What is information?†

Rebuilding the Habitable Zone from the Bottom up with Computational Zones

Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs and may be a fundamental measure of living systems. The opportunity for biological computation, represented in the propagation and selection-driven evolution of information-carrying organic molecular structures, has been partially characterized in terms of planetary habitable zones (HZs) based on primary conditions such as temperature and the presence of liquid water. A generalization of this concept to computational zones (CZs) is proposed, with constraints set by three principal characteristics: capacity (including computation rates), energy, and instantiation (or substrate, including spatial extent). CZs naturally combine traditional habitability factors, including those associated with biological function that incorporate the chemical milieu, constraints on nutrients and free energy, as well as element availability. Two example applications are presented by examining the fundamental thermodynamic work efficiency and Landauer limit of photon-driven biological computation on planetary surfaces and of generalized computation in stellar energy capture structures (a.k.a. Dyson structures). It is suggested that CZs that involve nested structures or substellar objects could manifest unique observational signatures as cool far-infrared emitters. While these latter scenarios are entirely hypothetical, they offer a useful, complementary introduction to the potential universality of CZs.

The QBIT theory of consciousness: Entropy and qualia

The QBIT theory is a recently introduced multi-disciplinary approach to the problem of consciousness. One of the main axioms of the theory is that when information-theoretic certainty of an observer about a stimulus goes beyond a certain threshold, the observer becomes conscious of that stimulus. This axiom could provide an explanation for how the brain generates consciousness.In short, the QBIT theory suggests that the brain generates consciousness by reducing the entropy of its internal representations below a critical threshold. This paper explains how the brain gradually minimizes the entropy of its internal representations and consequently generate minimum-entropy representations (also known as conscious representations or qualia). The paper also explores the consequences of this entropy-minimization process in the context of quantum information theory.

The QBIT Theory of Consciousness: Information, Correlation, and Coherence

The ultimate goal of the QBIT theory is to provide a scientific solution to the problem of consciousness. The theory assumes that qualia (plural for quale) are real physical entities. Each quale is a physical system consisting of qubits bonded together by quantum entanglement. The qubits of a quale are so intimately bonded together that they collectively form a unified whole that is more than (and different from) the sum of its parts. A quale is a highly organized, coherent system. Organization and coherence are manifestations of information. The more the amount of information in a system, the more organized, integrated, and coherent the system is. That is why the QBIT theory suggests that qualia are maximally entangled, maximally coherent systems containing high amounts of information, and extremely low amounts of entropy or uncertainty.

Alzheimer's disease as a fundamental disease of information processing systems: An information theory perspective

The human brain is a dynamic multiplex of information, both neural (neurotransmitter-to-neuron, involving 1.5×10¹⁵ action potentials per minute) and immunological (cytokine-to-microglia, providing continuous immune surveillance via 1.5×10¹⁰ immunocompetent cells). This conceptualization highlights the opportunity of exploiting "information" not only in the mechanistic understanding of brain pathology, but also as a potential therapeutic modality. Arising from its parallel yet interconnected proteopathic-immunopathic pathogeneses, Alzheimer's disease (AD) enables an exploration of the mechanistic and therapeutic contributions of information as a physical process central to brain disease progression. This review first considers the definition of information and its relevance to neurobiology and thermodynamics. Then we focus on the roles of information in AD using its two classical hallmarks. We assess the pathological contributions of β-amyloid peptides to synaptic dysfunction and reconsider this as a source of noise that disrupts information transfer between presynaptic and postsynaptic neurons. Also, we treat the triggers that activate cytokine-microglial brain processes as information-rich three-dimensional patterns, including pathogen-associated molecular patterns and damage-associated molecular patterns. There are structural and functional similarities between neural and immunological information with both fundamentally contributing to brain anatomy and pathology in health and disease. Finally, the role of information as a therapeutic for AD is introduced, particularly cognitive reserve as a prophylactic protective factor and cognitive therapy as a therapeutic contributor to the comprehensive management of ongoing dementia.

The QBIT Theory: Consciousness from Entangled Qubits

How does the brain generate consciousness? The present paper is an attempt to answer this question from the perspective of the QBIT theory. In sum, the theory argues that the brain has a prior belief (P) about the stimulus that has caused a sensory representation (R) to be created in the brain. When the conditional entropy of P given R becomes less than zero, the brain becomes more than certain about (i.e. becomes conscious of) the stimulus. Conditional entropy can become negative (and thus the brain can become more than certain) only if the brain uses entangled quantum information in its computations. The QBIT theory suggests that, at the most fundamental level, consciousness is nothing but a special kind of entangled information.

Learning size-adaptive molecular substructures for explainable drug-drug interaction prediction by substructure-aware graph neural network

Drug-drug interactions (DDIs) can trigger unexpected pharmacological effects on the body, and the causal mechanisms are often unknown. Graph neural networks (GNNs) have been developed to better understand DDIs. However, identifying key substructures that contribute most to the DDI prediction is a challenge for GNNs. In this study, we presented a substructure-aware graph neural network, a message passing neural network equipped with a novel substructure attention mechanism and a substructure-substructure interaction module (SSIM) for DDI prediction (SA-DDI). Specifically, the substructure attention was designed to capture size- and shape-adaptive substructures based on the chemical intuition that the sizes and shapes are often irregular for functional groups in molecules. DDIs are fundamentally caused by chemical substructure interactions. Thus, the SSIM was used to model the substructure-substructure interactions by highlighting important substructures while de-emphasizing the minor ones for DDI prediction. We evaluated our approach in two real-world datasets and compared the proposed method with the state-of-the-art DDI prediction models. The SA-DDI surpassed other approaches on the two datasets. Moreover, the visual interpretation results showed that the SA-DDI was sensitive to the structure information of drugs and was able to detect the key substructures for DDIs. These advantages demonstrated that the proposed method improved the generalization and interpretation capability of DDI prediction modeling.

Entropy and institutional theory

Purpose

Once introduced and conceptualized as a factor that causes erosion and decay of social institutions and subsequent deinstitutionalization, the notion of entropy is at odds with predictions of institutional isomorphism and seems to directly contradict the tendency toward ever-increasing institutionalization. The purpose of this paper is to offer a resolution of this theoretical inconsistency by revisiting the meaning of entropy and reconceptualizing institutionalization from an information-theoretic point of view.

Design/methodology/approach

It is a theoretical paper that offers an information perspective on institutionalization.

Findings

A mistaken understanding of the nature and role of entropy in the institutional theory is caused by conceptualizing it as a force that counteracts institutional tendencies and acts in opposite direction. Once institutionalization and homogeneity are seen as a product of natural tendencies in the organizational field, the role of entropy becomes clear. Entropy manifests itself at the level of information processing and corresponds with increasing uncertainty and the decrease of the value of information. Institutionalization thus can be seen as a special case of an increase in entropy and a decrease of knowledge. Institutionalization is a state of maximum entropy.

Originality/value

It is explained why institutionalization and institutional persistence are what to be expected in the long run and why information entropy contributes to this tendency. Contrary to the tenets of the institutional work perspective, no intentional efforts of individuals and collective actors are needed to maintain institutions. In this respect, the paper contributes to the view of institutional theory as a theory of self-organization.

From the origin of life to pandemics: emergent phenomena in complex systems

When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This non-trivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems-from physical to biological and social-and is often related to collective behaviour. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the theme issue Emergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Information Fragmentation, Encryption and Information Flow in Complex Biological Networks

Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network’s structure as opposed to its function. Here, we introduce a new information-theoretic tool—information fragmentation analysis—that, given full phenotypic data, allows us to localize information in complex networks, determine how fragmented (across multiple nodes of the network) the information is, and assess the level of encryption of that information. Using information fragmentation matrices we can also create information flow graphs that illustrate how information propagates through these networks. We illustrate the use of this tool by analyzing how artificial brains that evolved in silico solve particular tasks, and show how information fragmentation analysis provides deeper insights into how these brains process information and “think”. The measures of information fragmentation and encryption that result from our methods also quantify complexity of information processing in these networks and how this processing complexity differs between primary exposure to sensory data (early in the lifetime) and later routine processing.

Does Amount of Information Support Aesthetic Values?

Obtaining information from the world is important for survival. The brain, therefore, has special mechanisms to extract as much information as possible from sensory stimuli. Hence, given its importance, the amount of available information may underlie aesthetic values. Such information-based aesthetic values would be significant because they would compete with others to drive decision-making. In this article, we ask, "What is the evidence that amount of information support aesthetic values?" An important concept in the measurement of informational volume is entropy. Research on aesthetic values has thus used Shannon entropy to evaluate the contribution of quantity of information. We review here the concepts of information and aesthetic values, and research on the visual and auditory systems to probe whether the brain uses entropy or other relevant measures, specially, Fisher information, in aesthetic decisions. We conclude that information measures contribute to these decisions in two ways: first, the absolute quantity of information can modulate aesthetic preferences for certain sensory patterns. However, the preference for volume of information is highly individualized, with information-measures competing with organizing principles, such as rhythm and symmetry. In addition, people tend to be resistant to too much entropy, but not necessarily, high amounts of Fisher information. We show that this resistance may stem in part from the distribution of amount of information in natural sensory stimuli. Second, the measurement of entropic-like quantities over time reveal that they can modulate aesthetic decisions by varying degrees of surprise given temporally integrated expectations. We propose that amount of information underpins complex aesthetic values, possibly informing the brain on the allocation of resources or the situational appropriateness of some cognitive models.

Entropy: From Thermodynamics to Information Processing

Entropy is a concept that emerged in the 19th century. It used to be associated with heat harnessed by a thermal machine to perform work during the Industrial Revolution. However, there was an unprecedented scientific revolution in the 20th century due to one of its most essential innovations, i.e., the information theory, which also encompasses the concept of entropy. Therefore, the following question is naturally raised: “what is the difference, if any, between concepts of entropy in each field of knowledge?” There are misconceptions, as there have been multiple attempts to conciliate the entropy of thermodynamics with that of information theory. Entropy is most commonly defined as “disorder”, although it is not a good analogy since “order” is a subjective human concept, and “disorder” cannot always be obtained from entropy. Therefore, this paper presents a historical background on the evolution of the term “entropy”, and provides mathematical evidence and logical arguments regarding its interconnection in various scientific areas, with the objective of providing a theoretical review and reference material for a broad audience.

Mediated Electrochemical Probing: A Systems-Level Tool for Redox Biology

Biology uses well-known redox mechanisms for energy harvesting (e.g., respiration), biosynthesis, and immune defense (e.g., oxidative burst), and now we know biology uses redox for systems-level communication. Currently, we have limited abilities to "eavesdrop" on this redox modality, which can be contrasted with our abilities to observe and actuate biology through its more familiar ionic electrical modality. In this Perspective, we argue that the coupling of electrochemistry with diffusible mediators (electron shuttles) provides a unique opportunity to access the redox communication modality through its electrical features. We highlight previous studies showing that mediated electrochemical probing (MEP) can "communicate" with biology to acquire information and even to actuate specific biological responses (i.e., targeted gene expression). We suggest that MEP may reveal an extent of redox-based communication that has remained underappreciated in nature and that MEP could provide new technological approaches for redox biology, bioelectronics, clinical care, and environmental sciences.

Karyotype coding: The creation and maintenance of system information for complexity and biodiversity

The mechanism of biological information flow is of vital importance. However, traditional research surrounding the genetic code that follows the central dogma to a phenotype faces challengers, including missing heritability and two-phased evolution. Here, we propose the karyotype code, which by organizing genes along chromosomes at once preserves species genome information and provides a platform for other genetic and nongenetic information to develop and accumulate. This specific genome-level code, which exists in all living systems, is compared to the genetic code and other organic codes in the context of information management, leading to the concept of hierarchical biological codes and an 'extended' definition of adaptor where the adaptors of a code can be not only molecular structures but also, more commonly, biological processes. Notably, different levels of a biosystem have their own mechanisms of information management, and gene-coded parts inheritance preserves "parts information" while karyotype-coded system inheritance preserves the "system information" which organizes parts information. The karyotype code prompts many questions regarding the flow of biological information, including the distinction between information creation, maintenance, modification, and usage, along with differences between living and non-living systems. How do biological systems exist, reproduce, and self-evolve for increased complexity and diversity? Inheritance is mediated by organic codes which function as informational tools to organize chemical reactions, create new information, and preserve frozen accidents, transforming historical miracles into biological routines.

Current understanding of biological identity at the nanoscale and future prospects

Nanoscale objects are processed by living organisms using highly evolved and sophisticated endogenous cellular networks, specifically designed to manage objects of this size. While these processes potentially allow nanostructures unique access to and control over key biological machineries, they are also highly protected by cell or host defence mechanisms at all levels. A thorough understanding of bionanoscale recognition events, including the molecules involved in the cell recognition machinery, the nature of information transferred during recognition processes and the coupled downstream cellular processing, would allow us to achieve a qualitatively novel form of biological control and advanced therapeutics. Here we discuss evolving fundamental microscopic and mechanistic understanding of biological nanoscale recognition. We consider the interface between a nanostructure and a target cell membrane, outlining the categories of nanostructure properties that are recognized, and the associated nanoscale signal transduction and cellular programming mechanisms that constitute biological recognition.

Informational architecture across non-living and living collectives

Collective behavior is widely regarded as a hallmark property of living and intelligent systems. Yet, many examples are known of simple physical systems that are not alive, which nonetheless display collective behavior too, prompting simple physical models to often be adopted to explain living collective behaviors. To understand collective behavior as it occurs in living examples, it is important to determine whether or not there exist fundamental differences in how non-living and living systems act collectively, as well as the limits of the intuition that can be built from simpler, physical examples in explaining biological phenomenon. Here, we propose a framework for comparing non-living and living collectives as a continuum based on their information architecture: that is, how information is stored and processed across different degrees of freedom. We review diverse examples of collective phenomena, characterized from an information-theoretic perspective, and offer views on future directions for quantifying living collective behaviors based on their informational structure.

Driven progressive evolution of genome sequence complexity in Cyanobacteria

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.

Evolution of communication signals and information during species radiation

Communicating species identity is a key component of many animal signals. However, whether selection for species recognition systematically increases signal diversity during clade radiation remains debated. Here we show that in woodpecker drumming, a rhythmic signal used during mating and territorial defense, the amount of species identity information encoded remained stable during woodpeckers' radiation. Acoustic analyses and evolutionary reconstructions show interchange among six main drumming types despite strong phylogenetic contingencies, suggesting evolutionary tinkering of drumming structure within a constrained acoustic space. Playback experiments and quantification of species discriminability demonstrate sufficient signal differentiation to support species recognition in local communities. Finally, we only find character displacement in the rare cases where sympatric species are also closely related. Overall, our results illustrate how historical contingencies and ecological interactions can promote conservatism in signals during a clade radiation without impairing the effectiveness of information transfer relevant to inter-specific discrimination.

The QBIT Theory of Consciousness

The QBIT theory is an attempt toward solving the problem of consciousness based on empirical evidence provided by various scientific disciplines including quantum mechanics, biology, information theory, and thermodynamics. This theory formulates the problem of consciousness in the following four questions, and provides preliminary answers for each question: Question 1: What is the nature of qualia?

ANSWER

A quale is a superdense pack of quantum information encoded in maximally entangled pure states. Question 2: How are qualia generated?

ANSWER

When a pack of quantum information is compressed beyond a certain threshold, a quale is generated. Question 3: Why are qualia subjective?

ANSWER

A quale is subjective because a pack of information encoded in maximally entangled pure states are essentially private and unshareable. Question 4: Why does a quale have a particular meaning?

ANSWER

A pack of information within a cognitive system gradually obtains a particular meaning as it undergoes a progressive process of interpretation performed by an internal model installed in the system. This paper introduces the QBIT theory of consciousness, and explains its basic assumptions and conjectures.

Studying Lexical Dynamics and Language Change via Generalized Entropies: The Problem of Sample Size

Recently, it was demonstrated that generalized entropies of order α offer novel and important opportunities to quantify the similarity of symbol sequences where α is a free parameter. Varying this parameter makes it possible to magnify differences between different texts at specific scales of the corresponding word frequency spectrum. For the analysis of the statistical properties of natural languages, this is especially interesting, because textual data are characterized by Zipf’s law, i.e., there are very few word types that occur very often (e.g., function words expressing grammatical relationships) and many word types with a very low frequency (e.g., content words carrying most of the meaning of a sentence). Here, this approach is systematically and empirically studied by analyzing the lexical dynamics of the German weekly news magazine Der Spiegel (consisting of approximately 365,000 articles and 237,000,000 words that were published between 1947 and 2017). We show that, analogous to most other measures in quantitative linguistics, similarity measures based on generalized entropies depend heavily on the sample size (i.e., text length). We argue that this makes it difficult to quantify lexical dynamics and language change and show that standard sampling approaches do not solve this problem. We discuss the consequences of the results for the statistical analysis of languages.

Replicating and Cycling Stores of Information Perpetuate Life

Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.

Biological information systems: Evolution as cognition-based information management

An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.

DNA as information: at the crossroads between biology, mathematics, physics and chemistry

On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems-or parts of them-within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate.

The meaning of biological information

Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

DNA as information

This article reviews contributions to this theme issue covering the topic 'DNA as information' in relation to the structure of DNA, the measure of its information content, the role and meaning of information in biology and the origin of genetic coding as a transition from uninformed to meaningful computational processes in physical systems.