Consulta: creatorFacets:"Rodrick Wallace"
Registros recuperados: 42
Data/hora: 02/06/2024 13:18:45

The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?
Provedor de dados: 17
Autores: 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 &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3894/version/1

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; 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 &amp;#x27;physics&amp;#x27; 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&amp;#x27;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

Two &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;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 &amp;#x27;normal&amp;#x27; globular and a &amp;#x27;pathological&amp;#x27; amyloid version. The underlying normal &amp;#x27;protein folding code error network&amp;#x27; is found to have one major, highly dominant, &amp;#x27;spherical&amp;#x27; 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

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; transition, enabled a punctuated sequence of increasingly complex genetic codes. These evolved until the ancestor to the present narrow spectrum of nearly maximal codes became locked-in by path dependence.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4120/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/1

On biological homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalizing Landau&amp;#x27;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 &amp;#x27;freeze&amp;#x27; 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 &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3902/version/1

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: 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

Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having &amp;#x27;dual&amp;#x27; information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/1

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6115/version/2

Extending Astrobiology: Consciousness and Culture
Provedor de dados: 17
Autores: 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

Evolution as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a &amp;#x27;language&amp;#x27; 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 &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5339/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/1

On the social induction of Alzheimer&amp;#x27;s disease: An index theorem aging model for amyloid formation
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
The central &amp;#x27;risk factor&amp;#x27; for Alzheimer&amp;#x27;s disease (AD) is age. From first principles, we construct a mathematical model of protein folding and its in vivo regulation that gives this result in a natural manner. We extend the basic approach using topological information theory methods, and examine a case history of socially-induced premature aging in the United States.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6012/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; 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 &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/2

The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?
Provedor de dados: 17
Autores: 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 &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3894/version/2

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: 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 &amp;#x27;energy&amp;#x27; 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 &amp;#x27;developmental&amp;#x27; 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

Cancer and the social induction of aging
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
Age has long been known as the primary population &amp;#x27;risk factor&amp;#x27; 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 &amp;#x27;small molecule&amp;#x27; 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

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein &amp;#x27;molten globule&amp;#x27;. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty&amp;#x27;s (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1

The Evolution of Homochirality
Provedor de dados: 17
Autores: 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&amp;#x27;s spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; 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 &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3902/version/2

Tuning and regulating the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;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

Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; 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 &amp;#x27;language&amp;#x27; 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 &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/1

Lost in translation: Toward a formal model of multilevel, multiscale medicine
Provedor de dados: 17
Autores: 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

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; 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 &amp;#x27;physics&amp;#x27; 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&amp;#x27;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/2

Extending Tlusty&amp;#x27;s method to the glycome: Tuning the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a cognitive paradigm for protein folding regulation will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/2

Unnatural Selection: A new formal approach to punctuated equilibrium in economic systems
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalized Darwinian evolutionary theory has emerged as central to the description of economic process (e.g., Aldrich et. al., 2008). Here we demonstrate that, just as Darwinian principles provide necessary, but not sufficient, conditions for understanding the dynamics of social entities, in a similar manner the asymptotic limit theorems of information theory provide another set of necessary conditions that constrain the evolution of socioeconomic process. These latter constraints can, however, easily be formulated as a statistics-like analytic toolbox for the study of empirical data that is consistent with a generalized Darwinism, and this is no small thing.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5612/version/1

Hunter-Gatherers in a Howling Wilderness: Farming economic systems for human needs
Provedor de dados: 17
Autores: Rodrick Wallace.
Recent advances in evolutionary theory applied to economic structure and process may permit construction of both new economic theory and new tools for data analysis that can help in the design of more robust economic policies and practices, resulting in less frequent and less disruptive Knightian transitions, and enabling as well the design of institutions that are, in turn, less disrupted by those that do occur.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/2

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4120/version/4

The &amp;#x27;consciousness&amp;#x27; of the living state: Extending the Baars global broadcast model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
For the broad spectrum of cognitive biological phenomena having &amp;#x27;dual&amp;#x27; information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/2

Roman roads: The hierarchical endosymbiosis of cognitive modules
Provedor de dados: 17
Autores: Rodrick Wallace.
Serial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of &amp;#x27;Roman roads&amp;#x27; constituting channels for the transmission of information between modules.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3892/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/3

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6115/version/1

Empirical predictions of an intrinsically disordered protein theory approach to glycan/lectin reaction kinetics
Provedor de dados: 17
Autores: 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 &amp;#x27;arm-in-sleeve&amp;#x27; model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated &amp;#x27;spectral&amp;#x27; 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

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/2

Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Provedor de dados: 17
Autores: Rodrick Wallace.
We examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of &amp;#x27;herd infection&amp;#x27; inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5864/version/1

Internal conformation of the &amp;#x27;protein folding code&amp;#x27; inferred from empirical tertiary structural classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying &amp;#x27;protein folding code network&amp;#x27; is found to have one major, highly dominant &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4640/version/1

Medicine beyond magic bullets: a formal case for multilevel interventions
Provedor de dados: 17
Autores: Rodrick Wallace.
Western medicine&amp;#x27;s paradigmatic search for &amp;#x27;magic bullet&amp;#x27; interventions is facing increasing difficulty: Between 1950 and 2010 the inflation-adjusted cost per USFDA-approved drug has increased exponentially in time, a draconian inverse of the famous Moore&amp;#x27;s Law of computing. A sequence of empirically-oriented statistical models suggests that carefully designed synergistic multifactorial and multiscale strategies might evade this relationship.
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6780/version/1

Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Provedor de dados: 17
Autores: 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 &amp;#x27;biological renormalization&amp;#x27; 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

Many in vivo  &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;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 &amp;#x27;protein folding codes&amp;#x27; 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 &amp;#x27;protein folding code&amp;#x27; 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

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: 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

Astrobiological Perspectives on Consciousness
Provedor de dados: 17
Autores: 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

Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the &amp;#x27;logic gate&amp;#x27; spectrum
Provedor de dados: 17
Autores: Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological &amp;#x27;logic gates&amp;#x27; having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6413/version/1