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arXiv2010

Equations of Motion that Recognize Biochemical Patterns

Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical patterns are spatiotemporal distributions of multiple biochemical components that can be regarded as a continuum in concentration and mass flux. Recognizing biochemical patterns lead to a universal property of the equations, which is also mathematically demonstrated, that the devised equations are sufficient to approximate any orbits in an arbitrary dynamical system, even though that of expectedly seen in complex biological systems. This theory can be applied to also a non-biological system that can be regarded as a continuum comprised of any multiple components such as liquids, solids, and nonlinear viscoelastic materials.

physics.bio-ph↗

arXiv2010

On applications of Ulam-Hyers stability in biology and economics

We argue that Ulam-Hyers stability concept is quite significant in realistic problems in numerical analysis, biology and economics. A generalization to nonlinear systems is proposed and applied to the logistic equation (both differential and difference), SIS epidemic model, Cournot model in economics and a reaction diffusion equation. To the best of our knowledge this is the first time Ulam-Hyers stability is considered from the applications point of view.

nlin.CD↗

arXiv2013

Towards a mathematical theory of meaningful communication

Despite its obvious relevance, meaning has been outside most theoretical approaches to information in biology. As a consequence, functional responses based on an appropriate interpretation of signals has been replaced by a probabilistic description of correlations between emitted and received symbols. This assumption leads to potential paradoxes, such as the presence of a maximum information associated to a channel that would actually create completely wrong interpretations of the signals. Game-theoretic models of language evolution use this view of Shannon's theory, but other approaches considering embodied communicating agents show that the correct (meaningful) match resulting from agent-agent exchanges is always achieved and natural systems obviously solve the problem correctly. How can Shannon's theory be expanded in such a way that meaning -at least, in its minimal referential form- is properly incorporated? Inspired by the concept of {\em duality of the communicative sign} stated by the swiss linguist Ferdinand de Saussure, here we present a complete description of the minimal system necessary to measure the amount of information that is consistently decoded. Several consequences of our developments are investigated, such the uselessness of an amount of information properly transmitted for communication among autonomous agents.

cs.IT↗

arXiv2010

A heuristic view about the evolution and species

The controversy concerning both the definition of the species and methods for inferring the boundaries and numbers of species has occupied biologists for centuries, and the debate itself has become known as the species problem. The modern theory of evolution depends on a fundamental redefinition of "species". Here we show that based on the model of evolutionary continuum combined with fuzzy theory that the evolution system is a uncountable infinite set and species is a fuzzy set, the contradiction between discrete biological entities and continuous evolution system is solved, i.e. when a species evolved, the individuals scattered in space but continuously distributed on time sequences. Moreover, the calculation methods for species are suggested both in theory and practice.

q-bio.OT↗

arXiv2010

Anxiety as a Factor in the Development of Autistic Spectrum Symptoms: an Experimental Study

It is well known that psychoemotional disorders may be accompanied by decreased sociability in humans. It has been shown that repeated social defeats in 10 daily agonistic interactions in male mice led to development of the expressed level of anxiety and to reduction of communication estimated in the elevated plus-maze and partition tests, respectively. In the social interactions test, sociable behavior toward unfamiliar partner and exploratory activity were dramatically decreased in defeated male mice. Avoidance of approaching partner was significantly increased. Demonstration of self-grooming behavior was increased in defeated males. Chronic diazepam treatment (0.5 mg/kg, i.p., 2 weeks) led to significant decrease of anxiety level estimated in the elevated plus maze test and to improvement of communication in the partition test. In the social interaction test diazepam completely restored the level of sociability and exploratory activity and reduced avoidance behavior of approaching partner. Diazepam did not affect self-grooming demonstration. It is concluded that main factor which provokes decrease in communication in defeated male mice is the high level of anxiety. Similarity between changes in social behavior in defeated mice and symptoms of autism in humans is discussed. It is supposed that this behavioral approach may be useful for studying the molecular mechanisms of autistic spectrum disorders, developing under chronic negative social experiences.

q-bio.OT↗

arXiv2010

Mobilisation readiness state and the frequency structure of heart rate variability

A number of studies showed association of mental status with heart rate variability. This work discovered a feature of frequency structure of heart rate variability that is associated with mental readiness. In three independent groups of 64, 39, and 19 volunteers by the factor analysis of heart rate periodograms, it has been discovered that there are at least two other heart rate oscillation phenomena apart from the well known low frequency oscillations and respiratory arrhythmia. They have periods of 3 and 4 heart beats. Association of amplitude of 3-beats oscillation with level of mental readiness was shown due to further observation in two independent groups of 12 and 7. Moreover, possibility of assessment of mental readiness by the mathematical model based on heart rate periodogram was suggested.

q-bio.TO↗

arXiv2010

Matrix genetics, part 5: genetic projection operators and direct sums

The article is devoted to phenomena of symmetries and algebras in matrix presentations of the genetic code. The Kronecker family of the genetic matrices is investigated, which is based on the alphabetical matrix [C A; U G], where C, A, U, G are the letters of the genetic alphabet. The matrix P=[C A; U G] in the third Kronecker power is the (8*8)-matrix, which contains 64 triplets. Peculiarities of the degeneracy of the genetic code are reflected in the symmetrical black-and-white mosaic of this genetic (8*8)-matrix of 64 triplets. Phenomena of connections of this mosaic matrix (and many other genetic matrices) with projection operators are revealed. Taking into account an important role of projection operators in quantum mechanics, theory of digital codes, computer science, logic and in many other fields of applied mathematics, we study algebraic properties and biological meanings of these phenomena. Using of notions and formalisms of theory of finite-dimensional vector spaces in bioinformatics and theoretical biology is proposed on the bases of the described results.

q-bio.OT↗

arXiv2010

Triadic Conceptual Structure of the Maximum Entropy Approach to Evolution

Many problems in evolutionary theory are cast in dyadic terms, such as the polar oppositions of organism and environment. We argue that a triadic conceptual structure offers an alternative perspective under which the information generating role of evolution as a physical process can be analyzed, and propose a new diagrammatic approach. Peirce's natural philosophy was deeply influenced by his reception of both Darwin's theory and thermodynamics. Thus, we elaborate on a new synthesis which puts together his theory of signs and modern Maximum Entropy approaches to evolution. Following recent contributions to the naturalization of Peircean semiosis, we show that triadic structures involve the conjunction of three different kinds of causality, efficient, formal and final. We apply this on Ulanowicz's analysis of autocatalytic cycles as primordial patterns of life. This paves the way for a semiotic view of thermodynamics which is built on the idea that Peircean interpretants are systems of physical inference devices evolving under natural selection. In this view, the principles of Maximum Entropy, Maximum Power, and Maximum Entropy Production work together to drive the emergence of information carrying structures, which at the same time maximize information capacity as well as the gradients of energy flows, such that ultimately, contrary to Schroedinger's seminal contribution, the evolutionary process is seen to be a physical expression of the Second Law.

nlin.AO↗

arXiv2010

Technical performance and interpretation of physical experiment in problems of cell biology

The lecture summarises main results of my team over last five years in the field of technical experiment design and interpretation of results of experiments for cell bi-ology. I introduce the theoretical concept of the experiment, based mainly on ideqas of stochastic systems theory, and confront it with general ideas of systems theory. In the next part I introduce available experiments and discuss their information con-tent. Namely, I show that light microscopy may be designed to give resolution com-parable to that of electron microscopy and that may be used for experiments using living cells. I show avenues to objective analysis of cell behavior observation. I pro-pose new microscope design, which shall combine advantages of all methods, and steps to be taken to build a model of living cells with predictive power for practical use

q-bio.OT↗

arXiv2010

A Hybrid Model for Disease Spread and an Application to the SARS Pandemic

Pandemics can cause immense disruption and damage to communities and societies. Thus far, modeling of pandemics has focused on either large-scale difference equation models like the SIR and the SEIR models, or detailed micro-level simulations, which are harder to apply at a global scale. This paper introduces a hybrid model for pandemics considering both global and local spread of infections. We hypothesize that the spread of an infectious disease between regions is significantly influenced by global traffic patterns and the spread within a region is influenced by local conditions. Thus we model the spread of pandemics considering the connections between regions for the global spread of infection and population density based on the SEIR model for the local spread of infection. We validate our hybrid model by carrying out a simulation study for the spread of SARS pandemic of 2002-2003 using available data on population, population density, and traffic networks between different regions. While it is well-known that international relationships and global traffic patterns significantly influence the spread of pandemics, our results show that integrating these factors into relatively simple models can greatly improve the results of modeling disease spread.

cs.MA↗

arXiv2010

Thermodynamics of chemical free energy generation in off-axis hydrothermal vent systems and its consequences for compartmentalization and the emergence of life

In this paper we demonstrate how chemical free energy can be produced by a geological process. We provide a thermodynamic framework in which to assess how life emerged at the off-axis hydrothermal vent system; the RNA - clays system has been investigated from the entropic point of view, showing that the stabilization of the system in a state further away from equilibrium state, by an inorganic heterogeneous compartmetalization phenomena, is able to produce chemical free energy useful for RNA self - replication.

physics.bio-ph↗

arXiv2010

'Genesis': A takeover from field-responsive matter?

Cairns-Smith (2008) has argued for a pre-Darwinian era, with a simpler basis for life's functioning via primitive "crystal genes" (information transfer, kinetic control on metabolic reactions). At the other extreme, guided by the structural similarity of clusters in early-evolved enzymes to iron-sulphide minerals like greigite, the hydrothermal mound scenario of Russell and coworkers (1994) presents how non-equilibrium forces rooted in geochemistry could be extrapolated to understand the metabolic functioning of living systems. The informational vs metabolic aspects of life in these respective scenarios can be linked together via a framboid-based theory of Sawlowicz (2000), as these assemblies typically form in colloidal environments. In this background, we consider the ramifications of a magnetic rock field on the mound scenario, asking if soft matter assemblies are compatible with a coherent order.

physics.bio-ph↗

arXiv2010

The Entropy of Morbidity Trauma and Mortality

In this paper it is shown that statistical mechanics in the form of thermodynamic entropy can be used as a measure of the severity of individual injuries (AIS), and that the correct way to account for multiple injuries is to sum the entropies. It is further shown that summing entropies according to the Planck-Boltzmann (P-B) definition of entropy is formally the same as ISS, which is why ISS works. Approximate values of the probabilities of fatality are used to calculate the Gibb's entropy, which is more accurate than the P-B entropy far from equilibrium, and are shown to be again proportional to ISS. For the categorisation of injury using entropies it is necessary to consider the underlying entropy of the individuals morbidity to which is added the entropy of trauma, which then may result in death. Adding in the underlying entropy and summing entropies of all AIS3+ values gives a more extended scale than ISS, and so entropy is considered the preferred measure. A small scale trial is conducted of these concepts using the APROSYS In-Depth Pedestrian database, and the differences between the measures are illustrated. It is shown that adopting an entropy approach to categorising injury severity highlights the position of the elderly, who have a reduced physiological reserve to resist further traumatic onslaught. There are other informational entropy-like measures, here called i-entropy, which can also be used to classify injury severity, which are outlined. A large scale trial of these various entropy or i-entropy measures needs to be conducted to assess the usefulness of the measures. In the meantime, an age compensated ISS measure such as ASCOT or TRISS is recommended.

physics.med-ph↗

arXiv2010

Synthesis of Sugar and fixation of CO2 through Artificial Photosynthesis driving by Hydrogen or Electricity

The overall process of photosynthesis consists of two main phases, the so-called light and dark eactions: light energy is absorbed by chlorophyll molecules and transferred to regenerate NADH and ATP, then drive Calvin-Benson cycle to synthesize sugar. In order to synthesize sugar through artificial photosynthesis, one of the key is to regenerate ATP economically and improve the efficiency of dark reactions. Here 9 kinds of dark reaction pathways are proposed, which only NADH is regenearated from hydrogen or electricity for driving, the efficiency of dark reactions is improved, combined with solar photovoltaic or solar hydrogen technology, the total efficiency of artificial photosynthesis can reach 30%, several ten times more than natural photosynthesis. One of them, to use chemical synthesis of formaldehyde from CO2 and H2, no NADH and ATP is need, to synthesize sugar efficiently through 9 enzymes, so it will be easier to produce in large scale, and the sugar will be a good energy carrier as the sugar can be efficiently converted to energy carrier hydrogen through enzymes.

physics.chem-ph↗

arXiv2012

Diagonalizing the genome I: navigation in tree spaces

The orientable cover of the moduli space of real genus zero algebraic curves with marked points is a compact aspherical manifold tiled by associahedra, which resolves the singularities of the space of phylogenetic trees. The resolution maps planar metric trees to their underlying abstract representatives, collapsing and folding an explicit geometric decomposition of the moduli space into cubes. This decomposition endows the resolving space with an interesting canonical pseudometric. The second part of this paper defines a related (stacky) resolution of a space of real quadratic forms, and suggests, perhaps without much justification, that systems of oscillators parametrized by such objects may provide useful models in genomics.

math.AG↗

arXiv2010

Motion Parallax is Asymptotic to Binocular Disparity

Researchers especially beginning with (Rogers & Graham, 1982) have noticed important psychophysical and experimental similarities between the neurologically different motion parallax and stereopsis cues. Their quantitative analysis relied primarily on the "disparity equivalence" approximation. In this article we show that retinal motion from lateral translation satisfies a strong ("asymptotic") approximation to binocular disparity. This precise mathematical similarity is also practical in the sense that it applies at normal viewing distances. The approximation is an extension to peripheral vision of (Cormac & Fox's 1985) well-known non-trig central vision approximation for binocular disparity. We hope our simple algebraic formula will be useful in analyzing experiments outside central vision where less precise approximations have led to a number of quantitative errors in the vision literature.

physics.bio-ph↗

arXiv2010

Information Maximization Fails to Maximize Expected Utility in a Simple Foraging Model

Information theory has explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Some scholars have proposed that information should provide the central explanatory principle in biology, in the sense that any behavioral strategy that is optimal for an organism's survival must necessarily involve efficient information processing. We challenge this view by providing a counterexample. We present an analytically tractable model for a particular instance of a perception-action loop: a creature searching for a food source confined to a one-dimensional ring world. The model incorporates the statistical structure of the creature's world, the effects of the creature's actions on that structure, and the creature's strategic decision process. The model takes the form of a Markov process on an infinite dimensional state space. To analyze it we construct an exact coarse graining that reduces the model to a Markov process on a finite number of "information states". This technique allows us to make quantitative comparisons between the performance of an information-theoretically optimal strategy with other candidate strategies on a food gathering task. We find that: 1. Information optimal search does not necessarily optimize utility (expected food gain). 2. The rank ordering of search strategies by information performance does not predict their ordering by expected food obtained. 3. The relative advantage of different strategies depends on the statistical structure of the environment, in particular the variability of motion of the source. We conclude that there is no simple relationship between information and utility. Behavioral optimality does not imply information efficiency, nor is there a simple tradeoff between gaining information about a food source versus obtaining the food itself.

q-bio.OT↗

arXiv2010

Identificación de nuevos medicamentos a través de métodos computacionales

Resumen: El desarrollo de nuevos medicamentos es un problema complejo que carece de una solución única y automática desde un punto de vista computacional, debido a la carencia de programas que permitan manejar grandes volúmenes de información que están distribuidos a lo largo de todo el mundo entre múltiples bases de datos. Por ello se describe una metodología que permita realizar experimentos in silico para la identificación actual de nuevos medicamentos. Abstract: The development of new drugs is a problem that nowadays has no solution in terms of computational power due to the lack of software for handling the big volume of available information; besides, these data are stored in multiple formats and are distributed all around the world. To resolve that, a development of an in silico drug design methodology.

q-bio.OT↗