http://www.mdpi.com/journal/information/special_issues/matter/ Dear Colleagues, We stand on the edge of one more major leap in our understanding of the universe. One of many indications for the need of radical re-conceptualization is the fact that in our current understanding most of the universe seems to consist of something we know next to nothing about - dark energy and dark matter. All our knowledge about physics however is based on ordinary energy/matter which makes up less than 5% of what we know as the universe. There are several strategies for attacking this problem of understanding of physical reality, and already today we can see the beginnings of the development of a new conception of the world, where physics is placed in a broader context of human knowledge. It goes via basic ideas of information and computation. This development is a consequence of the advances in information processing technologies which affect knowledge production and our grasp of the fundamental ideas of reality, human mind and cognition, knowledge, sciences, humanities, engineering and arts. Many have already declared that reality basically is an informational phenomenon. To name but a few: Wheeler with IT FROM BIT; Floridi with Informational Structural Realism; Lloyd, Seife, Vedral with Decoding Reality; Frieden with Physics from Fisher Information and more. How does this information relate to energy/matter? The essential for new approaches is closure - coming back to human which is the center of all knowledge production about the world. This self-reflective process has traditionally been avoided because of the practical problems in addressing it computationally. Nowadays we have tools at our disposal which help us understand self-reflective dynamical structures, so this does not present a problem for modeling anymore. The idea is to explore how the framework for knowledge production relates to what can be known (and all of our knowledge is structured information so laws of physics are information about the informational structure of the world – a meta-information). It connects information with matter-energy as we find it in the world and in the observer of the world. This special issue will explore all the different facets of the relationship between the world (physical world as we know it in form of energy/matter) and information. Dr. Gordana Dodig Crnkovic Guest Editor {snippet name="submission_info"} http://www.mdpi.com/2078-2489/3/1/21/ 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. http://www.mdpi.com/2078-2489/3/1/21/ Mon, 16 Jan 2012 00:00:00 CET Information 2012-01-16 3 1 Article 21 35 2078-2489 Chemical Affinity as Material Agency for Naturalizing Contextual Meaning 2012-01-16 doi: 10.3390/info3010021 Koichiro Matsuno Stanley N. Salthe http://www.mdpi.com/2078-2489/3/1/1/ 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. http://www.mdpi.com/2078-2489/3/1/1/ Wed, 04 Jan 2012 00:00:00 CET Information 2012-01-04 3 1 Article 1 15 2078-2489 Self-Organized Complexity and Coherent Infomax from the Viewpoint of Jaynes’s Probability Theory 2012-01-04 doi: 10.3390/info3010001 William A. Phillips http://www.mdpi.com/2078-2489/2/3/560/ Semiotics is widely applied in theories of information. Following the original triadic characterization of reality by Peirce, the linguistic processes involved in information—production, transmission, reception, and understanding—would all appear to be interpretable in terms of signs and their relations to their objects. Perhaps the most important of these relations is that of the representation-one, entity, standing for or representing some other. For example, an index—one of the three major kinds of signs—is said to represent something by being directly related to its object. My position, however, is that the concept of symbolic representations having such roles in information, as intermediaries, is fraught with the same difficulties as in representational theories of mind. I have proposed an extension of logic to complex real phenomena, including mind and information (Logic in Reality; LIR), most recently at the 4th International Conference on the Foundations of Information Science (Beijing, August, 2010). LIR provides explanations for the evolution of complex processes, including information, that do not require any entities other than the processes themselves. In this paper, I discuss the limitations of the standard relation of representation. I argue that more realistic pictures of informational systems can be provided by reference to information as an energetic process, following the categorial ontology of LIR. This approach enables naïve, anti-realist conceptions of anti-representationalism to be avoided, and enables an approach to both information and meaning in the same novel logical framework. http://www.mdpi.com/2078-2489/2/3/560/ Mon, 19 Sep 2011 00:00:00 CEST Information 2011-09-19 2 3 Article 560 578 2078-2489 On Representation in Information Theory 2011-09-19 doi: 10.3390/info2030560 Joseph E. Brenner