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At least 163 records · Page 9Linked to original sources

arXiv2012

Three-stage Origin of Life as a Result of Directional Darwinian Evolution

The original hypothesis about Three-stage origin of life (TOL) on the Earth is developed and discussed. The role of the temperature factor in life origin is considered. It is supposed, that three stages of abiogenesis (DNA world, RNA world and the Protein world) consistently followed each other during Darwinian evolution. At the same time, the natural directional selection of the most stable macromolecules and effective catalytic reactions took place. The direction of this selection is related to action of the principle of «Increasing Independence from the Environment» (IIE) and is caused by temperature evolution of the atmosphere of the Earth. The direction of Anagenesis and inevitability of occurrence of genetic mechanisms is discussed.

q-bio.OT↗

arXiv2022

Experimental Evidence Supporting a New "Osmosis Law & Theory" Derived New Formula that Improves van't Hoff Osmotic Pressure Equation

Experimental data were used to support a new concept of osmotic force and a new osmotic law that can explain the osmotic process without the difficulties encountered with van't Hoff osmotic pressure theory. Derived new osmotic formula with curvilinear equation (via new osmotic law) overcomes the limitations and incompleteness of van't Hoff (linear) osmotic pressure equation, $π=(n/v)RT$, (for ideal dilute solution only). The application of this classical theory often resulted in contradiction regardless of miscellaneous explaining efforts. This is due to the lack of a scientific concept like "osmotic force" that we believe can elaborate the osmotic process. Via this new concept, the proposed new osmotic law and derived new osmotic pressure equation will greatly complete and improve the theoretical consistency within the scientific framework of osmosis.

q-bio.OT↗

arXiv2012

No entailing laws, but enablement in the evolution of the biosphere

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phenotypes, niches, ecosystems. We wish to argue that the evolution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon discussing the variability of the very "contexts of life": the interactions between organisms, biological niches and ecosystems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of time the "niches" which constitute the boundary conditions on selection. More generally, by the mathematical unprestatability of the "phase space" (space of possibilities), no laws of motion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound conceptual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of (theoretical) symmetries as invariant preserving transformations will allow us to understand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of "enablement". This will restrict causal analyses to differential cases (a difference that causes a difference). Mutations or other causal differences will allow us to stress that "non conservation principles" are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as symmetries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to "extended criticality" as a conceptual frame for a better understanding of the living state of matter.

q-bio.OT↗

arXiv2012

A classification scheme of Amino Acids in the Genetic Code by Group Theory

We derive the amino acid assignment to one codon representation (typical 64-dimensional irreducible representation) of the basic classical Lie superalgebra osp(5|2) from biochemical arguments. We motivate the approach of mathematical symmetries to the classification of the building constituents of the biosphere by analogy of its success in particle physics and chemistry. The model enables to calculate polarity and molecular volume of amino acids to a good approximation.

physics.gen-ph↗

arXiv2012

p-Adic Structure of the Genetic Code

The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end of genes, i.e. it terminates process of protein synthesis. This article is a review of simple modelling of the genetic code and related subjects by concept of p-adic distance. It also contains some new results. In particular, the article presents appropriate structure of the codon space, degeneration and possible evolution of the genetic code. p-Adic modelling of the genetic code is viewed as the first step in further application of p-adic tools in the information sector of life science.

q-bio.OT↗

arXiv2015

Health Matters: Human Organ Donations, Sales, and the Black Market

In this paper I explore the human organ procurement system. Which is better for saving lives and limiting black market use, the present altruistic system of donations or a free and open sales market? I explain that there is a risk with maintaining the present system, the altruistic vision, and that people may die who might otherwise live if the sale of organs was permitted. But there is no guarantee that permitting organ sales would effectively address the current supply-side shortage and global use of the black market. In addition to discussing the implications of these procurement systems, I look at methods to increase organ donations and I explore the differences between presumed and explicit consent. Ultimately, I conclude that the altruistic donation system, bolstered by the addition of a policy of presumed consent and appropriate financial incentives, is a better choice than a legal sales market in spite of its shortcomings.

q-bio.OT↗

arXiv2012

Field-control, phase-transitions, and life's emergence

Instances of critical-like characteristics in living systems at each organizational level as well as the spontaneous emergence of computation (Langton), indicate the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics--lacking the 'soft matter' response properties of today's bio-molecules--have dissipated energy from primordial reactions in a controlled manner for their 'ordering'? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the 'functional-takeover' of a soft magnetic scaffold by organics (c.f. Cairns-Smith's 'crystal-scaffold'). A field-controlled structure offers a mechanism for bootstrapping--bottom-up assembly with top-down control: its super-paramagnetic components obey reversible dynamics, but its dissipation of H-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically-oriented system towards a series of phase-transitions with appropriate organic replacements 'taking-over' its functions.

q-bio.OT↗

arXiv2012

Using Mimicry to Learn about Mental Representations

Phonology typically describes speech in terms of discrete signs like features. The field of intonational phonology uses discrete accents to describe intonation and prosody. But, are such representations useful? The results of mimicry experiments indicate that discrete signs are not a useful representation of the shape of intonation contours. Human behaviour seems to be better represented by a attractors where memory retains substantial fine detail about an utterance. There is no evidence that discrete abstract representations that might be formed that have an effect on the speech that is subsequently produced. This paper also discusses conditions under which a discrete phonology can arise from an attractor model and why - for intonation - attractors can be inferred without the implying a discrete phonology.

cs.SD↗

arXiv2012

Quantifying Limits to Detection of Early Warning for Critical Transitions

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls, or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model based approach in order to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favorable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different data sets, and suggest that uncertainty quantification become a more central part of early warning predictions.

q-bio.OT↗

arXiv2013

Dyadic groups, dyadic trees and symmetries in long nucleotide sequences

The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with well-known notions of dyadic groups and dyadic-shift matrices. Matrix genetics shows relations of the genetic alphabets with some types of hypercomplex numbers including dual numbers and bicomplex numbers together with their extensions. A possibility of new approach is mentioned to simulate genetically inherited phenomena of biological spirals and phyllotaxis laws on the base of screw theory and Fibonacci matrices. Dyadic trees for sub-sets of triplets of the whole human genome are constructed. A new notion is put forward about square matrices with internal complementarities on the base of genetic matrices. Initial results of the study of such matrices are described. Our results testify that living matter possesses a profound algebraic essence. They show new promising ways to develop algebraic biology.

q-bio.OT↗

arXiv2011

Fundamental Complexity Measures of Life

At present, there is a great deal of confusion regarding complexity and its measures (reviews on complexity measures are found in, e.g. Lloyd, 2001 and Shalizi, 2006 and more references therein). Moreover, there is also confusion regarding the nature of life. In this situation, it seems the task of determining the fundamental complexity measures of life is especially difficult. Yet this task is just part of a greater task: obtaining substantial insights into the nature of biological evolution. We think that without a firm quantitative basis characterizing the most fundamental aspects of life, it is impossible to overcome the confusion so as to clarify the nature of biological evolution. The approach we present here offers such quantitative measures of complexity characterizing biological organization and, as we will see, evolution.

physics.bio-ph↗

arXiv2013

The Geometry of Morphogenesis and the Morphogenetic Field Concept

The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of postulates and possible approaches for discovering the correspondence between molecular biological information and its realization in a given geometry of an organism in space-time. First, we suggest that the geometry of the organism and its parts is coded by a molecular code located on the cell surfaces in such a way that, with each cell, there can be associated a corresponding matrix, containing this code. As a particular model, we propose coding by several types of oligosaccharide residues of glycoconjugates. Second, we provide a notion of cell event, and suggest a description of development as a tree of cell events, where under cell event we understand the changing of cell state, e.g. the processes of cell division, cell growth/death, shift or differentiation. Next we suggest describing these cell motion laws using the notion of a "morphogenetic field", meaning by the field an object in an "event space" over a "cell space", which govern the transformation of the coded biological information into an instructive signal for a cell event for a given cell, depending on the position of a cell in the developing embryo. The matrix on a cell surface will be changed after each cell event according to the rule(s) dictated by the morphogenetic field of an organism. Finally, we provide some ideas on the connection between morphogenetic code on a cell surface, cell motion law(s) and the geometry of an embryo.

q-bio.OT↗

arXiv2012

Photonic Communications and Information Encoding in Biological Systems

The structure of optical radiation emitted by the samples of loach fish eggs is studied. It was found earlier that such radiation perform the communications between distant samples, which result in the synchronization of their development. The photon radiation in form of short quasi-periodic bursts was observed for fish and frog eggs, hence the communication mechanism can be similar to the exchange of binary encoded data in the computer nets via the noisy channels. The data analysis of fish egg radiation demonstrates that in this case the information encoding is similar to the digit to time analogue algorithm.

q-bio.OT↗

arXiv2012

Free flight of the mosquito Aedes aegypti

High speed video observations of free flying male Aedes aegypti mosquitoes, the dengue and yellow fever vector, along with custom measurement methods, enable measurement of wingbeat frequency, body position and body orientation of mosquitoes during flight. We find these mosquitoes flap their wings at approximately 850 Hz. We also generate body yaw, body pitch and wing deviation measurements with standard deviations of less than 1 degree and find that sideways velocity and acceleration are important components of mosquito motion. Rapid turns involving changes in flight direction often involve large sideways accelerations. These do not correspond to commensurate changes in body heading, and the insect's flight direction and body heading are decoupled during flight. These findings call in to question the role of yaw control in mosquito flight. In addition, using orientation data, we find that sideways accelerations are well explained by roll-based rotation of the lift vector. In contrast, the insect's body pitch angle does not correlate with its forward acceleration. This implies that controlling body roll is important to mosquito dynamics. The dynamic importance of stabilizing body pitch and body yaw is less clear.

physics.bio-ph↗

arXiv2012

Entromics -- thermodynamics of sequence dependent base incorporation into DNA reveals novel long-distance genome organization

Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously uncharacterized physical property of DNA, the incorporation reaction chemical potential Δμ. We use the combination of graph theory and statistical thermodynamics to derive entromics - a series of results providing the thermodynamic model of Δμ. We also show that Δμi is quantitatively characterized as incorporation entropy. We present formulae for computing Δμ from the genome DNA sequence. We then derive important restrictions on DNA properties and genome assembly that follow from thermodynamic properties of Δμ. Finally, we show how these genome assembly restrictions lead directly to the evolution of detectable coherences in incorporation entropy along the entire genome. Examples of entromic applications, demonstrating functional and biological importance are shown.

q-bio.OT↗

arXiv2012

Living Devices

The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long time. Physiologists have successfully analyzed a broad range of biological systems using a 'device-oriented' approach similar to the approach an engineer would use to investigate her devices. The present generation views biology through the powerful lenses of structural and (molecular) dynamic analysis, understandably enough because of the beauty and power of the analysis, and the ease of using these structures with present freely available software. The problem is that these powerful lenses offer such magnification that the engineering approach cannot be seen. High magnification means limited field of view, because the (spatial) dynamic range cannot cover everything. The function of the structures and molecular dynamics cannot be seen in the work of many biologists, probably because function cannot be immediately seen in the structures and molecular dynamics they compute. It is just as important for biologists to measure the inputs and outputs of their systems as it is to measure their structures. It seems clear, at least to one physiologist, that this research will be catalyzed by assuming that most biological systems are devices that can be analyzed with the same strategies one would use to analyze engineering devices. Thinking today about your biological preparation as a device tells you what experiments to do tomorrow. An important task for many of us is to transmit the physiological tradition to the next generation of biophysicists to help them adapt traditional questions to the new length scales and techniques of molecular and atomic biology.

q-bio.OT↗

arXiv2012

Affordability, cost and cost-effectiveness of universal anti-retroviral therapy for HIV

If people at risk of HIV infection are tested annually and started on treatment as soon as they are found to be HIV-positive it should be possible to reduce the case reproduction number for HIV to less than one, eliminate transmission and end the epidemic. If this is to be done it is essential to know if it would be affordable, and cost effective. Here we show that in all but eleven countries of the world it is affordable by those countries, that in these eleven countries it is affordable for the international community, and in all countries it is highly cost-effective.

q-bio.OT↗

arXiv2012

Soft Active Matter

In this review we summarize theoretical progress in the field of active matter, placing it in the context of recent experiments. Our approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of the review is to integrate the several approaches proposed in the literature, from semi-microscopic to phenomenological. In particular, we first consider "dry" systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium, and clarify the differences and similarities between two types of orientationally ordered states, the nematic and the polar. We then consider the active hydrodynamics of a suspension, and relate as well as contrast it with the dry case. We further highlight various large-scale instabilities of these nonequilibrium states of matter. We discuss and connect various semi-microscopic derivations of the continuum theory, highlighting the unifying and generic nature of the continuum model. Throughout the review, we discuss the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular materials. We suggest promising extensions towards greater realism in specific contexts from cell biology to ethology, and remark on some exotic active-matter analogues. Lastly, we summarize the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents.

cond-mat.soft↗