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| Registros recuperados: 42 | |
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| Rodrick Wallace. |
| A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the 'energy' picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual 'developmental' perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4280/version/2 |
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| Rodrick Wallace. |
| The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward. |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5286/version/1 |
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| Rodrick Wallace. |
| Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a 'biological renormalization' perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6849/version/1 |
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| Rodrick Wallace; Deborah Wallace. |
| Age has long been known as the primary population 'risk factor' for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by 'small molecule' interventions at the individual level, but must involve comprehensive prevention... |
| Tipo: Manuscript |
Palavras-chave: Cancer; Immunology; Pharmacology; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6146/version/1 |
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| Rodrick Wallace. |
| Newly-developed methods from the theory of intrinsically disordered proteins can be applied to the flexible glycan structures that coat cellular surfaces and provide rich channels for biological information transmission. Extension of a mechanistic 'arm-in-sleeve' model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated 'spectral' classifications in glycan/lectin interaction, parameterized by an appropriate index of glycan frond length or other index of topological complexity, possibly requiring groupoid classifications analogous to quasicrystals. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6752/version/1 |
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| Rodrick Wallace. |
| The 'self-referential' character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a 'language' model in which genes, gene expression, and environment are represented as interacting information sources. The larger, composite, source that characterizes the high probability evolutionary paths then becomes, in a real sense, a language that speaks itself. The approach represents a significant extension of nonequilibrium condensed matter formalism in which the asymptotic limit theorems of information theory beat back the mathematical thicket a full step, providing necessary, but not sufficient, conditions for punctuated evolutionary transitions that can themselves be expressed as highly... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5339/version/1 |
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| Rodrick Wallace. |
| Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5059/version/1 |
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| Rodrick Wallace. |
| Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5059/version/2 |
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| Rodrick Wallace. |
| The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct. |
| Tipo: Manuscript |
Palavras-chave: Ecology; Neuroscience; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5286/version/2 |
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| Rodrick Wallace. |
| The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction, and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of communication theory, that instantiates the punctuated dynamic relations of organisms with their embedding environments, including the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis, making application to both relatively rapid evolutionary punctuated equilibrium and to the conservation of ecological interactions across deep evolutionary time. |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4496/version/2 |
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| Rodrick Wallace. |
| The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis. |
| Tipo: Manuscript |
Palavras-chave: Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4496/version/1 |
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| Rodrick Wallace. |
| The 'self-referential' character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a 'language' model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics; Earth & Environment; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5650/version/1 |
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| Rodrick Wallace. |
| For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Immunology; Molecular Cell Biology; Pharmacology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6973/version/1 |
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| Rodrick Wallace. |
| Tlusty's topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous 'protein folding codes' can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the 'protein folding code' is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4665/version/2 |
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| Registros recuperados: 42 | |
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