Darwinian Evolution

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J. C. Phillips - One of the best experts on this subject based on the ideXlab platform.

  • Self-Organized Networks: Darwinian Evolution of Myosin-1
    arXiv: Other Quantitative Biology, 2020
    Co-Authors: J. C. Phillips
    Abstract:

    Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian Evolution enables them to approach optimized functionality (self-organized criticality). The principal features of the eukaryotic Evolution of the cytoskeleton motor protein myosin-1 parallel those of actin and tubulin, but also show striking differences connected to its dynamical function. Optimized (long) hydropathic waves characterize the molecular level Darwinian Evolution towards optimized functionality (self-organized criticality). The N-terminal and central domains of myosin-1 have evolved in eukaryotes at different rates, with the central domain hydropathic extrema being optimally active in humans. A test shows that hydropathic scaling can yield accuracies of better than 1% near optimized functionality. Evolution towards synchronized level extrema is connected to a special function of Mys-1 in humans involving Golgi complexes.

  • Darwinian Evolution of Taste
    arXiv: Other Quantitative Biology, 2020
    Co-Authors: J. C. Phillips
    Abstract:

    What is life. Schrodingers question is discussed here for a specific protein, villin, which builds cells in tissues that detect taste and sound. Villin is represented by a sequence of 827 amino acids bound to a peptide backbone chain. We focus attention on a limited problem, the Darwinian Evolution of villin sequences from chickens to humans. This biophysical problem is analyzed using a new physicical method based on thermodynamic domain scaling, a technique that bridges the gap between physical concepts, self-organized criticality, and conventional biostructural practice. It turns out that the Evolutionary changes can be explained by Darwinian selection, which is not generally accepted by biologists at the protein level. The presentation is self-contained, and requires no prior experience with proteins at the molecular level.

  • Self-Organized Networks with Long-Range Interactions: Tandem Darwinian Evolution of $\alpha$ and $\beta$ Tubulin
    arXiv: Other Quantitative Biology, 2020
    Co-Authors: J. C. Phillips
    Abstract:

    Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian Evolution enables them to approach optimized functionality (self-organized criticality). Our theoretical analysis uses hydropathic waves to identify and contrast the functional differences between the polymerizing $\alpha$ and $\beta$ tubulin monomers, which are similar in length and secondary structures, as well as having indistinguishable phylogenetic trees. We show how Evolution has improved water-driven flexibility especially for $\alpha$ tubulin, and thus facilitated heterodimer microtubule assembly, in agreement with recent atomistic simulations and topological models. We conclude that the failure of phylogenetic analysis to identify functionally specific positive Darwinian Evolution has been caused by 20th century technical limitations. These are overcome using 21st century quantitative mathematical methods based on thermodynamic scaling and hydropathic modular averaging. Our most surprising result is the identification of large level sets, especially in hydrophobic extrema, with both thermodynamically first- and second-order scaled water waves. Our calculations include explicitly long-range water-protein interactions described by fractals. We also suggest a much-needed corrective for large protein drug development costs.

  • Self-organized networks: Darwinian Evolution of dynein rings, stalks, and stalk heads.
    Proceedings of the National Academy of Sciences of the United States of America, 2020
    Co-Authors: J. C. Phillips
    Abstract:

    Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin, and dynein. Their positive Darwinian Evolution enables them to approach optimized functionality (self-organized criticality). Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1,500 amino acids away. Here, we show how many details of this extremely distant interaction are explained by water waves quantified by thermodynamic scaling. Water waves have shaped all proteins throughout positive Darwinian Evolution, and many aspects of long-range water-protein interactions are universal (described by self-organized criticality). Dynein water waves resembling tsunami produce nearly optimal energy transport over 1,500 amino acids along dynein's one-dimensional peptide backbone. More specifically, this paper identifies many similarities in the function and Evolution of dynein compared to other cytoskeleton proteins such as actin, myosin, and tubulin.

  • Self-Organized Networks, Darwinian Evolution of Self-Organized Networks, Darwinian Evolution of Dynein Rings, Stalks and Stalk Heads
    arXiv: Molecular Networks, 2020
    Co-Authors: J. C. Phillips
    Abstract:

    Cytoskeletons are self organized networks based on polymerized proteins, actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian Evolution enables them to approach optimized functionality self organized criticality. Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1500 amino acids away.

Ute Schechter - One of the best experts on this subject based on the ideXlab platform.

Marc Tessera - One of the best experts on this subject based on the ideXlab platform.

  • Is pre-Darwinian Evolution plausible?
    Biology direct, 2018
    Co-Authors: Marc Tessera
    Abstract:

    Background This essay highlights critical aspects of the plausibility of pre-Darwinian Evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian Evolution had emerged and that resulted in the origin of the first systems capable of Darwinian Evolution. The researchers’ responses to eight crucial questions are reviewed. The majority of the researchers claim that there would have been an Evolutionary continuity between chemistry and “biology”. A key question is how did this Evolution begin before Darwinian Evolution had begun? In other words the question is whether pre-Darwinian Evolution is plausible.

  • Research program for a search of the origin of Darwinian Evolution
    Origins of Life and Evolution of Biospheres, 2017
    Co-Authors: Marc Tessera
    Abstract:

    The search for origin of ‘life’ is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian Evolution (Cleland and Chyba 2002 ). Within a physical approach which has been defined as a level-4 Evolution (Tessera and Hoelzer 2013 ), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

  • Research program for a search of the origin of Darwinian Evolution. Research program for a vesicle-based model of the origin of Darwinian Evolution on prebiotic early Earth
    Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life, 2016
    Co-Authors: Marc Tessera
    Abstract:

    The search for origin of 'life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian Evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 Evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

Sylvia Baker - One of the best experts on this subject based on the ideXlab platform.

  • Rejecting Darwinian Evolution: The Effects of Education, Church Tradition, and Individual Theological Stance Among UK Churchgoers
    Review of Religious Research, 2018
    Co-Authors: Andrew Village, Sylvia Baker
    Abstract:

    A sample of 2232 committed churchgoers from a range of churches in the UK completed a questionnaire that included a measure of rejection of Darwinian Evolution. Respondents with undergraduate or postgraduate qualifications had slightly lower odds of rejecting Evolution than those without degrees, but whether qualifications were in non-biological science, biology or theology made little difference to the likelihood of rejection. Those who attended Anglican or Methodist (AM) churches were much less likely to reject Evolution than those who attended Evangelical or Pentecostal (EP) churches, but the effect of education on reducing rejection was similar in both groups. Individual theological conservatism was strongly associated with rejection, but whereas liberals showed declining rejection with increased education, there was no such effect for conservatives. Frequent church attendance and Bible reading both predicted rejection, and the effect of Bible reading was most pronounced among AM churchgoers. Higher education of any kind may reduce the likelihood of rejection of Evolution among many UK churchgoers, but theological conservatives from any tradition will tend to maintain their belief that Darwinian Evolution does not explain the origin of species whatever their educational experience.

  • Rejecting Darwinian Evolution: The Effects of Education, Church Tradition, and Individual Theological Stance Among UK Churchgoers
    Review of Religious Research, 2018
    Co-Authors: Andrew Village, Sylvia Baker
    Abstract:

    A sample of 2232 committed churchgoers from a range of churches in the UK completed a questionnaire that included a measure of rejection of Darwinian Evolution. Respondents with undergraduate or postgraduate qualifications had slightly lower odds of rejecting Evolution than those without degrees, but whether qualifications were in non-biological science, biology or theology made little difference to the likelihood of rejection. Those who attended Anglican or Methodist (AM) churches were much less likely to reject Evolution than those who attended Evangelical or Pentecostal (EP) churches, but the effect of education on reducing rejection was similar in both groups. Individual theological conservatism was strongly associated with rejection, but whereas liberals showed declining rejection with increased education, there was no such effect for conservatives. Frequent church attendance and Bible reading both predicted rejection, and the effect of Bible reading was most pronounced among AM churchgoers. Higher education of any kind may reduce the likelihood of rejection of Evolution among many UK churchgoers, but theological conservatives from any tradition will tend to maintain their belief that Darwinian Evolution does not explain the origin of species whatever their educational experience.

  • Rejection of Darwinian Evolution Among Churchgoers in England: The Effects of Psychological Type
    Journal for the Scientific Study of Religion, 2013
    Co-Authors: Andrew Village, Sylvia Baker
    Abstract:

    Rejection of Darwinian Evolution (implying rejection of the common origin of all species, including humans) was assessed among 1,100 churchgoers from a range of Christian denominations in England. The main predictors of rejecting Evolution were denominational affiliation and attendance. Individuals from Pentecostal or evangelical denominations were twice as likely to reject Evolution compared with those from Anglican or Methodist churches. In all denominations, higher attendance was associated with greater rejection of Evolution. Education in general, and theological education in particular, had some effect on reducing rejection, but this was not dependent on having specifically scientific or biological educational qualifications. Psychological type preferences for sensing over intuition and for thinking over feeling also predicted greater rejection, after allowing for the association of type preferences and general religiosity. Reasons for the association between psychological type and rejection of Evolution are discussed in the light of the known characteristics of different function preferences.

Martha Higgins - One of the best experts on this subject based on the ideXlab platform.

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