A morphomechanical aspect of epigenesis

Epigenesis in classical embryology is regarded as self-complication of spatial organization of the embryo during its development. The reality of the phenomenon of self-complication at the cellular and supracellular levels has been demonstrated by classical experimental embryology. Today, in light of studies of cell differentiation mechanisms, this problem acquired a molecular aspect. However, the attempt to solve it within the limits of molecular level leads to the paradox of "unreducible complexity". The discovery of a physical factor that concurrently would influence the processes of supracellular and molecular levels would be the best way to solve the problem of self-complication. The mechanical tension in cells and tissues of a developing organism may play the role of such factor. The paper considers facts on the role of mechanical stresses in morphogenesis and gene expression.     

Changes in the circadian biorhythms in animal and human ontogeny

It has been demonstrated that from the early stages of postnatal life up to adult age, gradual development of circadian amplitudes invariably takes place which may lead up to a complete absence of the diurnal rhythm in senile organisms. These changes are observed at various levels of organization of homeostatic systems (from cellular to organismic ones). A discussion is made of a possibility of evaluation of the level of adaptability and reliability of biological systems, as well as of their functional optimum via the analysis of circadian organization in ontogenesis, including gerontological problems (differentiation into age periods, biological age).     

Physical mechanism of spatial organization in epithelial morphogenesis

The morphogenetic movements of embryonic epithelia are preceded by their marking into motor active and passive zones. It is carried out as a result of spontaneous splitting of the epithelial layer to domains of morphologically polarized (motor active) and isotropic cells. Processes of the cellular level are dependent on the global supracellular organization. The mechanism of selforganization of macroscopic supracellular order in the course of cell polarization is analysed. A number of more elementary properties of the embryonic material inferred from the experiments proves to be sufficient for the initiation of such mechanism.     

Macroevolution: macrogenesis and typogenesis

One can distinguish two levels (and stages) of macroevolutionary processes: the lower (macrogenesis) and higher (typogenesis) ones. The macrogenesis represents macroevolutionary alterations of separate structures; the typogenesis is the forming of general Bauplan (type of organization) of a new macrotaxon on a base of initial macrogenesis. Discrete (or quantum) character of many macroevolutionary transformations is caused by various mechanisms, which are based on properties of integrated organismic systems and are characterized by threshold effect of their action. Initial macrogenesis can be resulted from the morphofunctional preadaptations; the pattern (or regime) transformations of morphofunctional organismic systems; emerging of dichotomy of morphogenetic programs and their following switching; the ontogenetic heterochronies (in particular, paedomorphosis); the allometric structural changes (and possibly some other mechanisms). The initial macrogenesis forms a base for qualitatively new adaptation and essentially influences on other systems in whole organism. That changes the selection vectors significantly. All these alterations trigger the typogenesis. The latter represents a complex of organismic systems transformations, integrated by selection and interconnections of various systems in whole organism. The important role in typogenesis belongs to the key alterations of some limiting organismic system that trigger and direct evolutionary changes of depended organismic systems. In course of typogenesis evolution, new macrotaxon occupies new adaptive zone.     

Entomological biometeorology

Summary I would appear to have given a rather pessimistic picture of the problems in entomological biometeorology as a result of emphasizing the areas of research that are most vitally concerned with a full understanding of the insect's relation to its environment. An important part of continuing scientific study is capacity to define problems for future investigation from past experience. In spite of the fact that many research results in border fields between meteorology and biology have accumulated without any serious organization toward unifying concepts, it is encouraging that we have achieved enough insight to define some of the basic problems. Future research is in a position in many ways to contribute to the organized approach that is required to make biometeorology a science.It should also be observed that the major limiting problem of handling large volumes of data in complicated ecological studies has been solved in principle to a large extent by the digital and the analogue electronic computers. Digital computer programming has already been incorporated in some population studies for insects. Eventual extension of analogue computer methods to behaviour problems may well facilitate an understanding of more complicated systems,especially those basic to the dispersal and migration of insects.     

Mechanisms of cell adhesion: early-forming junctions between aggregating fibroblasts.

When cultured fibroblasts (16C) are mildly dissociated with EGTA or trypsin/EDTA, they aggregate rapidly. The formation of aggregates has been found to involve junctions of the gap and adhaerens types which are seen by electron microscopy within minutes of allowing cells to come together. The process of adhesion between freshly dissociated, transformed 16C fibroblasts is therefore organized and establishes its usefulness as a model for studying cellular interactions in relation to supracellular organization.     

Complex adaptation and system structure

The structural organization of biological systems is one of nature’s most fascinating aspects, but its origin and functional role is not yet fully understood. For instance, basic adaptational mechanisms like genetic mutation and Hebbian adaptation seem to be generic and invariant across many species and are, on their own, fairly well investigated and understood. However, it is the organism’s structure – the representations these mechanisms act upon – that bears the complex functional effects of these mechanisms. While typical technical approaches to system design require detailed problem models and suffer from the need to explicitly take care of all possible cases, the organization of biological systems seems to induce inherent adaptability, flexibility and robustness. In this discussion paper we address the concept of structured variability, particularly the role of system structure as implementing a certain representation on which basic variational mechanisms act on. The functional adaptability (or search distribution) depends crucially on this representation.     

Complex adaptation and system structure

The structural organization of biological systems is one of nature’s most fascinating aspects, but its origin and functional role is not yet fully understood. For instance, basic adaptational mechanisms like genetic mutation and Hebbian adaptation seem to be generic and invariant across many species and are, on their own, fairly well investigated and understood. However, it is the organism’s structure – the representations these mechanisms act upon – that bears the complex functional effects of these mechanisms. While typical technical approaches to system design require detailed problem models and suffer from the need to explicitly take care of all possible cases, the organization of biological systems seems to induce inherent adaptability, flexibility and robustness. In this discussion paper we address the concept of structured variability, particularly the role of system structure as implementing a certain representation on which basic variational mechanisms act on. The functional adaptability (or search distribution) depends crucially on this representation.     

Soluble peroxidase gradients in lupin hypocotyls and the control of the level of polarly transported indole-3yl-acetic acid

The distribution of basic soluble isoperoxidases along the growth gradient of lupin hypocotyl was studied in order to establish the role of these isoenzymes in controlling polarly transported indole-3yl-acetic acid (IAA) levels. The observation that the levels of basic isoperoxidases, which diminish from the young (vascular differentiating) to the older (vascular differentiated) tissues, are related with previously reported IAA oxidation rates in decapitated plants, suggests that these isoenzymes can play a role in the oxidation of IAA during polar transport. The fact that the level of basic isoperoxidases is controlled by IAA in hypocotyl sections harvested from different growth zones is in accordance with the previously described adaptative activation of basic isoperoxidases to IAA content. This adaptative activation of basic isoperoxidases might constitute the basic characteristic of a system of subcellular oscillators, coupled at the cellular level, necessary to generate the supracellular auxinwave associated with auxin transport.     

Soluble peroxidase gradients in lupin hypocotyls and the control of the level of polarly transported indole-3yl-acetic acid

The distribution of basic soluble isoperoxidases along the growth gradient of lupin hypocotyl was studied in order to establish the role of these isoenzymes in controlling polarly transported indole-3yl-acetic acid (IAA) levels. The observation that the levels of basic isoperoxidases, which diminish from the young (vascular differentiating) to the older (vascular differentiated) tissues, are related with previously reported IAA oxidation rates in decapitated plants, suggests that these isoenzymes can play a role in the oxidation of IAA during polar transport. The fact that the level of basic isoperoxidases is controlled by IAA in hypocotyl sections harvested from different growth zones is in accordance with the previously described adaptative activation of basic isoperoxidases to IAA content. This adaptative activation of basic isoperoxidases might constitute the basic characteristic of a system of subcellular oscillators, coupled at the cellular level, necessary to generate the supracellular auxinwave associated with auxin transport.     

Effects of extremely high-frequency electromagnetic radiation on the immune system and systemic regulation of homeostasis

Low-intensity of electromagnetic radiation of extremely high frequencies (EHF EMR) is effectively used in medical practice for diagnostics, prevention and treatment of a broad spectrum of diseases of different etiology. However, in spite of existence of many hypotheses about mechanisms of EHF EMR effects on the molecular and cellular levels of organization of living systems, there is not conception that could explain all diversity of the EHF-therapy effects from unified approach. In our opinion, the problem of determination of mechanisms of EHF EMR effects on living organism is divided into two basic tasks: first, determining subcellular structures which can receive radiation, and, second, studying physiological reactions of the organism which are caused by radiation. It is obviously, that investigation of functions of single cells and subcellular elements can not entirely explain therapeutic effects and mechanisms of EHF EMR influence on multicellular organism on the whole. Plenty of functional relationships between organs and systems of organs should be taken into account. In the present review, a realization of the EHF-therapy effects due to the influence on immune system functions and start of system mechanisms of maintenance of the homeostasis on the organism level is hypothesized. Potential targets for EHF EMR acception on the level of different systems of the organism are analysed. The material is formed so that functional relations between immune system and other regulatory systems (nervous and endocrine systems) are traced.     

Objectivistic views in biology: an obstacle to our understanding of self-organisation processes in aquatic ecosystems

• 1 Ecologists are frequently inspired by the mechanistic view of classical physics in which motion is reduced to the effect of external forces on defined states of observable objects. Accordingly, dynamic events in ecosystems are resolved into environmental influences acting upon given states of an organismic system. In this conceptional scheme, both the environmental influences and the organismic system are assumed to be describable by objectively determinable parameters.
• 2 The present article directs criticism at this objectivistic approach. Accordingly, it is shown that an objectivistic view of living systems does not account for the complexity of organismic interactions which are continuously modified in a directional manner to achieve certain end states. This is exemplified in the physiological adaptation of micro‐organisms to their abiotic and biotic environment. Here, a population of single cells tends towards a ‘multicellular organism’ in which energy utilisation is optimised. During an investigation of this physiological adaptation process the organisms also adapt to the imposed experimental conditions, rendering futile any analysis in mechanistic terms.
• 3 Owing to this property of physiological adaptation a distinct research strategy is called for to establish the nature and ecological significance of this directionality. This strategy must be based on the observation that the sensitivity of living systems to a given environmental stimulus depends on the organismic prehistory with respect to previous exposures to stimuli. Thus, from an analysis of the adaptive response of a natural population to a defined challenge, information about prior environmental conditions may be derived that could not be obtained by other means.
• 4 Examples for the application of this research strategy to environmental problems are given.

     

Modeling the topological organization of cellular processes

The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes.     

Senescence and apoptosis in yeast mother cell-specific aging and in higher cells: a short review

It is our intention to give the reader a short overview of the relationship between apoptosis and senescence in yeast mother cell-specific aging. We are studying yeast as an aging model because we want to learn something of the basic biology of senescence and apoptosis even from a unicellular eukaryotic model system, using its unrivalled ease of genetic analysis. Consequently, we will discuss also some aspects of apoptosis in metazoa and the relevance of yeast apoptosis and aging research for cellular (Hayflick type) and organismic aging of multicellular higher organisms. In particular, we will discuss the occurrence and relevance of apoptotic phenotypes for the aging process. We want to ask the question whether apoptosis (or parts of the apoptotic process) are a possible cause of aging or vice versa and want to investigate the role of the cellular stress response system in both of these processes. Studying the current literature, it appears that little is known for sure in this field and our review will therefore be, for a large part, more like a memorandum or a program for future research.     

A morphomechanical aspect of epigenesis

Epigenesis in classical embryology is regarded as self-complication of spatial organization of the embryo during its development. The reality of the phenomenon of self-complication at the cellular and supra-cellular levels has been demonstrated by classical experimental embryology. Today, in light of studies of cell differentiation mechanisms, this problem acquired a molecular aspect. However, the attempt to solve it within the limits of molecular level leads to the paradox of “irreducible complexity.” The discovery of a physical factor that concurrently would influence the processes of supracellular and molecular levels would be the best way to solve the problem of self-complication. The mechanical tension in cells and tissues of a developing organism may play the role of such factor. The paper considers facts on the role of mechanical stresses in morphogenesis and gene expression.     

Some Problems and Principles of Development

Certain supracellular aspects of embryonic differentiation,illustrated by studies of young chick blastoderms, are discussed.Specifically, the following principles and guidelines seem tobe involved in early development of the chick: egg organization,relative movement, differential growth, regulation, restrictionof regulative capacities, synonomy of regulation and growth,gradients and fields', developmental centers, dominance, integration,environmental control, and induction.     

Multi-Level Semiosis: a Paradigm of Emergent Innovation

In this introductory article to the special issue on Multi-level semiosis we attempt to stage the background for qualifying the notion of “multi-levelness” when considering communication processes and semiosis in all life forms, i.e. from the cellular to the organismic level. While structures are organized hierarchically, communication processes require a kind of processual organization that may be better described as being heterarchical. Theoretically, the challenge arises in the temporal domain, that is, in the developmental and evolutionary dimension of dynamic semiotic processes. We discuss the importance of this fundamental difference in order to explain how levels, domains and orders of magnitude, on the one hand, and synchronic and diachronic processes, on the other, contribute to the overall organization of every living being. To account for such multi-level organization, semiotic freedom is assumed to be a scalar property that endows living systems at different levels and domains with the capacity to ponder selectively the overall structural coherence and functional compatibility of their heterarchical processing, which is increasingly less conditioned by the underlying molecular determinism.     

Brain organization and behaviour

Central question of this essay is, whether it is possible to relate specific aspects of the organization of sensorimotor systems to specific aspects of the behaviour. The role of the auditory system as part of a system for vocalization (song-birds) or as part of a system for prey localization (owls) and the different roles of the trigeminal system in the feeding behaviour of different birds are considered. The ascending sensory systems seem to possess a comparable organization in the various species. Also the descending motor pathways from archistriatum and paleostriatal complex seem to be basically similar. Behavioural specialization may be expressed particularly in the organization of the intratelencephalic circuits and thus in the involvement of specific regions of neostriatum and hyperstriatum ventrale. In discussions on cerebralisation it will be necessary to take such differences in intratelencephalic organization into account.     

The GP problem: quantifying gene-to-phenotype relationships

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.     

Organismic sets: Outline of a general theory of biological and social organisms

The discussion as to whether societies are organisms andvice versa has been going on for a long time. The question is meaningless unless a clear definition of the term “organism” is made. Once such a definition is made, the question may be answered by studying whether there exists any relational isomorphism between what the biologist calls an organism and what the sociologist calls society. Such a study should also include animal societies studied by ecologists. Both human and animal societies are sets of individuals together with certain other objects which are the products of their activities. A multicellular organism is a set of cells together with some products of their activities. A cell itself may be regarded as a set of genes together with the products of their activities because every component of the cell is either directly or indirectly the result of the activities of the genes. Thus it is natural to define both biological and social organisms as special kinds of sets. A number of definitions are given in this paper which define what we call here organismic sets. Postulates are introduced which characterize such sets, and a number of conclusions are drawn. It is shown that an organismic set, as defined here, does represent some basic relational aspects of both biological organisms and societies. In particular a clarification and a sharpening of the Postulate of Relational Forces given previously (Bull. Math. Biophysics,28, 283–308, 1966) is presented. It is shown that from the basic definitions and postulates of the theory of organismic sets, it folows that only such elements of those sets will aggregate spontaneously, which are not completely “specialized” in the performance of only one activity. It is further shown that such “non-specialized” elements undergo a process of specialization, and as a result of it their spontaneous aggregation into organismic sets becomes impossible. This throws light on the problem of the origin of life on Earth and the present absence of the appearance of life by spontaneous generation. Some applications to problems of ontogenesis and philogenesis are made. Finally the relation between physics, biology, and sociology is discussed in the light of the theory of organismic sets.