For more than fifty years, taxonomists have proposed numerous alternative definitions of species while they searched for a unique, comprehensive, and persuasive definition. This monograph shows that these efforts have been unnecessary, and indeed have provably been a pursuit of a will o' the wisp because they have failed to recognize the theoretical impossibility of what they seek to accomplish. A clear and rigorous understanding of the logic underlying species definition leads both to a recognition of the inescapable ambiguity that affects the definition of species, and to a framework-relative approach to species definition that is logically compelling, i.e., cannot not be accepted without inconsistency. An appendix reflects upon the conclusions reached, applying them in an intellectually whimsical taxonomic thought experiment that conjectures the possibility of an emerging new human species.
{"title":"THE SPECIES PROBLEM AND ITS LOGIC:Inescapable Ambiguity and Framework-relativity","authors":"S. Bartlett","doi":"10.2139/SSRN.3073801","DOIUrl":"https://doi.org/10.2139/SSRN.3073801","url":null,"abstract":"For more than fifty years, taxonomists have proposed numerous alternative definitions of species while they searched for a unique, comprehensive, and persuasive definition. This monograph shows that these efforts have been unnecessary, and indeed have provably been a pursuit of a will o' the wisp because they have failed to recognize the theoretical impossibility of what they seek to accomplish. A clear and rigorous understanding of the logic underlying species definition leads both to a recognition of the inescapable ambiguity that affects the definition of species, and to a framework-relative approach to species definition that is logically compelling, i.e., cannot not be accepted without inconsistency. An appendix reflects upon the conclusions reached, applying them in an intellectually whimsical taxonomic thought experiment that conjectures the possibility of an emerging new human species.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73262183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Several papers published since 2006 describe effects of magnetic fields on elasmobranchs and assess their utility in reducing negative interactions between sharks and humans, including bycatch reduction. Most of these repeat a single untested hypothesis regarding physical mechanisms by which elasmobranchs detect magnetic fields and also neglect careful consideration of magnetoreception in teleosts. Several species of teleosts are known to have magnetoreception based in biogenic magnetite, and direct magnetic field detection also has support in several species of elasmobranchs. The overly narrow focus of earlier papers on the unsupported hypothesis that magnetoreception in elasmobranchs is based in the ampullae of Lorenzini creates the impression that all teleosts will be insensitive to magnetic deterrents. However, magnetite based magnetoreception has been demonstrated in several teleosts, and is supported in others. Furthermore, electroreception is present in many teleost species; therefore, the possibility of induction based indirect magnetoreception should be considered. Finally, experiments reported as demonstrating insensitivity in teleost species to magnetic deterrents suffer from inadequate design and sample sizes to reject the hypothesis of magnetic detection in any given species. Since adoption of deterrent hook technologies depends on both deterrent effects in sharks and the absence of effects in target teleosts, the hypothesis of detection in teleost species must be independently tested with adequate sample sizes.
{"title":"Review of Magnetic Shark Deterrents: Hypothetical Mechanisms and Evidence for Selectivity","authors":"Joshua M. Courtney, Y. Courtney, M. Courtney","doi":"10.5296/ast.v3i1.6670","DOIUrl":"https://doi.org/10.5296/ast.v3i1.6670","url":null,"abstract":"Several papers published since 2006 describe effects of magnetic fields on elasmobranchs and assess their utility in reducing negative interactions between sharks and humans, including bycatch reduction. Most of these repeat a single untested hypothesis regarding physical mechanisms by which elasmobranchs detect magnetic fields and also neglect careful consideration of magnetoreception in teleosts. Several species of teleosts are known to have magnetoreception based in biogenic magnetite, and direct magnetic field detection also has support in several species of elasmobranchs. The overly narrow focus of earlier papers on the unsupported hypothesis that magnetoreception in elasmobranchs is based in the ampullae of Lorenzini creates the impression that all teleosts will be insensitive to magnetic deterrents. However, magnetite based magnetoreception has been demonstrated in several teleosts, and is supported in others. Furthermore, electroreception is present in many teleost species; therefore, the possibility of induction based indirect magnetoreception should be considered. Finally, experiments reported as demonstrating insensitivity in teleost species to magnetic deterrents suffer from inadequate design and sample sizes to reject the hypothesis of magnetic detection in any given species. Since adoption of deterrent hook technologies depends on both deterrent effects in sharks and the absence of effects in target teleosts, the hypothesis of detection in teleost species must be independently tested with adequate sample sizes.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84364323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-10-01DOI: 10.1142/9789814667944_0022
N. Morozova, R. Penner
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell surface gradients. We assume that a spectrum of such cell surface markers determines an epigenetic code for organism shape. The union of cells in space at a moment in time is by definition the organism taken as a metric subspace of Euclidean space, which can be further equipped with an arbitrary measure. Each cell determines a point in space thus assigning a finite configuration of distinct points in space to an organism, and a bundle over this configuration space is introduced with fiber a Hilbert space recording specific epigenetic data. On this bundle, a Lagrangian formulation of morphogenetic dynamics is proposed based on Gromov-Hausdorff distance which at once describes both embryo development and regenerative growth.
{"title":"Geometry of Morphogenesis","authors":"N. Morozova, R. Penner","doi":"10.1142/9789814667944_0022","DOIUrl":"https://doi.org/10.1142/9789814667944_0022","url":null,"abstract":"We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell surface gradients. We assume that a spectrum of such cell surface markers determines an epigenetic code for organism shape. The union of cells in space at a moment in time is by definition the organism taken as a metric subspace of Euclidean space, which can be further equipped with an arbitrary measure. Each cell determines a point in space thus assigning a finite configuration of distinct points in space to an organism, and a bundle over this configuration space is introduced with fiber a Hilbert space recording specific epigenetic data. On this bundle, a Lagrangian formulation of morphogenetic dynamics is proposed based on Gromov-Hausdorff distance which at once describes both embryo development and regenerative growth.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75479644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2013-05-01DOI: 10.7546/JGSP-31-2013-1-56
V. Ivancevic, T. Ivancevic
Nonlinear space-time dynamics, defined in terms of celebrated 'solitonic' equations, brings indispensable tools for understanding, prediction and control of complex behaviors in both physical and life sciences. In this paper, we review sine-Gordon solitons, kinks and breathers as models of nonlinear excitations in complex systems in physics and in living cellular structures, both intra-cellular (DNA, protein folding and microtubules) and inter-cellular (neural impulses and muscular contractions). Key words: Sine-Gordon solitons, kinks and breathers, DNA, Protein folding, Microtubules, Neural conduction, Muscular contraction
{"title":"Sine-Gordon Solitons, Kinks and Breathers as Physical Models of Nonlinear Excitations in Living Cellular Structures","authors":"V. Ivancevic, T. Ivancevic","doi":"10.7546/JGSP-31-2013-1-56","DOIUrl":"https://doi.org/10.7546/JGSP-31-2013-1-56","url":null,"abstract":"Nonlinear space-time dynamics, defined in terms of celebrated 'solitonic' equations, brings indispensable tools for understanding, prediction and control of complex behaviors in both physical and life sciences. In this paper, we review sine-Gordon solitons, kinks and breathers as models of nonlinear excitations in complex systems in physics and in living cellular structures, both intra-cellular (DNA, protein folding and microtubules) and inter-cellular (neural impulses and muscular contractions). \u0000Key words: Sine-Gordon solitons, kinks and breathers, DNA, Protein folding, Microtubules, Neural conduction, Muscular contraction","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74098582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2012-12-03DOI: 10.1007/978-3-319-00395-5_63
M. Robert
{"title":"A Broader Perspective About Organization and Coherence in Biological Systems","authors":"M. Robert","doi":"10.1007/978-3-319-00395-5_63","DOIUrl":"https://doi.org/10.1007/978-3-319-00395-5_63","url":null,"abstract":"","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89162075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2012-11-28DOI: 10.1142/S1793048012500051
Yuri K. Shestopaloff
We present significantly advanced studies of the previously introduced physical growth mechanism and unite it with biochemical growth factors. Obtained results allowed formulating the general growth law which governs growth and evolutional development of all living organisms, their organs and systems. It was discovered that the growth cycle is predefined by the distribution of nutritional resources between maintenance needs and biomass production. This distribution is quantitatively defined by the growth ratio parameter, which depends on the geometry of an organism, phase of growth and, indirectly, organism's biochemical machinery. The amount of produced biomass, in turn, defines the composition of biochemical reactions. Changing amount of nutrients diverted to biomass production is what forces organisms to proceed through the whole growth and replication cycle. The growth law can be formulated as follows: the rate of growth is proportional to influx of nutrients and growth ratio. Considering specific biochemical components of different organisms, we find influxes of required nutrients and substitute them into the growth equation; then, we compute growth curves for amoeba, wild type fission yeast, fission yeast's mutant. In all cases, predicted growth curves correspond very well to experimental data. Obtained results prove validity and fundamental scientific value of the discovery.
{"title":"General law of growth and replication. Growth equation and its applications","authors":"Yuri K. Shestopaloff","doi":"10.1142/S1793048012500051","DOIUrl":"https://doi.org/10.1142/S1793048012500051","url":null,"abstract":"We present significantly advanced studies of the previously introduced physical growth mechanism and unite it with biochemical growth factors. Obtained results allowed formulating the general growth law which governs growth and evolutional development of all living organisms, their organs and systems. It was discovered that the growth cycle is predefined by the distribution of nutritional resources between maintenance needs and biomass production. This distribution is quantitatively defined by the growth ratio parameter, which depends on the geometry of an organism, phase of growth and, indirectly, organism's biochemical machinery. The amount of produced biomass, in turn, defines the composition of biochemical reactions. Changing amount of nutrients diverted to biomass production is what forces organisms to proceed through the whole growth and replication cycle. The growth law can be formulated as follows: the rate of growth is proportional to influx of nutrients and growth ratio. Considering specific biochemical components of different organisms, we find influxes of required nutrients and substitute them into the growth equation; then, we compute growth curves for amoeba, wild type fission yeast, fission yeast's mutant. In all cases, predicted growth curves correspond very well to experimental data. Obtained results prove validity and fundamental scientific value of the discovery.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90374621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2012-10-31DOI: 10.1142/S2010194512007945
L. T. Handoko
A new approach to model the biomatter dynamics based on the field theory is presented. It is shown that some well known tools in field theory can be utilized to describe the physical phenomena in life matters, in particular at elementary biomatters like DNA and proteins. In this approach, the biomatter dynamics are represented as results of interactions among its elementary matters in the form of lagrangian. Starting from the lagrangian would provide stronger underlying theoretical consideration for further extension. Moreover, it also enables us to acquire rich physical observables using statistical mechanics instead of relying on the space-time dynamics from certain equation of motions which is not solvable due to its nonlinearities. Few examples from previous results are given and explained briefly.
{"title":"FIELD THEORY APPROACH IN THE DYNAMICS OF BIOMATTER","authors":"L. T. Handoko","doi":"10.1142/S2010194512007945","DOIUrl":"https://doi.org/10.1142/S2010194512007945","url":null,"abstract":"A new approach to model the biomatter dynamics based on the field theory is presented. It is shown that some well known tools in field theory can be utilized to describe the physical phenomena in life matters, in particular at elementary biomatters like DNA and proteins. In this approach, the biomatter dynamics are represented as results of interactions among its elementary matters in the form of lagrangian. Starting from the lagrangian would provide stronger underlying theoretical consideration for further extension. Moreover, it also enables us to acquire rich physical observables using statistical mechanics instead of relying on the space-time dynamics from certain equation of motions which is not solvable due to its nonlinearities. Few examples from previous results are given and explained briefly.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76903805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nucleic acids theoretically possess a Szilard engine function that can convert the energy associated with the Shannon entropy of molecules for which they have coded recognition, into the useful work of geometric reconfiguration of the nucleic acid molecule. This function is logically reversible because its mechanism is literally and physically constructed out of the information necessary to reduce the Shannon entropy of such molecules, which means that this information exists on both sides of the theoretical engine, and because information is retained in the geometric degrees of freedom of the nucleic acid molecule, a quantum gate is formed through which multi-state nucleic acid qubits can interact. Entangled biophotons emitted as a consequence of symmetry breaking nucleic acid Szilard engine (NASE) function can be used to coordinate relative positioning of different nucleic acid locations, both within and between cells, thus providing the potential for quantum coherence of an entire biological system. Theoretical implications of understanding biological systems as such "quantum adaptive systems" include the potential for multi-agent based quantum computing, and a better understanding of systemic pathologies such as cancer, as being related to a loss of systemic quantum coherence.
{"title":"A Theoretical Mechanism of Szilard Engine Function in Nucleic Acids and the Implications for Quantum Coherence in Biological Systems","authors":"F. Mihelic","doi":"10.1063/1.3536440","DOIUrl":"https://doi.org/10.1063/1.3536440","url":null,"abstract":"Nucleic acids theoretically possess a Szilard engine function that can convert the energy associated with the Shannon entropy of molecules for which they have coded recognition, into the useful work of geometric reconfiguration of the nucleic acid molecule. This function is logically reversible because its mechanism is literally and physically constructed out of the information necessary to reduce the Shannon entropy of such molecules, which means that this information exists on both sides of the theoretical engine, and because information is retained in the geometric degrees of freedom of the nucleic acid molecule, a quantum gate is formed through which multi-state nucleic acid qubits can interact. Entangled biophotons emitted as a consequence of symmetry breaking nucleic acid Szilard engine (NASE) function can be used to coordinate relative positioning of different nucleic acid locations, both within and between cells, thus providing the potential for quantum coherence of an entire biological system. Theoretical implications of understanding biological systems as such \"quantum adaptive systems\" include the potential for multi-agent based quantum computing, and a better understanding of systemic pathologies such as cancer, as being related to a loss of systemic quantum coherence.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85066278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2012-05-05DOI: 10.1007/978-3-642-20164-6_20
N. Morozova, M. Shubin
{"title":"The Geometry of Morphogenesis and the Morphogenetic Field Concept","authors":"N. Morozova, M. Shubin","doi":"10.1007/978-3-642-20164-6_20","DOIUrl":"https://doi.org/10.1007/978-3-642-20164-6_20","url":null,"abstract":"","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89818982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-02DOI: 10.1038/NPRE.2011.6176.1
Wan-Chung Hu
{"title":"Parkinson disease is a TH17 dominant autoimmune disorder against accumulated alpha-synuclein","authors":"Wan-Chung Hu","doi":"10.1038/NPRE.2011.6176.1","DOIUrl":"https://doi.org/10.1038/NPRE.2011.6176.1","url":null,"abstract":"","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72739677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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