Generation of valuable information and the problem of goal self-setting in living systems

The problem of origination of capacity for goal self-setting is discussed. It was shown that the definition "goal" in living systems differs from the definition "target function" in physical problems concerned with nonliving systems. It was also shown that the main goal of the elements of a system is the storage of information. In biology, this goal is the extension of the principle of struggle for existence. Conditions were determined that the dynamic system describing the goal self-setting process must satisfy. It was shown that living systems meet these conditions. In inorganic nature, such systems may also arise but only as a result of long-term evolution, after which they become living.     

Revealing biological information using data structuring and automated learning

The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.     

Redundancies, development and the flow of information.

There is increasing evidence for the wide-spread existence of functionally redundant genetic pathways in developmental processes. However, both their significance and manner of evolution are still matters of debate. I will argue here that redundancy of gene actions may, in fact, be a necessary requirement for the development and evolution of complex life forms. One can view development as a process that transmits information from the egg to the adult organism. Transmission of information is, however, always an error-prone process, which can only be safeguarded by including redundancies in the message. Molecular examples for well analysed redundant processes indicate that redundancies may best be understood within a conceptual framework of overlaps between different gene functions.     

Chemistry in living systems

Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community--the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.     

Genes, information and sense: complexity and knowledge retrieval

Information capacity of nucleotide sequences measures the unexpectedness of a continuation of a given string of nucleotides, thus having a sound relation to a variety of biological issues. A continuation is defined in a way maximizing the entropy of the ensemble of such continuations. The capacity is defined as a mutual entropy of real frequency dictionary of a sequence with respect to the one bearing the most expected continuations; it does not depend on the length of strings contained in a dictionary. Various genomes exhibit a multi-minima pattern of the dependence of information capacity on the string length, thus reflecting an order within a sequence. The strings with significant deviation of an expected frequency from the real one are the words of increased information value. Such words exhibit a non-random distribution alongside a sequence, thus making it possible to retrieve the correlation between a structure, and a function encoded within a sequence.

Genes, gene flow and adaptation of Diabrotica virgifera virgifera

1  Diabrotica virgifera virgifera has emerged as a major pest of cultivated maize, due to a combination of its high capacity to inflict economic damage, adaptability to pest management techniques and invasiveness.
2 This review presents a survey of the current state of knowledge about the genetics of D.   v.   virgifera . In addition, the tools and resources currently available to Diabrotica geneticists are identified, as are areas where knowledge is lacking and research should be prioritized.
3 A substantial amount of information has been published concerning the molecular phylogenetic relationships of D.   v.   virgifera to other chrysomelids.
4 There is a growing literature focused on the population genetics and evolution of the species. Several adaptations to anthropogenic selection pressure have been studied, with resistance to synthetic insecticides providing some particularly well-characterized examples.
5 A notable deficiency is a lack of studies directed toward the formal genetics of D.   v.   virgifera .     

Quantum computation, non-demolition measurements, and reflective control in living systems

Internal computation underlies robust non-equilibrium living process. The smallest details of living systems are molecular devices that realize non-demolition quantum measurements. These smaller devices form larger devices (macromolecular complexes), up to living body. The quantum device possesses its own potential internal quantum state (IQS), which is maintained for a prolonged time via reflective error-correction. Decoherence-free IQS can exhibit itself by a creative generation of iteration limits in the real world. It resembles the properties of a quasi-particle, which interacts with the surround, applying decoherence commands to it. In this framework, enzymes are molecular automata of the extremal quantum computer, the set of which maintains highly ordered robust coherent state, and genome represents a concatenation of error-correcting codes into a single reflective set. The biological evolution can be viewed as a functional evolution of measurement constraints in which limits of iteration are established, possessing criteria of perfection and having selective values.     

Information dynamics in living systems: prokaryotes, eukaryotes, and cancer

Background

Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established.

Findings

We propose that stable entropy in living systems, in the absence of thermodynamic equilibrium, requires an information extremum (maximum or minimum), which is invariant to first order perturbations. Proliferation and death represent key feedback mechanisms that promote stability even in a non-equilibrium state. A system moves to low or high information depending on its energy status, as the benefit of information in maintaining and increasing order is balanced against its energy cost. Prokaryotes, which lack specialized energy-producing organelles (mitochondria), are energy-limited and constrained to an information minimum. Acquisition of mitochondria is viewed as a critical evolutionary step that, by allowing eukaryotes to achieve a sufficiently high energy state, permitted a phase transition to an information maximum. This state, in contrast to the prokaryote minima, allowed evolution of complex, multicellular organisms. A special case is a malignant cell, which is modeled as a phase transition from a maximum to minimum information state. The minimum leads to a predicted power-law governing the in situ growth that is confirmed by studies measuring growth of small breast cancers.

Conclusions

We find living systems achieve a stable entropic state by maintaining an extreme level of information. The evolutionary divergence of prokaryotes and eukaryotes resulted from acquisition of specialized energy organelles that allowed transition from information minima to maxima, respectively. Carcinogenesis represents a reverse transition: of an information maximum to minimum. The progressive information loss is evident in accumulating mutations, disordered morphology, and functional decline characteristics of human cancers. The findings suggest energy restriction is a critical first step that triggers the genetic mutations that drive somatic evolution of the malignant phenotype.     

Biostructural theory of the living systems

Eugen Macovschi is among the few scientists who tried, and partly succeeded, to explain the differences between "dead" and "living" in biological sciences. He discovered and characterized the so-called biostructure of the living bodies and worked out a biostructural theory, which is the first supramolecular conception in biology. Nevertheless, complex biological systems are currently considered only from the molecular point of view, although they may be regarded as specific phenomena on highly structured bodies within the four-dimensional Universe. According to Macovschi, the biostructure provides organisms with life properties and controls their life processes and chemical changes. Nevertheless, plant cells or bacterial ones differ much from the animal or human cells. In fact, there are various biostructures which are related with cell properties. Hence, this theory creates confusions and cannot be easily used to explain all the properties of the biosystems. Consequently, it is our goal to highlight the principles, advantages, limitations, and applications of the biostructural theory, which might support new ideas and theories in modern life sciences.     

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.     

Some order-disorder considerations in living systems

Order and disorder in biological systems are considered quantitatively in terms of information and entropy. After discussing the factors contributing to the information content of a living cell, a calculation is made of this parameter. The value for a typical bacterial cell is 4.6×10¹⁰ bits. This value is compared with an experimental value of the heat of growth and entropy production ofE. Coli. A discussion of methods of improving the calculation is also presented.