Origin of life on earth and Shannon's theory of communication

Exploring species taxonomic kingdom using information entropy and nucleotide compositional features of coding sequences based on machine learning methods

The flow of genetic information from DNA to protein is governed by the central dogma of molecular biology. Genetic drift and mutations usually lead to changes in DNA composition, thereby affecting the coding sequences (CDS) that encode functional proteins. Analyzing the nucleotide distribution in the coding regions of species is crucial for understanding their evolution. In this study, we applied Markov processes to analyze codon formation in 37,031,061 CDSs across 3,735 species genomes, spanning viruses, archaea, bacteria, and eukaryotes, to explore compositional changes. Our results revealed species preferences for different nucleotides. Information entropies and Markov information densities show that eukaryotes exhibit higher redundancy, followed by viruses, suggesting more gene duplication in eukaryotes and high mutation rates in viruses. Evolutionary trends showed an increase in information entropy and a decrease in Markov entropy, with negative correlations between first- and second-order Markov information densities. Furthermore, uniform manifold approximation and projection (UMAP) was used to reduce information redundancy for revealing unique evolutionary patterns in species classification. The machine learning methods demonstrated excellent performance in species classification accuracy, providing profound insights into CDS evolution and protein synthesis.

The calculus of codes - From entropy, complexity, and information to life

Exploring the core components that define living systems and their operational mechanisms within emerging biological entities is a complex endeavor. In the realm of biological systems literature, the terms matter, energy, information, complexity, and entropy are frequently referenced. However, possessing these concepts alone does not guarantee a comprehensive understanding or the ability to reconstruct the intricate nature of life. This study aims to illuminate the trajectory of these organic attributes, presenting a theoretical framework that delves into the integrated role of these concepts in biology. We assert that Code Biology serves as a pivotal steppingstone for unraveling the mechanisms underlying life. Biological codes (BCs) emerge not only from the interplay of matter and energy but also from Information. Contrary to deriving information from the former elements, we propose that information holds its place as a fundamental physical aspect. Consequently, we propose a continuum perspective called Calculus of Fundamentals involving three fundamentals: Matter, Energy, and Information, to depict the dynamics of BCs. To achieve this, we emphasize the necessity of studying Entropy and Complexity as integral organic descriptors. This perspective also facilitates the introduction of a mathematical theoretical framework that aids in comprehending continuous changes, the driving dynamics of biological fundamentals. We posit that Energy, Matter, and Information constitute the essential building blocks of living systems, and their interactions are governed by Entropy and Complexity analyses, redefined as biological descriptors. This interdisciplinary perspective of Code Biology sheds light on the intricate interplay between the controversial phenomenon of life and advances the idea of constructing a theory rooted in information as an organic fundamental.

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

Ethylene-bridged oligoureas characterized by a continuous, switchable chain of hydrogen bonds and carrying a binding site (an N,N′-disubstituted urea) for a hydrogen-bond-accepting ligand (a phosphine oxide) were synthesized. These oligomers show stronger ligand binding when the binding site is located at the hydrogen-bond-donating terminus than when the same binding site is at the hydrogen-bond-accepting terminus. An acidic group at the terminus remote from the binding site allows hydrogen bond polarity, and hence ligand binding ability, to be controlled remotely by a deprotonation/reprotonation cycle. Addition of base induces a remote conformational change that is relayed through up to five urea linkages, reducing the ability of the binding site to retain an intermolecular association to its ligand, which is consequently released into solution. Reprotonation returns the polarity of the oligomer to its original directionality, restoring the function of the remote binding site, which consequently recaptures the ligand. This is the first example of a synthetic molecular structure that relays intermolecular binding information, and these “dynamic foldamer” structures are prototypes of components for chemical systems capable of controlling chemical function from a distance.

Defining life and evolution: Essay on the origin, expansion, and evolution of living matter

This essay aims to define the origin, expansion, and evolution of living matter. The first formations, identified as remains, fossils, traces etc. of life are almost as old as the Earth itself. During four billion years, life on the Earth has continuously existed and been implemented in the range of conditions, ensuring the liquid state of water. During the entire period of life existence, its evolution was proceeding with the tendency of multidirectionality, after each catastrophe tending to the diversity and vastness of distribution, and all the currently living species, regardless of their complexity, have the same evolutionary age. The property of reproductive surplus (multiplication) is inherent in all the living matter. The reproduction of all the living matter is implemented via the "development" - a process of continuous occurrence of something new that did not exist in the previous moment in the reproduced individual at each specific moment of time with the tendency towards the reproduction of a "copy". In its fundamental basis, Life is based on a programme, its material support is implemented and exists not in the field of causative-consecutive events, but in the field of programmed-causative-consecutive events. This predetermines the "biology laws", the behaviour of the material constituent of Life at each time period, and the future of the material constituent of life.

A model of k-mer surprisal to quantify local sequence information content surrounding splice regions

Molecular sequences carry information. Analysis of sequence conservation between homologous loci is a proven approach with which to explore the information content of molecular sequences. This is often done using multiple sequence alignments to support comparisons between homologous loci. These methods therefore rely on sufficient underlying sequence similarity with which to construct a representative alignment. Here we describe a method using a formal metric of information, surprisal, to analyse biological sub-sequences without alignment constraints. We applied our model to the genomes of five different species to reveal similar patterns across a panel of eukaryotes. As the surprisal of a sub-sequence is inversely proportional to its occurrence within the genome, the optimal size of the sub-sequences was selected for each species under consideration. With the model optimized, we found a strong correlation between surprisal and CG dinucleotide usage. The utility of our model was tested by examining the sequences of genes known to undergo splicing. We demonstrate that our model can identify biological features of interest such as known donor and acceptor sites. Analysis across all annotated coding exon junctions in Homo sapiens reveals the information content of coding exons to be greater than the surrounding intron regions, a consequence of increased suppression of the CG dinucleotide in intronic space. Sequences within coding regions proximal to exon junctions exhibited novel patterns within DNA and coding mRNA that are not a function of the encoded amino acid sequence. Our findings are consistent with the presence of secondary information encoding features such as DNA and RNA binding sites, multiplexed through the coding sequence and independent of the information required to define the corresponding amino-acid sequence. We conclude that surprisal provides a complementary methodology with which to locate regions of interest in the genome, particularly in situations that lack an appropriate multiple sequence alignment.

A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory

We propose a framework to convert the protein intrinsic disorder content to structural entropy (H) using Shannon’s information theory (IT). The structural capacity (C), which is the sum of H and structural information (I), is equal to the amino acid sequence length of the protein. The structural entropy of the residues expands a continuous spectrum, ranging from 0 (fully ordered) to 1 (fully disordered), consistent with Shannon’s IT, which scores the fully-determined state 0 and the fully-uncertain state 1. The intrinsically disordered proteins (IDPs) in a living cell may participate in maintaining the high-energy-low-entropy state. In addition, under this framework, the biological functions performed by proteins and associated with the order or disorder of their 3D structures could be explained in terms of information-gains or entropy-losses, or the reverse processes.

What is information?

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that the information of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the 'chemical paradigm', the idea that 'life is chemistry', or, more precisely, that 'life is an extremely complex form of chemistry'. The other is the 'information paradigm', the view that chemistry is not enough, that 'life is chemistry plus information'. This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able to prove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today. Here, it is shown that a solution to the ontological problem of information does exist. It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding rules in addition to the quantities of physics and chemistry. More precisely, it is shown that the production of artefacts requires new observables that are referred to as nominable entities because they can be described only by naming their components in their natural order. From an ontological point of view, in conclusion, information is a nominable entity, a fundamental but not-computable observable.

The problems of biological information

The discovery of genetic encoding in the DNA molecule, and its mode of translation into protein structures, secured the modern view of biology as an information science. But it remains unclear what kind of information science it is. The all-too-ready analogy with computer programs stored on spools of magnetic tape has been hard to relinquish, even while the complexity of information storage and flow in the cell has become ever more apparent. To understand how life is sustained and evolves through encoding and processing of information, new ideas are now required, within which genetic encoding in DNA seems likely to provide only one part of a much broader and more profound puzzle. In particular, it seems likely that the emerging picture will need to take a more subtle view of causation, context and meaning in the orchestrated, hierarchical processes that make life possible.

Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes

Information theory has been used for quite some time in the area of computational biology. In this paper we present a pattern discovery method, named Fast Entropic Profiler, that is based on a local entropy function that captures the importance of a region with respect to the whole genome. The local entropy function has been introduced by Vinga and Almeida in , here we discuss and improve the original formulation. We provide a linear time and linear space algorithm called Fast Entropic Profiler ( FastEP), as opposed to the original quadratic implementation. Moreover we propose an alternative normalization that can be also efficiently implemented. We show that FastEP is suitable for large genomes and for the discovery of patterns with unbounded length. FastEP is available at http://www.dei.unipd.it/~ciompin/main/FastEP.html.

Quantum information and the problem of mechanisms of biological evolution

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed.

Is life unique?

Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity-heat agitation and the cause-and-effect determinism of nature's orderliness-cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

Effects of ionizing radiation on cell-to-cell communication

Cell-to-cell signaling has become a significant issue in radiation biology due to experimental evidence, accumulated primarily since the early 1990s, of radiation-induced bystander effects. Several candidate mediators involved in cell-to-cell communication have been investigated and proposed as being responsible for this phenomenon, but the current investigation techniques (both theoretical and experimental) of the mechanisms involved, due to the particular set-up of each experiment, result in experimental data that often are not directly comparable. In this study, a comprehensive approach was adopted to describe cell-to-cell communication (focusing on cytokine signaling) and its modulation by external agents such as ionizing radiation. The aim was also to provide integrated theoretical instruments and experimental data to help in understanding the peculiarities of in vitro experiments. Theoretical/modeling activities were integrated with experimental measurements by (1) redesigning a cybernetic model (proposed in its original form in the 1950s) to frame cell-to-cell communication processes, (2) implementing and developing a mathematical model, and (3) designing and carrying out experiments to quantify key parameters involved in intercellular signaling (focusing as a pilot study on the release and decay of IL-6 molecules and their modulation by radiation). This formalization provides an interpretative framework for understanding the intercellular signaling and in particular for focusing on the study of cell-to-cell communication in a "step-by-step" approach. Under this model, the complex phenomenon of signal transmission was reduced where possible into independent processes to investigate them separately, providing an evaluation of the role of cell communication to guarantee and maintain the robustness of the in vitro experimental systems against the effects of perturbations.

The role of biomacromolecular crowding, ionic strength, and physicochemical gradients in the complexities of life's emergence

We have developed a general scenario of prebiotic physicochemical evolution during the Earth's Hadean eon and reviewed the relevant literature. We suggest that prebiotic chemical evolution started in microspaces with membranous walls, where external temperature and osmotic gradients were coupled to free-energy gradients of potential chemical reactions. The key feature of this scenario is the onset of an emergent evolutionary transition within the microspaces that is described by the model of complex vectorial chemistry. This transition occurs at average macromolecular crowding of 20 to 30% of the cell volume, when the ranges of action of stabilizing colloidal forces (screened electrostatic forces, hydration, and excluded volume forces) become commensurate. Under these conditions, the macromolecules divide the interior of microspaces into dynamically crowded macromolecular regions and topologically complementary electrolyte pools. Small ions and ionic metabolites are transported vectorially between the electrolyte pools and through the (semiconducting) electrolyte pathways of the crowded macromolecular regions from their high electrochemical potential (where they are biochemically produced) to their lower electrochemical potential (where they are consumed). We suggest a sequence of tentative transitions between major evolutionary periods during the Hadean eon as follows: (i) the early water world, (ii) the appearance of land masses, (iii) the pre-RNA world, (iv) the onset of complex vectorial chemistry, and (v) the RNA world and evolution toward Darwinian thresholds. We stress the importance of high ionic strength of the Hadean ocean (short Debye's lengths) and screened electrostatic interactions that enabled the onset of the vectorial structure of the cytoplasm and the possibility of life's emergence.

Evolution of the Genetic Triplet Code via Two Types of Doublet Codons

Explaining the apparent non-random codon distribution and the nature and number of amino acids in the 'standard' genetic code remains a challenge, despite the various hypotheses so far proposed. In this paper we propose a simple new hypothesis for code evolution involving a progression from singlet to doublet to triplet codons with a reading mechanism that moves three bases each step. We suggest that triplet codons gradually evolved from two types of ambiguous doublet codons, those in which the first two bases of each three-base window were read ('prefix' codons) and those in which the last two bases of each window were read ('suffix' codons). This hypothesis explains multiple features of the genetic code such as the origin of the pattern of four-fold degenerate and two-fold degenerate triplet codons, the origin of its error minimising properties, and why there are only 20 amino acids.

Early assembly of cellular life

Popular hypotheses that attempt to explain the origin of prebiotic molecules and cellular life capable of growth and division are not always agreed upon. In this manuscript, information on early bacterial life on Earth is examined using information from several disciplines. For example, knowledge can be integrated from physics, thermodynamics, planetary sciences, geology, biogeochemistry, lipid chemistry, primordial cell structures, cell and molecular biology, microbiology, metabolism and genetics. The origin of life also required a combination of elements, compounds and environmental physical-chemical conditions that allowed cells to assemble in less than a billion years. This may have been widespread in the subsurface of the early Earth located at microscopic physical domains.