Microscopic-macroscopic interface in biological information processing

Recent experimental work suggests that chemical messengers associated with the neuron membrane serve as a link between macroscopic and microscopic information processes in the brain. Arguments based on the physical limits of computing, on computational parallelism, and on evolution theory suggest that microphysical computing processes enormously enhance the brain's computing power. A number of models are briefly sketched which illustrate how molecular switching processes could be recruited for useful biological functions. The flow of information between microscopic and macroscopic forms is suggestive of processes which occur in a measuring apparatus, and the implications of this analogy are considered.     

Entropy and information in evolving biological systems

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor ming energy from one state to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes.Authorship alphabetical     

Encoding and processing biologically relevant temporal information in electrosensory systems

Wave-type weakly electric fish are specialists in time-domain processing: behaviors in these animals are often tightly correlated with the temporal structure of electrosensory signals. Behavioral responses in these fish can be dependent on differences in the temporal structure of electrosensory signals alone. This feature has facilitated the study of temporal codes and processing in central nervous system circuits of these animals. The temporal encoding and mechanisms used to transform temporal codes in the brain have been identified and characterized in several species, including South American gymnotid species and in the African mormyrid genus Gymnarchus. These distantly related groups use similar strategies for neural computations of information on the order of microseconds, milliseconds, and seconds. Here, we describe a suite of mechanisms for behaviorally relevant computations of temporal information that have been elucidated in these systems. These results show the critical role that behavioral experiments continue to have in the study of the neural control of behavior and its evolution.     

Quantum mechanics in the present progressive mode and its significance in biological information processing

Quantum mechanics practiced in the present progressive mode can incorporate into itself the propagation of a signal of a local character. It is possible to view that any movement in the present progressive mode is mutli-agential in the sense of internal interactions due to the absence of an external agency coordinating the global situation simultaneously. The idea of living memory is discussed as carrying the leftover from those actions completed and registered in the present perfect mode and surviving at any present moment. The occurrence of both the signal propagation of a local character and living memory is upheld upon exchange interaction of a quantum mechanical origin. Empirical evidence suggesting the likelihood of such an exchange interaction is found in the neurotransmitter-gated ion channels located on the plasma membrane of the muscle cell in the vicinity of secretory vesicles containing acetylcholine near the nerve terminal. Another case from the empirical evidence is seen in the actomyosin system demonstrating the unidirectional propagation of variations in the acceleration of the displacement of an actin filament sliding on myosin molecules in the presence of ATP molecules.     

From sparks to spikes: information processing in the electrosensory systems of fish

Recent work on electrosensory systems in fish has combined traditional neuroethological approaches with quantitative methods for characterizing neural coding. These studies have shed light on general issues in sensory processing, including how peripheral sensory receptors encode external stimuli and how these representations are transformed at subsequent stages of processing.     

From population dynamics to ecoinformatics: Ecosystems as multilevel information processing systems

In classical ecological theory the concept population plays a central role. Most models are formulated in terms of changes in the number/biomass/fraction of interacting populations. In the passed 30 years slowly alternative viewpoints have been developed. In this paper we trace some of these alternative developments which lead to viewing ecosystems in terms of local multilevel information processing and evolution. We will sketch the methodological developments, indicate some fundamental insight gained through the methodological innovations and focus our discussion on the central problem of the development and maintenance of diversity in ecosystems. We will explore the circumstances in which individual based diversity (plasticity, regulatory adaptation, intelligence) or population based diversity (speciation) develops.     

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems

The amount of genomic and proteomic data that is entered each day into databases and the experimental literature is outstripping the ability of experimental scientists to keep pace. While generic databases derived from automated curation efforts are useful, most biological scientists tend to focus on a class or family of molecules and their biological impact. Consequently, there is a need for molecular class-specific or other specialized databases. Such databases collect and organize data around a single topic or class of molecules. If curated well, such systems are extremely useful as they allow experimental scientists to obtain a large portion of the available data most relevant to their needs from a single source. We are involved in the development of two such databases with substantial pharmacological relevance. These are the GPCRDB and NucleaRDB information systems, which collect and disseminate data related to G protein-coupled receptors and intra-nuclear hormone receptors, respectively. The GPCRDB was a pilot project aimed at building a generic molecular class-specific database capable of dealing with highly heterogeneous data. A first version of the GPCRDB project has been completed and it is routinely used by thousands of scientists. The NucleaRDB was started recently as an application of the concept for the generalization of this technology. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm/ and the NucleaRDB at http://www.receptors.org/NR/.     

Mapping of statistical physics to information theory with application to biological systems

The problem of achieving a mapping of formalisms in statistical physics and theoretical biology to information theory is discussed using an example for canonical ensembles. We extend the meaning of the Handscomb Monte-Carlo method to a general recipe for the transformation from a "configuration" space to a "sentence" space. The ensemble of "sentences" and its corresponding source uncertainty function are introduced. A possible mapping procedure based on a generalization of the Handscomb representation is described. For a biological illustration, we present a way to introduce a pathway representation to describe metabolic processes in living systems.     

Stochastic Penna model for biological aging

Summary A stochastic genetic model for biological aging is introduced bridging the gap between the bit-string Penna model and the Pletcher-Neuhauser approach. The phenomenon of exponentially increasing mortality function at intermediate ages and its deceleration at advanced ages is reproduced for both the evolutionary steady-state population and the genetically homogeneous individuals.     

Stochastic model of domain kinetics in biological membranes

A stochastic storage model based on the behavior of macroscopic variables of the system is used to describe the kinetics of raft-like domains in biological membranes. For a simple output model, we examine the features of the system behavior corresponding to the noise-induced nonequilibrium phase transitions. Characteristics of the behavior of the statistical system are obtained: an explicit form of the stationary distribution of the number of domains; ratios for the phase transition points; the expression for the first two moments of the random domain concentration, and the expression for the lifetime of membrane domains in the stationary state.     

Self-organization in biological systems

Biological systems are considered that are capable of dynamic self-organization, i.e., spontaneous emergence of spatio-temporal order with the formation of various spatio-temporal patterns. A cell is involved in the organization of ontogenesis of all stages. Embryonic cells exhibit coordinated social behavior and generate ordered morphological patterns displaying variability and equifinality of development. Physical and topological patterns are essential for biological systems as an imperative that restricts and directs biological morphogenesis. Biological self-organization is directed and fixed by natural selection during which selection of the most sustainable, flexible, modular systems capable of adaptive self-organization occurs.