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Entropy, Volume 12, Issue 4 (April 2010), Pages 631-995

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Research

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Open AccessArticle The Antithesis of Entropy: Biosemiotic Communication from Genetics to Human Language with Special Emphasis on the Immune Systems
Entropy 2010, 12(4), 631-705; doi:10.3390/e12040631
Received: 12 January 2010 / Revised: 9 March 2010 / Accepted: 24 March 2010 / Published: 31 March 2010
Cited by 9 | PDF Full-text (2564 KB) | HTML Full-text | XML Full-text
Abstract
Entropy can be defined as the antithesis of well-formed true reports that agree with each other and with the material facts accessible through the experience of one or more competent observers. The abstract convergence (strictly formal, logical agreement) of true narrative representations (TNRs)—ordinary
[...] Read more.
Entropy can be defined as the antithesis of well-formed true reports that agree with each other and with the material facts accessible through the experience of one or more competent observers. The abstract convergence (strictly formal, logical agreement) of true narrative representations (TNRs)—ordinary valid reports of facts of experience—makes them formally more complete than fictions, errors, lies, and nonsense. A limit of absolute entropy is theoretically reached if all resemblance to a TNR is lost. As argued here, TNRs—formally defined along the lines of Peirce's exact logic—provide the necessary foundation for functional human languages and for biosemiotic systems. The theoretical concepts of pragmatic mapping—the fitting of a TNR to whatever facts it represents—and the constructive cycle of abstraction that enables a child to discover the systems underlying such mappings are introduced and illustrated from child development and then shown to apply to the human neuroarchitecture, genetics, fetal development, and our immune systems. It is also argued that biological disorders and disease conditions logically must involve corrupted (damaged, undeveloped, or otherwise incomplete) representations at one or many levels. Full article
Open AccessArticle Entropy-Related Extremum Principles for Model Reduction of Dissipative Dynamical Systems
Entropy 2010, 12(4), 706-719; doi:10.3390/e12040706
Received: 12 February 2010 / Revised: 23 March 2010 / Accepted: 1 April 2010 / Published: 1 April 2010
Cited by 11 | PDF Full-text (1808 KB) | HTML Full-text | XML Full-text
Abstract
Chemical kinetic systems are modeled by dissipative ordinary differential equations involving multiple time scales. These lead to a phase flow generating anisotropic volume contraction. Kinetic model reduction methods generally exploit time scale separation into fast and slow modes, which leads to the occurrence
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Chemical kinetic systems are modeled by dissipative ordinary differential equations involving multiple time scales. These lead to a phase flow generating anisotropic volume contraction. Kinetic model reduction methods generally exploit time scale separation into fast and slow modes, which leads to the occurrence of low-dimensional slow invariant manifolds. The aim of this paper is to review and discuss a computational optimization approach for the numerical approximation of slow attracting manifolds based on entropy-related and geometric extremum principles for reaction trajectories. Full article
(This article belongs to the Special Issue Entropy in Model Reduction)
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Open AccessArticle Statistical Information and Uncertainty: A Critique of Applications in Experimental Psychology
Entropy 2010, 12(4), 720-771; doi:10.3390/e12040720
Received: 11 February 2010 / Revised: 10 March 2010 / Accepted: 1 April 2010 / Published: 7 April 2010
Cited by 8 | PDF Full-text (446 KB) | HTML Full-text | XML Full-text
Abstract
This paper presents, first, a formal exploration of the relationships between information (statistically defined), statistical hypothesis testing, the use of hypothesis testing in reverse as an investigative tool, channel capacity in a communication system, uncertainty, the concept of entropy in thermodynamics, and Bayes’
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This paper presents, first, a formal exploration of the relationships between information (statistically defined), statistical hypothesis testing, the use of hypothesis testing in reverse as an investigative tool, channel capacity in a communication system, uncertainty, the concept of entropy in thermodynamics, and Bayes’ theorem. This exercise brings out the close mathematical interrelationships between different applications of these ideas in diverse areas of psychology. Subsequent illustrative examples are grouped under (a) the human operator as an ideal communications channel, (b) the human operator as a purely physical system, and (c) Bayes’ theorem as an algorithm for combining information from different sources. Some tentative conclusions are drawn about the usefulness of information theory within these different categories. (a) The idea of the human operator as an ideal communications channel has long been abandoned, though it provides some lessons that still need to be absorbed today. (b) Treating the human operator as a purely physical system provides a platform for the quantitative exploration of many aspects of human performance by analogy with the analysis of other physical systems. (c) The use of Bayes’ theorem to calculate the effects of prior probabilities and stimulus frequencies on human performance is probably misconceived, but it is difficult to obtain results precise enough to resolve this question. Full article
(This article belongs to the Special Issue Complexity of Human Language and Cognition)
Open AccessArticle Engineering Model Reduction and Entropy-based Lyapunov Functions in Chemical Reaction Kinetics
Entropy 2010, 12(4), 772-797; doi:10.3390/e12040772
Received: 23 February 2010 / Revised: 21 March 2010 / Accepted: 23 March 2010 / Published: 8 April 2010
Cited by 16 | PDF Full-text (350 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, the structural properties of chemical reaction systems obeying the mass action law are investigated and related to the physical and chemical properties of the system. An entropy-based Lyapunov function candidate serves as a tool for proving structural stability, the existence
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In this paper, the structural properties of chemical reaction systems obeying the mass action law are investigated and related to the physical and chemical properties of the system. An entropy-based Lyapunov function candidate serves as a tool for proving structural stability, the existence of which is guaranteed by the second law of thermodynamics. The commonly used engineering model reduction methods, the so-called quasi equilibrium and quasi steady state assumption based reductions, together with the variable lumping are formally defined as model transformations acting on the reaction graph. These model reduction transformations are analysed to find conditions when (a) the reduced model remains in the same reaction kinetic system class, (b) the reduced model retains the most important properties of the original one including structural stability. It is shown that both variable lumping and quasi equilibrium based reduction preserve both the reaction kinetic form and the structural stability of reaction kinetic models of closed systems with mass action law kinetics, but this is not always the case for the reduction based on quasi steady state assumption. Full article
(This article belongs to the Special Issue Entropy in Model Reduction)
Open AccessArticle Article Omission in Dutch Children with SLI: A Processing Approach
Entropy 2010, 12(4), 798-817; doi:10.3390/e12040798
Received: 21 December 2009 / Revised: 5 March 2010 / Accepted: 7 April 2010 / Published: 8 April 2010
Cited by 4 | PDF Full-text (270 KB) | HTML Full-text | XML Full-text
Abstract
Children with Specific Language Impairment (SLI) show difficulties with grammatical morphology. Based on the data from 12 Dutch children with SLI, an information-theoretical model is proposed in which the noun-article set dependency is modeled as a channel. We propose that reduced capacity of
[...] Read more.
Children with Specific Language Impairment (SLI) show difficulties with grammatical morphology. Based on the data from 12 Dutch children with SLI, an information-theoretical model is proposed in which the noun-article set dependency is modeled as a channel. We propose that reduced capacity of this channel is responsible for article omission. The Kullback-Leibler divergence between input and output distribution of article production provides an index of the channel capacity, which is shown to correlate with the percentage of article omission and to lag behind in SLI development as compared to typically developing children. Full article
(This article belongs to the Special Issue Complexity of Human Language and Cognition)
Open AccessArticle Parametric Bayesian Estimation of Differential Entropy and Relative Entropy
Entropy 2010, 12(4), 818-843; doi:10.3390/e12040818
Received: 16 November 2009 / Revised: 28 March 2010 / Accepted: 2 April 2010 / Published: 9 April 2010
Cited by 17 | PDF Full-text (356 KB) | HTML Full-text | XML Full-text
Abstract
Given iid samples drawn from a distribution with known parametric form, we propose the minimization of expected Bregman divergence to form Bayesian estimates of differential entropy and relative entropy, and derive such estimators for the uniform, Gaussian, Wishart, and inverse Wishart distributions. Additionally,
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Given iid samples drawn from a distribution with known parametric form, we propose the minimization of expected Bregman divergence to form Bayesian estimates of differential entropy and relative entropy, and derive such estimators for the uniform, Gaussian, Wishart, and inverse Wishart distributions. Additionally, formulas are given for a log gamma Bregman divergence and the differential entropy and relative entropy for the Wishart and inverse Wishart. The results, as always with Bayesian estimates, depend on the accuracy of the prior parameters, but example simulations show that the performance can be substantially improved compared to maximum likelihood or state-of-the-art nonparametric estimators. Full article
(This article belongs to the Special Issue Distance in Information and Statistical Physics Volume 2)
Open AccessArticle Sound Symbolism in Basic Vocabulary
Entropy 2010, 12(4), 844-858; doi:10.3390/e12040844
Received: 23 December 2009 / Revised: 2 April 2010 / Accepted: 7 April 2010 / Published: 9 April 2010
Cited by 10 | PDF Full-text (164 KB) | HTML Full-text | XML Full-text
Abstract
The relationship between meanings of words and their sound shapes is to a large extent arbitrary, but it is well known that languages exhibit sound symbolism effects violating arbitrariness. Evidence for sound symbolism is typically anecdotal, however. Here we present a systematic approach.
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The relationship between meanings of words and their sound shapes is to a large extent arbitrary, but it is well known that languages exhibit sound symbolism effects violating arbitrariness. Evidence for sound symbolism is typically anecdotal, however. Here we present a systematic approach. Using a selection of basic vocabulary in nearly one half of the world’s languages we find commonalities among sound shapes for words referring to same concepts. These are interpreted as due to sound symbolism. Studying the effects of sound symbolism cross-linguistically is of key importance for the understanding of language evolution. Full article
(This article belongs to the Special Issue Complexity of Human Language and Cognition)
Open AccessArticle Air Conditioning Systems from a 2nd Law Perspective
Entropy 2010, 12(4), 859-877; doi:10.3390/e12040859
Received: 18 December 2009 / Revised: 16 February 2010 / Accepted: 6 April 2010 / Published: 13 April 2010
Cited by 4 | PDF Full-text (310 KB) | HTML Full-text | XML Full-text
Abstract
In this paper exergy analysis is used to assess the performance of the three most common air conditioning plant schemes: all-air, dual-duct and fan-coil systems. The results are presented in terms of flow diagrams to provide a clear picture of the exergy flow
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In this paper exergy analysis is used to assess the performance of the three most common air conditioning plant schemes: all-air, dual-duct and fan-coil systems. The results are presented in terms of flow diagrams to provide a clear picture of the exergy flow across the systems. The most relevant outcomes are that the air cooling and dehumidification is the process most responsible for the exergy loss and that the exergy efficiency of the overall systems is rather low; thus the quest for more appropriate technologies. Solar-assisted air-conditioning is also discussed, outlining the possibilities and the constraints. Full article
(This article belongs to the Special Issue Exergy: Analysis and Applications)
Open AccessArticle The Cybersemiotics and Info-Computationalist Research Programmes as Platforms for Knowledge Production in Organisms and Machines
Entropy 2010, 12(4), 878-901; doi:10.3390/e12040878
Received: 23 February 2010 / Revised: 1 April 2010 / Accepted: 12 April 2010 / Published: 13 April 2010
Cited by 6 | PDF Full-text (102 KB) | HTML Full-text | XML Full-text
Abstract
Both Cybersemiotics and Info-computationalist research programmes represent attempts to unify understanding of information, knowledge and communication. The first one takes into account phenomenological aspects of signification which are insisting on the human experience "from within". The second adopts solely the view "from the
[...] Read more.
Both Cybersemiotics and Info-computationalist research programmes represent attempts to unify understanding of information, knowledge and communication. The first one takes into account phenomenological aspects of signification which are insisting on the human experience "from within". The second adopts solely the view "from the outside" based on scientific practice, with an observing agent generating inter-subjective knowledge in a research community. The process of knowledge production, embodied into networks of cognizing agents interacting with the environment and developing through evolution is studied on different levels of abstraction in both frames of reference. In order to develop scientifically tractable models of evolution of intelligence in informational structures from pre-biotic/chemical to living networked intelligent organisms, including the implementation of those models in artificial agents, a basic level language of Info-Computationalism has shown to be suitable. There are however contexts in which we deal with complex informational structures essentially dependent on human first person knowledge where high level language such as Cybersemiotics is the appropriate tool for conceptualization and communication. Two research projects are presented in order to exemplify the interplay of info-computational and higher-order approaches: The Blue Brain Project where the brain is modeled as info-computational system, a simulation in silico of a biological brain function, and Biosemiotics research on genes, information, and semiosis in which the process of semiosis is understood in info-computational terms. The article analyzes differences and convergences of Cybersemiotics and Info-computationalist approaches which by placing focus on distinct levels of organization, help elucidate processes of knowledge production in intelligent agents. Full article
Open AccessArticle On the Problem of Formulating Principles in Nonequilibrium Thermodynamics
Entropy 2010, 12(4), 926-931; doi:10.3390/e12040926
Received: 24 March 2010 / Accepted: 8 April 2010 / Published: 14 April 2010
Cited by 4 | PDF Full-text (73 KB) | HTML Full-text | XML Full-text
Abstract
In this work, we consider the choice of a system suitable for the formulation of principles in nonequilibrium thermodynamics. It is argued that an isolated system is a much better candidate than a system in contact with a bath. In other words, relaxation
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In this work, we consider the choice of a system suitable for the formulation of principles in nonequilibrium thermodynamics. It is argued that an isolated system is a much better candidate than a system in contact with a bath. In other words, relaxation processes rather than stationary processes are more appropriate for the formulation of principles in nonequilibrium thermodynamics. Arguing that slow varying relaxation can be described with quasi-stationary process, it is shown for two special cases, linear nonequilibrium thermodynamics and linearized Boltzmann equation, that solutions of these problems are in accordance with the maximum entropy production principle. Full article
(This article belongs to the Special Issue What Is Maximum Entropy Production and How Should We Apply It?)
Open AccessArticle Entropy in the Present and Early Universe: New Small Parameters and Dark Energy Problem
Entropy 2010, 12(4), 932-952; doi:10.3390/e12040932
Received: 22 March 2010 / Revised: 7 April 2010 / Accepted: 10 April 2010 / Published: 14 April 2010
Cited by 14 | PDF Full-text (286 KB) | HTML Full-text | XML Full-text
Abstract
It is demonstrated that entropy and its density play a significant role in solving the problem of the vacuum energy density (cosmological constant) of the Universe and hence the dark energy problem. Taking this in mind, two most popular models for dark energy—Holographic
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It is demonstrated that entropy and its density play a significant role in solving the problem of the vacuum energy density (cosmological constant) of the Universe and hence the dark energy problem. Taking this in mind, two most popular models for dark energy—Holographic Dark Energy Model and Agegraphic Dark Energy Model—are analysed. It is shown that the fundamental quantities in the first of these models may be expressed in terms of a new small dimensionless parameter that is naturally occurring in High Energy Gravitational Thermodynamics and Gravitational Holography (UV-limit). On this basis, the possibility of a new approach to the problem of Quantum Gravity is discussed. Besides, the results obtained on the uncertainty relation of the pair “cosmological constant–volume of space-time”, where the cosmological constant is a dynamic quantity, are reconsidered and generalized up to the Generalized Uncertainty Relation. Full article
(This article belongs to the Special Issue Feature Papers: Entropy Concepts and Applications)
Open AccessArticle Entropy of Bounding Tori
Entropy 2010, 12(4), 953-960; doi:10.3390/e12040953
Received: 27 January 2010 / Revised: 5 March 2010 / Accepted: 13 April 2010 / Published: 15 April 2010
PDF Full-text (221 KB) | HTML Full-text | XML Full-text
Abstract
Branched manifolds that describe strange attractors in R3 can be enclosed in, and are organized by, canonical bounding tori. Tori of genus g are labeled by a symbol sequence, or “periodic orbit”, of period g-1. We show that the number of
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Branched manifolds that describe strange attractors in R3 can be enclosed in, and are organized by, canonical bounding tori. Tori of genus g are labeled by a symbol sequence, or “periodic orbit”, of period g-1. We show that the number of distinct canonical bounding tori grows exponentially like N(g) ~ eγ(g-1), with eγ = 3, so that the “bounding tori entropy” is log(3). Full article
Open AccessArticle Effect of Counterion and Configurational Entropy on the Surface Tension of Aqueous Solutions of Ionic Surfactant and Electrolyte Mixtures
Entropy 2010, 12(4), 983-995; doi:10.3390/e12040983
Received: 2 March 2010 / Revised: 10 April 2010 / Accepted: 17 April 2010 / Published: 23 April 2010
Cited by 4 | PDF Full-text (198 KB) | HTML Full-text | XML Full-text
Abstract
In order to clarify the adsorption behavior of cationic surfactants on the air/aqueous electrolyte solution surface, we derived the theoretical equation for the surface tension. The equation includes the electrical work required for charging the air/water surface and the work attributable to the
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In order to clarify the adsorption behavior of cationic surfactants on the air/aqueous electrolyte solution surface, we derived the theoretical equation for the surface tension. The equation includes the electrical work required for charging the air/water surface and the work attributable to the configurational entropy in the adsorbed film. By fitting the equation to the experimental data, we determined the binding constant between adsorbed surfactant ion and counterion, and found that the bromide ions, rather than the chloride ions, are preferentially adsorbed by the air/water surface. Furthermore, it was suggested that the contribution of configurational entropy to the surface tension is predominant in the presence of electrolytes because of the increase in the surface density of surfactant molecules associated with decreasing the repulsive interaction between their hydrophilic groups. Full article
(This article belongs to the Special Issue Configurational Entropy)
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Review

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Open AccessReview Exergy as a Tool for Ecosystem Health Assessment
Entropy 2010, 12(4), 902-925; doi:10.3390/e12040902
Received: 31 December 2009 / Revised: 7 March 2010 / Accepted: 10 March 2010 / Published: 13 April 2010
Cited by 18 | PDF Full-text (387 KB) | HTML Full-text | XML Full-text
Abstract
Exergy is demonstrated to be a useful measurable parameter reflecting the state of the ecosystem, and allowing estimation of the severity of its anthropogenous damage. Exergy is shown to have advantages such as good theoretical basis in thermodynamics, close relation to information theory,
[...] Read more.
Exergy is demonstrated to be a useful measurable parameter reflecting the state of the ecosystem, and allowing estimation of the severity of its anthropogenous damage. Exergy is shown to have advantages such as good theoretical basis in thermodynamics, close relation to information theory, rather high correlation with others ecosystem goal functions and relative ease of computation. Nowadays exergy is often used in ecological assessment. This paper reviews the application of exergy in ecology in the fields of ecological modeling and natural ecosystem monitoring. Special attention is paid to the use of exergy for aquatic ecosystem studies, particularly, assessment of the lake Baikal ecosystem state. Full article
(This article belongs to the Special Issue Exergy: Analysis and Applications)
Open AccessReview Influence of Conformational Entropy on the Protein Folding Rate
Entropy 2010, 12(4), 961-982; doi:10.3390/e12040961
Received: 30 December 2009 / Revised: 15 March 2010 / Accepted: 30 March 2010 / Published: 16 April 2010
Cited by 6 | PDF Full-text (939 KB) | HTML Full-text | XML Full-text
Abstract
One of the most important questions in molecular biology is what determines folding pathways: native structure or protein sequence. There are many proteins that have similar structures but very different sequences, and a relevant question is whether such proteins have similar or different
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One of the most important questions in molecular biology is what determines folding pathways: native structure or protein sequence. There are many proteins that have similar structures but very different sequences, and a relevant question is whether such proteins have similar or different folding mechanisms. To explain the differences in folding rates of various proteins, the search for the factors affecting the protein folding process goes on. Here, based on known experimental data, and using theoretical modeling of protein folding based on a capillarity model, we demonstrate that the relation between the average conformational entropy and the average energy of contacts per residue, that is the entropy capacity, will determine the possibility of the given chain to fold to a particular topology. The difference in the folding rate for proteins sharing more ball-like and less ball-like folds is the result of differences in the conformational entropy due to a larger surface of the boundary between folded and unfolded phases in the transition state for proteins with a more ball-like fold. The result is in agreement with the experimental folding rates for 67 proteins. Proteins with high or low side chain entropy would have extended unfolded regions and would require some additional agents for complete folding. Such proteins are common in nature, and their structural properties are of biological importance. Full article
(This article belongs to the Special Issue Entropies of Polymers)

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