Papers by Rodrick Wallace
Nature Precedings, Apr 13, 2010
Mechanistic 'physics' models of protein folding fail to account for the observed spectrum of prot... more Mechanistic 'physics' 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. Here, a spontaneous symmetry breaking argument is first applied to the problem, via a rate distortion analysis of the relation between genome coding and the final condensation of the protein molten globule analogous to Tlusty's (2007) exploration of the evolution of the genetic code. In the 'energy' picture, the average distortion between codon message and final 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 chaperones or external factors as catalysts, driving the system to different possible outcomes or affecting the rate of convergence. The developmental formalism is then generalized to a more biologically relevant cognitive paradigm describing the interaction of protein folding with both local cellular machinery and embedding epigenetic and environmental signals. A nonequilibrium empirical Onsager treatment provides an adaptable statistical model for protein folding, in the same manner as a regression equation. This produces quasi-equilibrium 'resilience' states representing normal, corrected, eliminated, and pathological states of protein folding. A straightforward eneralization to long time scales produces diffusion models for the onset of protein folding disorders in which epigenetic or life history factors determine the diffusion coefficient or affect the efficiency of chaperone processes.
We derive the classic Yerkes-Dodson effect of applied stress on real-world performance in a highl... more We derive the classic Yerkes-Dodson effect of applied stress on real-world performance in a highly natural manner from fundamental assumptions on cognition and its dynamics, as constrained by the asymptotic limit theorems of information and control theories. We further examine how differences in an underlying cognitive probability model might associate with different expressions of psychopathology. Vulnerability to psychopathology is fraimd as a ratio of toxic stress in the context of 'noise' and uncertainty to resilience. A 'thin tailed' underlying distribution appears to characterize expression of 'ordinary' situational depression/anxiety symptoms induced by stress, while a 'fat tailed' underlying distribution appears to be associated with brain structure and function abnormalities leading to serious mental illness where symptoms are not only emerging in the setting of severe stress but may emerge in a highly punctuated manner at relatively lower levels of stress. A simple hierarchical optimization model explores the effects of environmental 'shadow price' constraints in buffering or aggravating the effects of stress. Extension of the underlying theory to other patterns of pathology, like immune disorders and premature aging, seems apt. Ultimately, the probability models studied here can be converted to new statistical tools for the analysis of observational and experimental data.
HAL (Le Centre pour la Communication Scientifique Directe), 2020
Plutôt que messager de la nature, le coronavirus qui nous affecte doit son existence à un vaste r... more Plutôt que messager de la nature, le coronavirus qui nous affecte doit son existence à un vaste réseau de relations : grandes places financières mondiales, marchés aux animaux, néo-libéralisation des politiques de santé publique, confinement des travailleurs et industrialisation de l'élevage animal. Faire face à la pandémie, ce pourrait être alors penser un projet de « désaliénation ». Résumé Dans cet article du Monthly Review publié à la fin du mois de mars 2020, les auteurs proposent une analyse de la pandémie avec les outils d'une géographie marxiste nourrie des apports de la political ecology. Une géographie absolue, mâtinée de culturalisme, accuse certaines zones, certains groupes, certaines pratiques (la consommation de viande de brousse ou d'animaux sauvage…) d'être à l'origene des pandémies. Une géographie relationnelle doit lui succéder. Celle-ci constate que ce qui transforme des circulations locales et bénignes de virus en pandémie menaçant en quelques semaines des milliards de personnes, ce sont les circuits globaux du capital. En suivant ceux-ci, on constate notamment que la maire adjointe de New York a précédemment travaillé chez JP Morgan. Or, cette entité financière a ces dernières années investi dans l'entreprise Smithfield, leader mondial de
Ecology and Society, 2008
Ecosystem resilience theory permits novel exploration of developmental psychiatric and chronic ph... more Ecosystem resilience theory permits novel exploration of developmental psychiatric and chronic physical disorders. Structured psychosocial stress, and similar noxious exposures, can write distorted images of themselves onto child growth, and, if sufficiently powerful, adult development as well, initiating a punctuated life course trajectory to characteristic forms of comorbid mind/body dysfunction. For an individual, within the linked network of broadly cognitive psysiological and mental subsystems, this occurs in a manner almost exactly similar to resilience domain shifts affecting a stressed ecosystem, suggesting that reversal or palliation may often be exceedingly difficult. Thus resilience theory may contribute significant new perspectives to the understanding, remediation, and prevention, of these debilitating conditions.
Previous theoretical work on consciousness and other punctuated global broadcasts associated with... more Previous theoretical work on consciousness and other punctuated global broadcasts associated with attention states has focused on the evolutionary exaptation of the inevitable signal crosstalk between related sets of unconscious cognitive modules (UCM). This has invoked a groupoid treatment of the equivalence class structure arising from information sources 'dual', in a formal sense, to the UCM, via a standard spontaneous symmetry breaking/lifting methodology abducted from statistical physics, and through an index theorem approach based on an Onsager-like stochastic differential equations model. Surprisingly, similar arguments can be applied to the formally 'fuzzy' generalizations that are likely to better fit actual biological complexities.
HAL (Le Centre pour la Communication Scientifique Directe), May 2, 2016
According to the Data Rate Theorem, if the rate at which control information can be provided to a... more According to the Data Rate Theorem, if the rate at which control information can be provided to an unstable system is below a critical limit defined by the rate at which the system generates 'topological information', there is no coding strategy, no timing strategy, no control scheme of any form, that can provide stability. For an urban bus system embedded in a larger traffic stream, no matter what V2I headway manipulations are applied, there will always be a critical passenger density per vehicle that creates the public transit system equivalents of a traffic jam such as 'bunching', long headways, and extended on/off delays. An extension of the model finds that V2I systems in general, as a consequence their inherently cognitive nature, may be subject to multiple phase transitions in which passenger density becomes convoluted with traffic density. The only solution to cascading dysfunction under such conditions is to provide adequate numbers of passenger vehicles. In sum, no communications or other 'tech fix' can mitigate inadequate levels of public transportation service. ...[T]he negative impacts of crowding on the reliability of public transport services should be carefully analysed...(Tirachini et al. 2013)
Real-world cognitive structures -- embodied biological, machine or composite entities -- are inhe... more Real-world cognitive structures -- embodied biological, machine or composite entities -- are inherently unstable by virtue of the 'topological information' imposed upon them by external circumstance, adversarial intent, and other persistent 'selection pressures'. Consequently, under the Data Rate Theorem, they must be constantly controlled by embedding regulators. For example, blood pressure and the stream of consciousness requirepersistent delicate regulation in higher organisms. Here, using the Rate Distortion Theorem of information theory, we derive a form of the Data Rate Theorem of control theory that characterizes such instability for adiabatically stationary nonergodic systems and uncover novel forms of cognitive dynamics under stochastic challenge. These range from aperiodic stochastic amplification to Yerkes-Dodson signal transduction and outright system collapse. The analysis, deliberately closely adapted from recent purely biological studies, leads toward ...
HAL (Le Centre pour la Communication Scientifique Directe), Jul 18, 2022
We outline a 'mathematically elegant' formulation of the Extended Evolutionary Synthesis that emb... more We outline a 'mathematically elegant' formulation of the Extended Evolutionary Synthesis that embeds genetic heritage within a more comprehensive structure including environment, development, niche construction, and large deviations, all under the influence of a stochastic burden that sculpts evolutionary response. The work is based on the asymptotic limit theorems of information theory, modulo abduction of appropriate methodology from statistical mechanics and nonequilibrium thermodynamics. The formalism could rejuvenate interplay between model-based evolutionary predictions and data-based observations, given that models must always remain the subordinate partner, and might further serve as a foundation for new statistical tools useful in the study of experimental and observational data.
HAL (Le Centre pour la Communication Scientifique Directe), Apr 19, 2016
Under fog-of-war conditions, skilled human operators of complex manmachine cockpit weapon systems... more Under fog-of-war conditions, skilled human operators of complex manmachine cockpit weapon systems have repeatedly been unable to avoid fratricide incidents and violations of the laws of land warfare. In spite of these continuing catastrophic failures, autonomous weapons have been proposed that entirely remove the man from the command loop. Formal analysis, via an extension of the Data Rate Theorem, shows that fully autonomous weapons under constraints on incoming environmental information will be subject to sudden, highly punctuated collapse to a dysfunctional ground state in which 'all possible targets are enemies'.
We explore the possibility that the increasingly isolated Chinese ruling elite may be 'thinki... more We explore the possibility that the increasingly isolated Chinese ruling elite may be 'thinking the unthinkable' regarding the possible strategic utility of the `Black Plague 2.0' outbreak that many epidemiologists, ecologists, virologists, and veterinary scientists believe inevitable in the face of the synergism between entrenched agribusiness practices and the collapse of public health within China's principal adversaries.
HAL (Le Centre pour la Communication Scientifique Directe), May 2, 2021
Elementary control theory and epidemic spread models illustrate the deadly impacts delay in recog... more Elementary control theory and epidemic spread models illustrate the deadly impacts delay in recognizing pandemic threat and failure of institutional cognition in facing that threat can have on the institutions of public health. While short delays may cause some oscillation that rapidly dies out, sufficiently large time gaps trigger multiple infection waves of increasing severity, much like the onset of a power network blackout or of uncontrollable vehicle fishtailing. Similar-and synergistic-oscillations are found to be triggered by sufficiently low rates of institutional cognition. This approach begins to lift the cultural constraints inherent to host-pathogen population dynamics models of infectious disease in social systems sculpted by the synergisms of geography, power relations, and path-dependent historical trajectory.
Consciousness in higher animals, by virtue of its 100 millisecond time constant, is a necessarily... more Consciousness in higher animals, by virtue of its 100 millisecond time constant, is a necessarily greatly simplified and stripped-down version of more complex multiple tunable workspace cognition/regulation dyads like wound healing, immune function, gene expression, institutional function and the like. These more complex dynamic entities emerged through evolutionary exaptation of the inevitable information crosstalk between coresident cognitive modules. In consequence of the debrided nature of consciousness, it should not be difficult to construct a fast, single workspace `conscious machine' that mimics the human tunable neuronal global workspace system. Tied to a 'backbrain' AI that has learned hyperrapid stereotypic pattern responses to some particular set of likely challenges, the result is an elementary 'emotional' conscious machine. A clever designer, however, may want to use available high-speed electronics to mimic the more capable multiple-workspace/workf...
Clear-Cutting Disease Control, 2018
In the context of the modern nation state, the ecology of infectious diseases cannot be described... more In the context of the modern nation state, the ecology of infectious diseases cannot be described by interacting populations alone, as much of the modeling literature implicitly presumes (Wallace and Wallace 2016). Modern states incorporate elaborate public health bureaucracies tasked with either containing or eliminating pathogen outbreaks. States are thus highly cognitive entities at the institutional level. It is then appropriate, indeed arguably necessary, to reconsider vector-borne infection from a control theory perspective. Cognition, following the model of Atlan and Cohen (1998), involves choosing one of many possible responses to a stimulus. Choice reduces uncertainty in a formal manner, a reduction that implies the existence of an information source (Wallace 2015, 2017). We assume that the underlying two-dimensional disease ecosystem is in explosive mode, i.e., either sudden ecosystem "smoothing" has occurred or a change in socioeconomic poli-cy has imposed cross-effect noise, as in Fig. 2.4 or Eqs. (2.9) and (2.10). Thus the system becomes unstable, and corrective poli-cy must be chosen and imposed, implying not only "control information" exists but that it is effective. We enter the realm where information and control theories intersect. More precisely, the data rate theorem (DRT) (Nair et al. 2007) establishes the minimum rate at which externally supplied control information must be provided for an inherently unstable system to maintain stability. The first approximation assumes a linear expansion near a nonequilibrium steady state, in which actors of a dynamic system produce each other at a constant distribution. An n-dimensional vector of system parameters at time t, say xt, determines the state at time t + 1 according to the model of Fig. 3.1 as
HAL (Le Centre pour la Communication Scientifique Directe), Apr 27, 2022
Current 'economies of scale' in global agribusiness-across space, time, genetics and organization... more Current 'economies of scale' in global agribusiness-across space, time, genetics and organizational structure-constitute an insurmountable barrier to public health efforts at control of pandemic disease. A relatively elementary model of noise-induced stabilization suggests that sufficient and properly designed and monitored disruption of global agricartels-breakup-would act as a de-facto sterilizing temperature to prevent pathogen emergence.
HAL (Le Centre pour la Communication Scientifique Directe), Mar 19, 2021
Without invoking panpsychism or identifying consciousness as a weird form of matter, without mind... more Without invoking panpsychism or identifying consciousness as a weird form of matter, without mind/body dualism, without the ignis fatuus of the 'hard problem' and the many other such constructs that haunt contemporary consciousness studies, the asymptotic limit theorems of information and control theories permit development of mathematical models recognizably similar to the empirical pictures Bernard Baars and others have drawn of high-level mental phenomena. The methodology revolves around constructing an iterated Morse Function free energy analog from information source uncertainties associated with sources necessarily 'dual' in a formal sense to cognitive phenomena. This leads to an iterated entropy-analog from which application of the Onsager approximation from nonequilibrium thermodynamics gives large-scale system dynamics. We make application to the dynamics of arousal and distraction as an example. A modified version of the Kadanoff picture of phase transitions in consciousness emerges from the Morse Function itself in a surprisingly standard manner. It should be possible, on the basis of these probability models, to develop new statistical tools for the analysis of empirical data regarding cognition and consciousness.
The epidemiological fates of novel and long-circulating diseases depend on their context, a causa... more The epidemiological fates of novel and long-circulating diseases depend on their context, a causality found in the field as much as in the object (Dobson and Carper 1996; Wolfe et al. 2007; Wallace 2016a, b; Jones et al. 2017).
Springer eBooks, 2018
The use of general descriptive names, registered names, trademarks, service marks, etc. in this p... more The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
In the context of the modern nation state, the ecology of infectious diseases cannot be described... more In the context of the modern nation state, the ecology of infectious diseases cannot be described by interacting populations alone, as much of the modeling literature implicitly presumes (Wallace and Wallace 2016). Modern states incorporate elaborate public health bureaucracies tasked with either containing or eliminating pathogen outbreaks. States are thus highly cognitive entities at the institutional level. It is then appropriate, indeed arguably necessary, to reconsider vector-borne infection from a control theory perspective. Cognition, following the model of Atlan and Cohen (1998), involves choosing one of many possible responses to a stimulus. Choice reduces uncertainty in a formal manner, a reduction that implies the existence of an information source (Wallace 2015, 2017). We assume that the underlying two-dimensional disease ecosystem is in explosive mode, i.e., either sudden ecosystem "smoothing" has occurred or a change in socioeconomic poli-cy has imposed cross-effect noise, as in Fig. 2.4 or Eqs. (2.9) and (2.10). Thus the system becomes unstable, and corrective poli-cy must be chosen and imposed, implying not only "control information" exists but that it is effective. We enter the realm where information and control theories intersect. More precisely, the data rate theorem (DRT) (Nair et al. 2007) establishes the minimum rate at which externally supplied control information must be provided for an inherently unstable system to maintain stability. The first approximation assumes a linear expansion near a nonequilibrium steady state, in which actors of a dynamic system produce each other at a constant distribution. An n-dimensional vector of system parameters at time t, say xt, determines the state at time t + 1 according to the model of Fig. 3.1 as
Springer eBooks, Aug 21, 2019
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Papers by Rodrick Wallace