The theory of functional systems and purposeful behavior

The role of probability forecasting in the purposive behavior under conditions of subjective uncertainty is considered in terms of the theory of functional systems. Participation of the probability forecasting in the afferent synthesis, goal formation, formation of the acceptor of action result and action program, and, finally, in the action program actualization is substantiated. The model of behavior under conditions of subjective uncertainty is advanced. It includes all the classical elements of the model of behavioral act developed by P.K. Anokhin. In order to take into account the probability aspects of behavior, the role of probability forecasting is emphasized at every stage of the system functioning. In addition to the classical elements, two novel components are introduced. These are the "memory buffer" (results of searching reactions) and the apparatus of probability decisions about changes in the action program. By the memory buffer an apparatus is meant, which gathers and stores the information about the results of many behavioral acts performed during the actualization of the action program. This information is used in the process of making a probability decision as whether to alter or not the action program after each specific behavioral act. Such an approach integrates the probability forecasting and the theory of functional systems. The theory becomes universal, i.e., applicable not only to deterministic but also to probabilistic environments.     

Motor reaction time and probabilistic prognosis

The results of long-term studies demonstrating the predominant importance of probabilistic prognosis for quick motor reactions that have been carried out by the author and his research team are systematized and summarized. The results of experiments on the transition from a random to a fixed sequence of stimuli of different frequencies indicate that the reaction time upon presentation of stimuli depends on their expectation at a specific probability rather than on the frequency of their repetition. According to the experimental data, both prediction of the stimulus and prediction of the response are important: preadjustment is performed in both the motor and the sensory systems.     

Chaos theory: the transforming role of functional systems

The review of applications of chaos theory in physiology shows, that this theory makes possible to get quantitative measure of degree of the order for such processes as neuronal activity, heart rate, electroencephalogram etc. The basic concepts of chaos theory--fractal dimension. Liapunov exponents, entropy, some algorithms for obtaining of quantitative characteristics of degree of the order for different processes--have been considered in this paper. The main areas for application chaos theory in physiology and medicine have been revealed and some examples of practical and theoretical achievements in this new region of investigation are given, as well as existing limitations and problems with results interpretation. Entirely new possibilities for understanding of the order in physiological processes are shown when estimation is made from the point of view of the functional system theory.     

Effects of diffusion on the electrophoretic behavior of associating systems: The Gilbert-Jenkins theory revisited

The Gilbert-Jenkins theory predicts the asymptotic shape of moving-boundary sedimentation and electrophoretic patterns and broad zone molecular sieve chromatographic elution profiles for the class of interacting systems, A + B ⇄ C, in which two dissimilar macromolecules react reversibly to form a complex. A particularly provocative case is the one in which the complex has a greater migration velocity than that of either reactant, each of which has a different velocity. Depending upon conditions, this case predicts, for example, that in the asymptotic limit an ascending electrophoretic pattern or a frontal gel chromatographic elution profile can show two hypersharp reaction boundaries separated by a plateau. This prediction is now confirmed by numerical solution of transport equations which retain the second-order diffusional term and extrapolation of the computed patterns to zero diffusion coefficient. For finite diffusion coefficient, however, the two hypersharp reaction boundaries are separated by a weak negative gradient. These calculations are extended to an examination of the transitions between the three types of patterns admitted by the case under consideration in order to gain physical understanding and to define criteria for recognizing the transitions. Studies of this kind not only establish confidence in the Gilbert-Jenkins theory, but, in addition, they provide new insights which make for more effective application of the theory to real systems.     

A probabilistic and algebraic treatment of regular inbreeding systems

Summary A probabilistic and algebraic treatment of regular inbreeding systems is presented. Regular inbreeding systems can be thought of as graphs which have certain natural homogeneity properties. Random walks X_n and Y_n are introduced on the nodes of the graphs; the event {X_n = Y_n} is a renewal event by the homogeneity property. We show that in such regular inbreeding systems the population becomes genetically uniform if and only if the event {X_n = Y_n} is recurrent, which happens if 1/ A_n diverges, where A_n is the number of ancestors n generations into the past. We give two counterexamples to show the converse is false in general, but we verify the converse in the case of the graphs of certain finitely presented semigroups.An expended version of this paper was submitted as a doctoral thesis to Purdue University. This thesis was directed by Professor Stanley Sawyer.     

The characteristics of probabilistic prognosis and of the orienting reaction in children with learning difficulties]

Middle-aged school-children were examined with learning disabilities, differentiated by the parameters of probabilistic prognosis in two subgroups: with disturbances of attention (1) and memory (2). The first subgroup differed from the norm by intensified reaction of desynchronization of the projection areas of the cortex to irrelevant stimuli. Relevant information evoked an increase of activation of the associative zones, less expressed than in the norm. In the second subgroup a weak involvement of associative cortical areas in the reaction of desynchronization to relevant stimuli correlated with insufficient formation of alpha 2-rhythm and high frequency of meeting the signs of dysfunction of mesodiencephalic brain structure. The results are discussed in the aspect of the role of neurophysiological mechanisms of regulation and trace fixation for the formation of the integrative brain activity in the ontogenesis.     

The theory of impedance in biological systems

The basic relations of impedance as they pertain to biological systems is slowly varying electric fields are developed. One of the boundary conditions for the quasi-steady state is derived in terms of impedance rather than the limiting case of resistance. Then, given a complete schedule of conditions, the equation of Maxwell for a single membrane-covered sphere is derived in terms of impedance. Cole's relations are then obtained for a thin membrane. The analysis is extended to obtain Cole's relations for a suspension of spheres and alternative boundary conditions are suggested to remove ambiguities in Cole's work. A similar procedure is then applied to a membrane-covered cylinder and a flat sheet with membranous walls. Equations are also derived for experimental systems using electrodes with spherical or cylindrical symmetry.     

Density functional theory

Photosynthesis Research - Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point...     

Geometric and probabilistic stability criteria for delay systems.

A new approach to the study of the stability of delay systems is developed. The method is applicable to biological control systems and other systems where little information about time delays is available. The view proposed is that stability information can be deduced from the statistical properties of the probability distribution that encodes the structure of the time delay. The main statistical variables used are the usual expectation parameter E and a modified variance, called relative variance and denoted R, that is invariant under time-scale changes. In many cases, the stability of a model improves as R increases while E remains fixed. The statistical approach is shown to be closely related to a geometric method of Walther and Cushing that establishes stability in the case of a convex delay distribution function. In fact, it is shown that convex and concave distributions have R values respectively greater than and less than 1/2. A generalized version of the geometric theory is presented that relaxes the smoothness hypothesis on the density function; this brings it more into correspondence with statistical theory, which applies to general distributions irrespective of their smoothness.     

(In search of) probabilistic P systems

The aim of this paper is to (preliminarily) discuss various ways of introducing probabilities in membrane systems. We briefly present both ideas already circulated in the literature and new proposals, trying to have a systematic overview of possibilities of associating probabilities with the ingredients of a membrane system: with (localization of) single objects, with multiplicities of objects (hence with the multisets), with the rules (depending or not on the previous applied rule), with the communication targets. For a certain mode of using the probabilities associated with the evolution rules (in string-object P systems) we obtain the computational universality.     

Towards a definition of living systems: A theory of ecological support for behavior

It is proposed that the Darwinian theoretical approach and account of living systems has not yet been clearly given. A first approximation to this is attempted, focussing on behavior in evolving environments. A theoretical terminology is defined emphasizing the mutuality of organism and environment and the existence of biologically theoretical entities.     

Inferring functional modules of protein families with probabilistic topic models

Background  

Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.     

An integrated probabilistic model for functional prediction of proteins.

We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression networks, protein complex data, and domain structures of individual proteins to predict protein functions. The model is an extension of our previous model for protein function prediction based on Markovian random field theory. The model is flexible in that other protein pairwise relationship information and features of individual proteins can be easily incorporated. Two features distinguish the integrated approach from other available methods for protein function prediction. One is that the integrated approach uses all available sources of information with different weights for different sources of data. It is a global approach that takes the whole network into consideration. The second feature is that the posterior probability that a protein has the function of interest is assigned. The posterior probability indicates how confident we are about assigning the function to the protein. We apply our integrated approach to predict functions of yeast proteins based upon MIPS protein function classifications and upon the interaction networks based on MIPS physical and genetic interactions, gene expression profiles, tandem affinity purification (TAP) protein complex data, and protein domain information. We study the recall and precision of the integrated approach using different sources of information by the leave-one-out approach. In contrast to using MIPS physical interactions only, the integrated approach combining all of the information increases the recall from 57% to 87% when the precision is set at 57%-an increase of 30%.     

Evaluation of the role of the adaptive result in the theory of the functional systems

The fundamental of the theory of the functional systems, i.e., the concept of the useful adaptive result as a universal system-forming factor is considered. It is suggested that the adaptive result is not system-forming in behaviors actualized exclusively due to activity of systems developed earlier. It is argued that positive mutations may serve as the system-forming factor for hereditary determined behavioral forms. In all other cases of goal-directed behavior (except conditioning) the aim of performance as a model of the future result plays the decisive role. Only in conditioning the classical concept of the system-forming role of the adaptive result seems to be undeniable. The refined ideas about the mechanisms of formation of the functional systems may be useful in analysis of a number of animal and human functions (learning, emotional stress, neuroses, etc.).     

The structure and behavior of defoliating insect/forest systems

Using four detailed and complex simulation models we derive a framework for predicting behavior of any defoliating insect/forest system. The framework uses simple and easily gathered biological information on four sets of state variables, each with a characteristic temporal scale, to predict presence, absence or form of key ecological processes acting on or between the variables. The combination of these key processes enables prediction of system equilibrium structure and this structure can be used to derive the temporal behavior of the system. Four qualitatively different classes of system behavior arise from the equilibrium structures. The framework is tested against twelve other systems and field invalidation experiments are outlined. Forest defoliator research and management implications are discussed.     

Effects of diffusion on the electrophoretic behavior of associating systems: the Gilbert-Jenkins theory revisited

The Gilbert-Jenkins theory predicts the asymptotic shape of moving-boundary sedimentation and electrophoretic patterns and broad zone molecular sieve chromatographic elution profiles for the class of interacting systems, A + B in equilibrium C, in which two dissimilar macromolecules react reversibly to form a complex. A particularly provocative case is the one in which the complex has a greater migration velocity than that of either reactant, each of which has a different velocity. Depending upon conditions, this case predicts, for example, that in the asymptotic limit an ascending electrophoretic pattern or a frontal gel chromatographic elution profile can show two hypersharp reaction boundaries separated by a plateau. This prediction is now confirmed by numerical solution of transport equations which retain the second-order diffusional term and extrapolation of the computed patterns to zero diffusion coefficient. For finite diffusion coefficient, however, the two hypersharp reaction boundaries are separated by a weak negative gradient. These calculations are extended to an examination of the transitions between the three types of patterns admitted by the case under consideration in order to gain physical understanding and to define criteria for recognizing the transitions. Studies of this kind not only establish confidence in the Gilbert-Jenkins theory, but, in addition, they provide new insights which make for more effective application of the theory to real systems.