Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2021-01-02DOI: 10.1007/s12064-020-00329-z
Paul-Antoine Miquel, Su-Young Hwang
{"title":"On biological individuation.","authors":"Paul-Antoine Miquel, 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 (R<sub>1</sub>) 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 (R<sub>2</sub>). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R<sub>1</sub>R<sub>2</sub>) operators are applied to themselves, so that R<sub>N</sub> = (R<sub>1</sub>R<sub>2</sub>)<sub>N</sub>. 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":"141 2","pages":"203-211"},"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}
Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2021-06-06DOI: 10.1007/s12064-021-00348-4
Carlos Lobo
{"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":"141 2","pages":"175-202"},"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}
Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2021-05-06DOI: 10.1007/s12064-021-00342-w
Athel Cornish-Bowden, María Luz Cárdenas
{"title":"The essence of life revisited: how theories can shed light on it.","authors":"Athel Cornish-Bowden, María Luz Cárdenas","doi":"10.1007/s12064-021-00342-w","DOIUrl":"10.1007/s12064-021-00342-w","url":null,"abstract":"<p><p>Disagreement over whether life is inevitable when the conditions can support life remains unresolved, but calculations show that self-organization can arise naturally from purely random effects. Closure to efficient causation, or the need for all specific catalysts used by an organism to be produced internally, implies that a true model of an organism cannot exist, though this does not exclude the possibility that some characteristics can be simulated. Such simulations indicate that there is a limit to how small a self-organizing system can be: much smaller than a bacterial cell, but around the size of a typical virus particle. All current theories of life incorporate, at least implicitly, the idea of catalysis, but they largely ignore the need for metabolic regulation.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 2","pages":"105-123"},"PeriodicalIF":1.3,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8101340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38955724","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}
Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2021-06-11DOI: 10.1007/s12064-021-00351-9
Jürgen Jost
{"title":"Biology, geometry and information.","authors":"Jürgen Jost","doi":"10.1007/s12064-021-00351-9","DOIUrl":"10.1007/s12064-021-00351-9","url":null,"abstract":"<p><p>The main thesis developed in this article is that the key feature of biological life is the a biological process can control and regulate other processes, and it maintains that ability over time. This control can happen hierarchically and/or reciprocally, and it takes place in three-dimensional space. This implies that the information that a biological process has to utilize is only about the control, but not about the content of those processes. Those other processes can be vastly more complex that the controlling process itself, and in fact necessarily so. In particular, each biological process draws upon the complexity of its environment.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 2","pages":"65-71"},"PeriodicalIF":1.3,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9184451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39085553","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}
Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2020-07-01DOI: 10.1007/s12064-020-00320-8
Maël Montévil
{"title":"Historicity at the heart of biology.","authors":"Maël Montévil","doi":"10.1007/s12064-020-00320-8","DOIUrl":"https://doi.org/10.1007/s12064-020-00320-8","url":null,"abstract":"<p><p>Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration where equations no longer play a central role. We argue that all observations depend on objects defined by their historical origin instead of their relations as in physics. Therefore, we propose that biological variations and historicity come first, and regularities are constraints with limited validity in biology. Their proper theoretical and empirical use requires specific rationales.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 2","pages":"165-173"},"PeriodicalIF":1.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00320-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38108539","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}
Theory in BiosciencesPub Date : 2022-06-01Epub Date: 2021-06-15DOI: 10.1007/s12064-021-00350-w
Vincent Fleury, Alexis Peaucelle, Anick Abourachid, Olivia Plateau
{"title":"Second-order division in sectors as a prepattern for sensory organs in vertebrate development.","authors":"Vincent Fleury, Alexis Peaucelle, Anick Abourachid, Olivia Plateau","doi":"10.1007/s12064-021-00350-w","DOIUrl":"https://doi.org/10.1007/s12064-021-00350-w","url":null,"abstract":"<p><p>We present in vivo observations of chicken embryo development which show that the early chicken embryo presents a principal structure made out of concentric rings and a secondary structure composed of radial sectors. During development, physical forces deform the main rings into axially directed, antero-posterior tubes, while the sectors roll up to form cylinders that are perpendicular to the antero-posterior axis. As a consequence, the basic structure of the chicken embryo is a series of encased antero-posterior tubes (gut, neural tube, body envelope, amnion, chorion) decorated with smaller orifices (ear duct, eye stalk, nasal duct, gills, mouth) forming at right angles to the main body axis. We argue that the second-order divisions reflect the early pattern of cell cleavage, and that the transformation of radial and orthoradial lines into a body with sensory organs is a generic biophysical mechanism more general than the chicken embryo.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 2","pages":"141-163"},"PeriodicalIF":1.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00350-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39231888","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 historical nature of biological complexity and the ineffectiveness of the mathematical approach to it","authors":"Saverio Forestiero","doi":"10.1007/s12064-022-00369-7","DOIUrl":"https://doi.org/10.1007/s12064-022-00369-7","url":null,"abstract":"<p>Contemporary scientific knowledge is built on both methodological and epistemological reductionism. The discovery of the limitations of the reductionist paradigm in the mathematical treatment of certain physical phenomena originated the notion of complexity, both as a pattern and process. After clarifying some very general terms and ideas on biological evolution and biological complexity, the article will tackle to seek to summarize the debate on biological complexity and discuss the difference between complexities of living and inert matter. Some examples of the major successes of mathematics applied to biological problems will follow; the notion of an intrinsic limitation in the application of mathematics to biological complexity as a global, relational, and historical phenomenon at the individual and species level will also be advanced.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"25 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138543527","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":"Mathematics of life spaces: continuation of the 2018 large dimensions course","authors":"M. Gromov","doi":"10.1007/s12064-022-00362-0","DOIUrl":"https://doi.org/10.1007/s12064-022-00362-0","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 1","pages":"59 - 63"},"PeriodicalIF":1.1,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46360027","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":"Network representation and analysis of energy coupling mechanisms in cellular metabolism by a graph-theoretical approach","authors":"S. Nath","doi":"10.1007/s12064-022-00370-0","DOIUrl":"https://doi.org/10.1007/s12064-022-00370-0","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 1","pages":"249 - 260"},"PeriodicalIF":1.1,"publicationDate":"2022-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43388877","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":"A reappraisal of the form – function problem. Theory and phenomenology","authors":"Luciano Boi","doi":"10.1007/s12064-022-00368-8","DOIUrl":"https://doi.org/10.1007/s12064-022-00368-8","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"141 1","pages":"73 - 103"},"PeriodicalIF":1.1,"publicationDate":"2022-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48815471","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}