Koichiro Matsuno and Stanley N. Salthe
Article: Chemical Affinity as Material Agency for Naturalizing Contextual Meaning
Information 2012, 3(1), 21-35; doi:10.3390/info3010021 - published online 16 January 2012
Show/Hide AbstractAbstract: Chemical affinity involves the integration of two different types of interaction. One is the interaction operating between a pair of reactants while forming a chemical bond, and the other is the prior interaction between those reactants when they identify a reaction partner. The context of the environments under which chemical reactions proceed is identified by the interaction of the participating chemical reactants themselves unless the material process of internal measurement is substituted by theoretical artifacts in the form of imposed boundary conditions, as in the case, for example, of thermal equilibrium. The identification-interaction specific to each local participant serves as a preparation for the making of chemical bonds. The identification-interaction is intrinsically selective in precipitating those chemical bonds that are synthesized most rapidly among possible reactions. Once meta-stable products appear that mediate chemical syntheses and their partial decompositions without totally decomposing, those products would become selective because of their ongoing participation in the identification-interaction. One important natural example must have been the origin and evolution of life on Earth.

Raquel del Moral and Pedro C. Marijuán
Editorial: Introduction to the Special Issue on Information: Selected Papers from “FIS 2010 Beijing”
Information 2012, 3(1), 16-20; doi:10.3390/info3010016 - published online 4 January 2012
Show/Hide AbstractAbstract: During the last two decades, a systematic re-examination of the whole information science field has taken place around the FIS—Foundations of Information Science—initiative. With the occasion of its Fourth Conference in Beijing 2010, a group of selected contributors and leading practitioners of those fields have been invited to contribute to this Special Issue. What is the status of information science today? What is the relationship between information and the laws of nature? Is information merely “physical”? What is the difference between information and computation? Has the genomic revolution changed the contemporary views on information and life? And what about the nature of social information? Cogent answers to these questions and to quite many others are attempted in the contributions that follow.

William A. Phillips
Article: Self-Organized Complexity and Coherent Infomax from the Viewpoint of Jaynes’s Probability Theory
Information 2012, 3(1), 1-15; doi:10.3390/info3010001 - published online 4 January 2012
Show/Hide AbstractAbstract: This paper discusses concepts of self-organized complexity and the theory of Coherent Infomax in the light of Jaynes’s probability theory. Coherent Infomax, shows, in principle, how adaptively self-organized complexity can be preserved and improved by using probabilistic inference that is context-sensitive. It argues that neural systems do this by combining local reliability with flexible, holistic, context-sensitivity. Jaynes argued that the logic of probabilistic inference shows it to be based upon Bayesian and Maximum Entropy methods or special cases of them. He presented his probability theory as the logic of science; here it is considered as the logic of life. It is concluded that the theory of Coherent Infomax specifies a general objective for probabilistic inference, and that contextual interactions in neural systems perform functions required of the scientist within Jaynes’s theory.

Mark Burgin
Article: Epistemic Information in Stratified M-Spaces
Information 2011, 2(4), 697-726; doi:10.3390/info2040697 - published online 16 December 2011
Show/Hide AbstractAbstract: Information is usually related to knowledge. However, the recent development of information theory demonstrated that information is a much broader concept, being actually present in and virtually related to everything. As a result, many unknown types and kinds of information have been discovered. Nevertheless, information that acts on knowledge, bringing new and updating existing knowledge, is of primary importance to people. It is called epistemic information, which is studied in this paper based on the general theory of information and further developing its mathematical stratum. As a synthetic approach, which reveals the essence of information, organizing and encompassing all main directions in information theory, the general theory of information provides efficient means for such a study. Different types of information dynamics representation use tools of mathematical disciplines such as the theory of categories, functional analysis, mathematical logic and algebra. Here we employ algebraic structures for exploration of information and knowledge dynamics. In Introduction (Section 1), we discuss previous studies of epistemic information. Section 2 gives a compressed description of the parametric phenomenological definition of information in the general theory of information. In Section 3, anthropic information, which is received, exchanged, processed and used by people is singled out and studied based on the Componential Triune Brain model. One of the basic forms of anthropic information called epistemic information, which is related to knowledge, is analyzed in Section 4. Mathematical models of epistemic information are studied in Section 5. In Conclusion, some open problems related to epistemic information are given.

Stefan L. Frank and Gabriella Vigliocco
Article: Sentence Comprehension as Mental Simulation: An Information-Theoretic Perspective
Information 2011, 2(4), 672-696; doi:10.3390/info2040672 - published online 23 November 2011
Show/Hide AbstractAbstract: It has been argued that the mental representation resulting from sentence comprehension is not (just) an abstract symbolic structure but a “mental simulation” of the state-of-affairs described by the sentence. We present a particular formalization of this theory and show how it gives rise to quantifications of the amount of syntactic and semantic information conveyed by each word in a sentence. These information measures predict simulated word-processing times in a dynamic connectionist model of sentence comprehension as mental simulation. A quantitatively similar relation between information content and reading time is known to be present in human reading-time data.

Raquel del Moral , Mónica González , Jorge Navarro and Pedro C. Marijuán
Article: From Genomics to Scientomics: Expanding the Bioinformation Paradigm
Information 2011, 2(4), 651-671; doi:10.3390/info2040651 - published online 9 November 2011
Show/Hide AbstractAbstract: Contemporary biological research (particularly in systems biology and the “omic” disciplines) is factually answering some of the poignant questions associated with the information concept and the limitations of information theory. Here, rather than emphasizing and persisting on a focalized discussion about the i-concept, an ampler conception of “informational entities” will be advocated. The way living cells self-produce, interact with their environment, and collectively organize multi-cell systems becomes a paradigmatic case of what such informational entities consist of. Starting with the fundamentals of molecular recognition, and continuing with the basic cellular processes and subsystems, a new interpretation of the global organization of the living cell must be assayed, so that the equivalents of meaning, value, and intelligence will be approached along an emerging “bioinformational” perspective. Further insights on the informational processes of brains, companies, institutions and human societies at large, and even the sciences themselves, could benefit from—and cross-fertilize with—the advancements derived from the informational approach to living systems. The great advantage fuelling the expansion of the bioinformation paradigm is that, today, cellular information processes may be defined almost to completion at the molecular scale (at least in the case of prokaryotic cells). This is not the case, evidently, with nervous systems and the variety of human organizational, cultural, and social developments. Concretely, the crucial evolutionary phenomenon of protein-domain recombination—knowledge recombination—will be analyzed here as a showcase of, and even as a model for, the interdisciplinary and multidisciplinary mixing of the sciences so prevalent in contemporary societies. Scientomics will be proposed as a new research endeavor to assist advancement. Informationally, the “society of enzymes” appears as a forerunner of the “society of neurons”, and even of the “society of individuals”.