding our decisions to act, or can consciousness instead affect the brain activity leading to action? This has been much debated in philosophy, but also in science since the famous experiments by Libet in the 1980s, where the current most common interpretation is that conscious free will is an illusion. It seems that the brain knows, up to several seconds in advance what \"you\" decide to do. These studies have, however, been criticized, and alternative interpretations of the experiments can be given, some of which are discussed in this paper. In an attempt to elucidate the processes involved in decision-making (DM), as an essential part of volition, we have developed a computational model of relevant brain structures and their neurodynamics. While DM is a complex process, we have particularly focused on the amygdala and orbitofrontal cortex (OFC) for its emotional, and the lateral prefrontal cortex (LPFC) for its cognitive aspects. In this paper, we present a stochastic population model representing the neural information processing of DM. Simulation results seem to confirm the notion that if decisions have to be made fast, emotional processes and aspects dominate, while rational processes are more time consuming and may result in a delayed decision. Finally, some limitations of current science and computational modeling will be discussed, hinting at a future development of science, where consciousness and free will may add to chance and necessity as explanation for what happens in the world.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9184456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38946316","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":"On biological individuation.","authors":"Paul-Antoine Miquel,&nbsp;Su-Young Hwang","doi":"10.1007/s12064-020-00329-z","DOIUrl":"https://doi.org/10.1007/s12064-020-00329-z","url":null,"abstract":"<p><p>In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R₁) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change as the fact that their structure is the recursive result of their operations (R₂). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R₁R₂) operators are applied to themselves, so that R_N = (R₁R₂)_N. We suggest that under specific thermodynamic (open systems out of equilibrium) and chemical conditions (autocatalysis, kinetic dynamic stability), this mapping can go up to a limit characterized by a fixed-point equation: [Formula: see text]. In this equation, ([Formula: see text]) symbolizes a regime of permanent resonance characterizing the biosphere, as open from inside, by the recursive differential relation between the biosphere and all its holobionts. As such the biosphere is closed on itself as a pure differential entity. ([Formula: see text]) symbolizes the regime of permanent change characterizing the emergence of evolution in the biosphere. As such the biosphere is closed on itself, by the principle of descent with modifications, and by the fact that every holobiont evolves in a niche, while evolving with it.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00329-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38773749","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 limits of the mathematization of the living and the idea of formal morphology of the living world following Husserlian phenomenology.","authors":"Carlos Lobo","doi":"10.1007/s12064-021-00348-4","DOIUrl":"https://doi.org/10.1007/s12064-021-00348-4","url":null,"abstract":"<p><p>Through a presentation and a commentary of Husserl's little-known analyses of mathematization in the life sciences and on morphology, this article proposes three goals. First, it aims at establishing the real meaning and results of the critical analyses of the mathematization in natural sciences and of exactness put forth as a standard of scientific knowledge that we read in the Krisis. As a result, it will appear that these analyses belong to the perspective of a project of a formal morphology, understood as an extension of mathesis. It is then to explain why this project only makes sense in the larger framework of the description of the \"correlational a priori,\" i.e., the theory of constituting subjectivity, experiencing these morphologies, and engaging, theoretically, by induction, in the typification and categorial elaboration of possible explanatory models. After presenting the contours of this project and its achievements, we will conclude with some conjectural proposals concerning the profile of plausible mathematical structures likely to satisfy the minimal algebraic formal conditions for a model of stability and plasticity of the living and allowing to understand and express the dynamic stratification of morphological levels and the various forms of morphogenesis.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00348-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39065072","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}