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Riverside, NY, United States

Unlike the universal genetic code and ordered protein folding, direct application of Tlusty's method to the glycome produces a reducto ad absurdum: From the beginning a complicated system of chemical cognition is needed so that external information constrains and tunes what would otherwise be a monstrously large 'glycan code error network'. Further, the glycan manufacture machinery itself must be regulated by yet other levels of chemical cognition to ensure that what is produced matches what was chosen for production. Application of a rate distortion index theorem/operator method at this second stage appears possible, permitting analytic characterization of the complicated 'glycan spectra' associated with cellular interactions and their dynamics. The regulation of 'low level' biochemical processes, ranging from gene expression and protein folding through the production of flexible glycan surface signalling fronds, appears to require systems of chemical cognition whose sophistication may rival that of high order neural process. © 2011 Elsevier Ireland Ltd. Source

Wallace R.,The New York State Psychiatric Institute
BioSystems | Year: 2011

Tlusty's topological rate distortion analysis of the genetic code is applied to protein symmetries and protein folding rates. Unlike the genetic case, numerous thermodynamically accessible 'protein folding codes' can be identified from empirical classifications. Folding rates follow from a topologically driven rate distortion argument, a model that can, in principle, be extended to intrinsically disordered proteins. The elaborate cellular regulatory machinery of the endoplasmic reticulum and heat shock proteins is needed to prevent transition between the various thermodynamically 'natural' sets of hydrophobic-core protein conformations, and its corrosion by aging would account for the subsequent onset of many protein folding disorders. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the 'protein folding code' is really 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 components within a significantly larger 'protein folding groupoid'. © 2010 Elsevier Ireland Ltd. Source

Wallace R.,The New York State Psychiatric Institute
Cognitive Processing | Year: 2015

The stabilization of human cognition via feedback from embedding social and cultural contexts is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness at different scales: Cultural norms and social interaction are synergistic with individual and group cognition and their disorders. A canonical failure mode in atomistic cultures is found to be a ‘ground state’ collapse well represented by atomistic models of economic interaction that are increasingly characterized as divorced from reality by heterodox economists. That is, high rates of psychopathic and antisocial personality disorder and obsessive compulsive disorder emerge as culture-bound syndromes particular to Western or Westernizing societies, or to those undergoing social disintegration. © 2015, Marta Olivetti Belardinelli and Springer-Verlag Berlin Heidelberg. Source

Wallace R.,The New York State Psychiatric Institute
Ecological Modelling | Year: 2016

Applying biological versions of the Data Rate Theorem and the Arrhenius reaction rate relation, it becomes clear that the search-and-response feedback of developmental selection associated with phenotypic plasticity requires a significant rate of metabolic free energy. Too rapid change in environmental conditions, often coupled with decline in available sources of metabolic free energy, leads to highly punctuated local extinction events. The observed dynamic is likely to be that the animal seems to adapt to environmental alterations for a long time, but then, and quite suddenly, developmental selection fails, leading to local extirpation of the reproducing population. Conversely, mosaicking, by imposing selection demands associated with diversity in time, space, and mode - as in traditional and conservation agricultures - can create energy barriers limiting the evolution and spread of pest or pathogen populations. © 2015 Elsevier B.V. Source

Wallace R.,The New York State Psychiatric Institute
Connection Science | Year: 2014

Maturana's cognitive perspective on the living state, Dretske's insight on how information theory constrains cognition, the Atlan/Cohen cognitive paradigm, and models of intelligence without representation, permit construction of a spectrum of dynamic necessary conditions statistical models of signal transduction, regulation, and metabolism at and across the many scales and levels of organisation of an organism and its context. Nonequilibrium critical phenomena analogous to physical phase transitions, driven by crosstalk, will be ubiquitous, representing not only signal switching, but the recruitment of underlying cognitive modules into tunable dynamic coalitions that address changing patterns of need and opportunity at all scales and levels of organisation. The models proposed here, while certainly providing much conceptual insight, should be most useful in the analysis of empirical data, much as are fitted regression equations. © 2014, © 2014 Taylor & Francis. Source

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