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A special issue of Information (ISSN 2078-2489).

Deadline for manuscript submissions: closed (31 October 2016) | Viewed by 92806

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Prof. Dr. Pedro C. Marijuán

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Grupo de Bioinformación / Bioinformation Group, Instituto Aragonés de Ciencias de la Salud, Centro de Investigación Biomédica de Aragón (CIBA), 50009 Zaragoza, Spain
Interests: multidisciplinary research; systems biology; biology & information; scientomics; sensory-motor approach; laughter research; social information; information science; information philosophy
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Prof. Dr. Abir U. Igamberdiev

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Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
Interests: plant mitochondria; alternative oxidase; respiratory carbon metabolism; photorespiration; environmental and stress biology; interactions of respiration and photosynthesis; plant responses to global change; plant molecular genetics; plant epigenetics; mitochondrial stress-signaling; reactive oxygen and nitrogen species; anaerobic metabolism; cellular energetics; theoretical biology
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Dr. Lin Bi

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International Research Center for Philosophy of Information, Xi’an Jiaotong University,China
Interests: communication science; social information; philosophy of information; system science; history; ICTs

Special Issue Information

Dear Colleagues,

The present Special Issue on Information and Symmetry follows from the special session on Information & Symmetry to be organized in the Symmetry Festival 2016 (in Vienna, 18–22 July 2016, http://festival.symmetry.hu/). With this Special Issue, we try to deepen our understanding of the relationships between two of the most vexed concepts in theoretical science. In spite of clear and cut developments in both realms, their intersection is really problematic, either in mathematics, physics, biology, neurosciences, or social sciences. We will welcome exploratory contributions from any of those domains. With this Special Issue, we are also celebrating the near 20^th anniversary of the first joint session between Symmetrion (Symmetry Institute) and FIS (Foundations of Information Science) on information and symmetry matters (Washington 1995) and the subsequent special issues (Symmetry and Culture, 1996 and 1997). It will be a good occasion to meet again some of those contributors and pass over the views developed during this period.

Prof. Dr. Pedro C. Marijuán
Prof. Dr. Andrei (Abir) Igamberdiev
Dr. Lin Bi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Information is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (12 papers)

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Editorial

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182 KiB

Open AccessEditorial

Information and Symmetry: Adumbrating the Abstract Core of Complex Systems

by Lin Bi, Abir U. Igamberdiev and Pedro C. Marijuán

Information 2017, 8(1), 35; https://doi.org/10.3390/info8010035 - 14 Mar 2017

Viewed by 4562

Abstract

Information and symmetry are essential theoretical concepts that underlie the scientific explanation of a variety of complex systems. In spite of clear-cut developments around both concepts, their intersection is really problematic, either in fields related to mathematics, physics, and chemistry, or even more in those pertaining to biology, neurosciences, and social sciences. The present Special Issue explores recent developments, both theoretical and applied, in most of these disciplines. Full article

(This article belongs to the Special Issue Symmetry and Information)

Research

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11141 KiB

Open AccessArticle

Structural and Functional Modeling of Artificial Bioactive Proteins

by Nikola Štambuk and Paško Konjevoda

Information 2017, 8(1), 29; https://doi.org/10.3390/info8010029 - 5 Mar 2017

Cited by 5 | Viewed by 7166

Abstract

A total of 32 synthetic proteins designed by Michael Hecht and co-workers was investigated using standard bioinformatics tools for the structure and function modeling. The dataset consisted of 15 artificial α-proteins (Hecht_α) designed to fold into 102-residue four-helix bundles and 17 artificial six-stranded β-sheet proteins (Hecht_β). We compared the experimentally-determined properties of the sequences investigated with the results of computational methods for protein structure and bioactivity prediction. The conclusion reached is that the dataset of Michael Hecht and co-workers could be successfully used both to test current methods and to develop new ones for the characterization of artificially-designed molecules based on the specific binary patterns of amino acid polarity. The comparative investigations of the bioinformatics methods on the datasets of both de novo proteins and natural ones may lead to: (1) improvement of the existing tools for protein structure and function analysis; (2) new algorithms for the construction of de novo protein subsets; and (3) additional information on the complex natural sequence space and its relation to the individual subspaces of de novo sequences. Additional investigations on different and varied datasets are needed to confirm the general applicability of this concept. Full article

(This article belongs to the Special Issue Symmetry and Information)

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5628 KiB

Open AccessArticle

Waves as the Symmetry Principle Underlying Cosmic, Cell, and Human Languages

by Sungchul Ji

Information 2017, 8(1), 24; https://doi.org/10.3390/info8010024 - 20 Feb 2017

Cited by 7 | Viewed by 12318

Abstract

In 1997, the author concluded that living cells use a molecular language (cellese) that is isomorphic with the human language (humanese) based on his finding that the former shared 10 out of the 13 design features of the latter. In 2012, the author postulated that cellese and humanese derived from a third language called the cosmic language (or cosmese) and that what was common among these three kinds of languages was waves—i.e., sound waves for humanese, concentration waves for cellese, and quantum waves for cosmese. These waves were suggested to be the symmetry principle underlying cosmese, cellese, and humanese. We can recognize at least five varieties of waves—(i) electromagnetic; (ii) mechanical; (iii) chemical concentration; (iv) gravitational; and (v) probability waves, the last being non-material, in contrast to the first four, which are all material. The study of waves is called “cymatics” and the invention of CymaScope by J. S. Reid of the United Kingdom in 2002 is expected to accelerate the study of waves in general. CymaScope has been used to visualize not only human sounds (i.e., humanese) but also sounds made by individual cells (cellese) in conjunction with Atomic Force Microscopy (AFM) (unpublished observations of J. Gimzewski of UCLA and J. Reid). It can be predicted that the gravitational waves recently detected by the Interferometer Gravitational-Wave Observatory (LIGO) will be visualized with CymaScope one day, thereby transforming gravitational waves into CymaGlyphs. Since cellese in part depends on RNA concentration waves (or RNA glyphs) and humanese includes hieroglyphs that were decoded by Champollion in 1822, it seems reasonable to use cymaglyphs, RNA glyphs, and hieroglyphs as symbols of cosmese, cellese, and humanese, respectively, all based on the principle of waves as the medium of communication. Full article

(This article belongs to the Special Issue Symmetry and Information)

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207 KiB

Open AccessArticle

An Introduction to the Foundations of Chemical Information Theory. Tarski–Lesniewski Logical Structures and the Organization of Natural Sorts and Kinds

by Jerry L. R. Chandler

Information 2017, 8(1), 15; https://doi.org/10.3390/info8010015 - 25 Jan 2017

Cited by 2 | Viewed by 5154

Abstract

Organic mathematics is an applied mathematics of philosophical atomism. The order of the chemical elements in the table of elements is the source of order for the logical operations of addition and subtraction of atomic numbers. The inverse square laws of physics are the source of organization of subatomic structures of chemical atoms (atomic and molecular structures). These facts are foundational to the logic of the chemical sciences and are therefore the scientific basis for chemical information theory. The theories and facts of the chemical sciences are so perplex that several forms of symbolic representations are necessary to communicate the broad range of scientific concepts used to inquire into the nature of natural sorts and kinds. The logics proposed by Tarski, Lesniewski and Malatesta are applied to the construction of a numerical “spine” of perplex numbers representing atomic numbers as meta-symbols in meta-languages. The orbital angular momenta of certain collections of electrical particles (also known as “handedness”) are critical components in constructing the logical propositions of the perplex number “spine”. Biological communication channels can function if and only if the natural sorts and kinds are consistent with the matching patterns of the optical isomers. The terms spinners and twisters are introduced to express the electro-mechanical torques necessary for encoding chemical information. This hypothesis can be tested by several categories of experiments, including clinical pharmaco-dynamics and clinical toxico-dynamics of dissymmetric isomers of different sorts and kinds. Full article

(This article belongs to the Special Issue Symmetry and Information)

12860 KiB

Open AccessArticle

The Matrix Method of Representation, Analysis and Classification of Long Genetic Sequences

by Ivan V. Stepanyan and Sergey V. Petoukhov

Information 2017, 8(1), 12; https://doi.org/10.3390/info8010012 - 17 Jan 2017

Cited by 12 | Viewed by 8774

Abstract

The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed. Full article

(This article belongs to the Special Issue Symmetry and Information)

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1266 KiB

Open AccessArticle

The Genetic Codes: Mathematical Formulae and an Inverse Symmetry-Information Relationship

by Tidjani Négadi

Information 2017, 8(1), 6; https://doi.org/10.3390/info8010006 - 30 Dec 2016

Cited by 2 | Viewed by 12155

Abstract

First, mathematical formulae faithfully describing the distributions of amino acids and codons and reproducing the degeneracies in the various known genetic codes, including the standard genetic code, are constructed, by hand. Second, we summarize another mathematical approach relying on the use of q-deformations to describe these same genetic codes, and add a new application not considered before. Third, by considering these same genetic codes, we find, qualitatively, that an inverse symmetry-information relationship exists. Full article

(This article belongs to the Special Issue Symmetry and Information)

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2454 KiB

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Symmetries in Genetic Systems and the Concept of Geno-Logical Coding

by Sergey V. Petoukhov and Elena S. Petukhova

Information 2017, 8(1), 2; https://doi.org/10.3390/info8010002 - 25 Dec 2016

Cited by 10 | Viewed by 7433

Abstract

The genetic code of amino acid sequences in proteins does not allow understanding and modeling of inherited processes such as inborn coordinated motions of living bodies, innate principles of sensory information processing, quasi-holographic properties, etc. To be able to model these phenomena, the concept of geno-logical coding, which is connected with logical functions and Boolean algebra, is put forward. The article describes basic pieces of evidence in favor of the existence of the geno-logical code, which exists in parallel with the known genetic code of amino acid sequences but which serves for transferring inherited processes along chains of generations. These pieces of evidence have been received due to the analysis of symmetries in structures of molecular-genetic systems. The analysis has revealed a close connection of the genetic system with dyadic groups of binary numbers and with other mathematical objects, which are related with dyadic groups: Walsh functions (which are algebraic characters of dyadic groups), bit-reversal permutations, logical holography, etc. These results provide a new approach for mathematical modeling of genetic structures, which uses known mathematical formalisms from technological fields of noise-immunity coding of information, binary analysis, logical holography, and digital devices of artificial intellect. Some opportunities for a development of algebraic-logical biology are opened. Full article

(This article belongs to the Special Issue Symmetry and Information)

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548 KiB

Open AccessArticle

Retrocausality in Quantum Phenomena and Chemical Evolution

by Koichiro Matsuno

Information 2016, 7(4), 62; https://doi.org/10.3390/info7040062 - 29 Oct 2016

Cited by 15 | Viewed by 5652

Abstract

The interplay between retrocausality and the time-reversal symmetry of the dynamical law of quantum mechanics underscores the significance of the measurement dynamics with the use of indivisible and discrete quantum particles to be mediated. One example of empirical evidence demonstrating the significance of retrocausality going along with time-reversal symmetry is seen in the operation of a reaction cycle to be expected in chemical evolution. A reaction cycle can hold itself when the causative operation of the cycle remains robust, even when facing frequent retrocausal interventions of a quantum-mechanical origin. Quantum mechanics in and of itself has potential in raising a reaction cycle in the prebiotic phase of chemical evolution, even without any help of artefactual scaffoldings of an external origin. Full article

(This article belongs to the Special Issue Symmetry and Information)

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Review

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185 KiB

Open AccessReview

Information Flow in the Brain: Ordered Sequences of Metastable States

by Andrew A. Fingelkurts and Alexander A. Fingelkurts

Information 2017, 8(1), 22; https://doi.org/10.3390/info8010022 - 13 Feb 2017

Cited by 26 | Viewed by 7101

Abstract

In this brief overview paper, we analyse information flow in the brain. Although Shannon’s information concept, in its pure algebraic form, has made a number of valuable contributions to neuroscience, information dynamics within the brain is not fully captured by its classical description. These additional dynamics consist of self-organisation, interplay of stability/instability, timing of sequential processing, coordination of multiple sequential streams, circular causality between bottom-up and top-down operations, and information creation. Importantly, all of these processes are dynamic, hierarchically nested and correspond to continuous brain state change, even if the external environment remains constant. This is where metastable coordination comes into play. In a metastable regime of brain functioning, as a result of the simultaneous co-existence of tendencies for independence and cooperation, information is continuously created, preserved for some time and then dissipated through the formation of dynamical and nested spatio-temporal coalitions among simple neuronal assemblies and larger coupled conglomerates of them—so-called delocalised operational modules. Full article

(This article belongs to the Special Issue Symmetry and Information)

1260 KiB

Open AccessReview

A Symmetric Approach Elucidates Multisensory Information Integration

by Arturo Tozzi and James F. Peters

Information 2017, 8(1), 4; https://doi.org/10.3390/info8010004 - 27 Dec 2016

Cited by 5 | Viewed by 9236

Abstract

Recent advances in neuronal multisensory integration suggest that the five senses do not exist in isolation of each other. Perception, cognition and action are integrated at very early levels of central processing, in a densely-coupled system equipped with multisensory interactions occurring at all temporal and spatial stages. In such a novel framework, a concept from the far-flung branch of topology, namely the Borsuk-Ulam theorem, comes into play. The theorem states that when two opposite points on a sphere are projected onto a circumference, they give rise to a single point containing their matching description. Here we show that the theorem applies also to multisensory integration: two environmental stimuli from different sensory modalities display similar features when mapped into cortical neurons. Topological tools not only shed new light on questions concerning the functional architecture of mind and the nature of mental states, but also provide an empirically assessable methodology. We argue that the Borsuk-Ulam theorem is a general principle underlying nervous multisensory integration, resulting in a framework that has the potential to be operationalized. Full article

(This article belongs to the Special Issue Symmetry and Information)

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1572 KiB

Open AccessReview

Symmetries, Information and Monster Groups before and after the Big Bang

by Arturo Tozzi and James F. Peters

Information 2016, 7(4), 73; https://doi.org/10.3390/info7040073 - 21 Dec 2016

Cited by 3 | Viewed by 7382

Abstract

The Monster group, the biggest of the sporadic groups, is equipped with the highest known number of dimensions and symmetries. Taking into account variants of the Borsuk–Ulam theorem and a novel topological approach cast in a physical fashion that has the potential to be operationalized, the universe can be conceived as a lower-dimensional manifold encompassed in the Monster group. Our universe might arise from spontaneous dimension decrease and symmetry breaking that occur inside the very structure of the Monster Module. We elucidate how the energetic loss caused by projection from higher to lower dimensions and by the Monster group’s non-abelian features is correlated with the present-day asymmetry in the thermodynamic arrow. By linking the Monster Module to its theoretical physical counterparts, it is then possible to calculate its enthalpy and Lie group trajectories. Our approach also reveals how a symmetry break might lead to a universe based on multi-dimensional string theories and CFT/AdS (anti-de Sitter/conformal field theory) correspondence. Full article

(This article belongs to the Special Issue Symmetry and Information)

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Other

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135 KiB

Open AccessEssay

A Conjecture on the Nature of Information, with a “Simple” Example

by Stanley N. Salthe

Information 2017, 8(1), 21; https://doi.org/10.3390/info8010021 - 8 Feb 2017

Viewed by 4438

Abstract

Here, I take the position that information is a result of interactions between observers. In order to proceed with this, I construct a simple physical example, with forces standing in for observers. That example leads me to consider the relation between investigative work [...] Read more.

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