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| Registros recuperados: 42 | |
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| Rodrick Wallace. |
| We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Genetics & Genomics; Neuroscience. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3894/version/1 |
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| Rodrick Wallace. |
| Protein folding disorders of aging like Alzheimer's and Parkinson's diseases currently present intractable medical challenges. 'Small molecule' interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary 'physics' or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty's (2010a) elegant exploration of the genetic code. The formalism produces... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4847/version/1 |
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| Rodrick Wallace. |
| Tlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a 'normal' globular and a 'pathological' amyloid version. The underlying normal 'protein folding code error network' is found to have one major, highly dominant, 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4665/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. |
| Generalizing Landau's spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to 'freeze' the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Earth & Environment; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3902/version/1 |
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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 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 '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. |
| A mathematical model based on Tlusty's topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the 'aerobic' transition, enabled a punctuated sequence of increasingly complex genetic codes and protein translators under mechanisms similar to the Serial Endosymbiosis effecting the Eukaryotic transition. These evolved until the ancestor to the present narrow spectrum of nearly maximally robust codes became locked-in by path dependence. |
| Tipo: Manuscript |
Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4120/version/2 |
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| Rodrick Wallace. |
| We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of... |
| Tipo: Manuscript |
Palavras-chave: Developmental Biology; Genetics & Genomics; Neuroscience. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3894/version/2 |
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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; 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. |
| It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau's spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to 'freeze' the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Ecology; Molecular Cell Biology; Earth & Environment; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/3902/version/2 |
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| Rodrick Wallace; Deborah Wallace. |
| We apply Tlusty's information-theoretic index theorem analysis of the genetic code to the glycome, using a cognitive paradigm by which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The model suggests spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity, an effect that may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition. Once focused on a subset of the glycan error code network however, the glycan production machinery must then be regulated by an elaborate cognitive process to ensure that what is produced matches... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Molecular Cell Biology; Pharmacology; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5932/version/2 |
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| Registros recuperados: 42 | |
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