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arXiv2009

A Unified Theory on Construction and Evolution of the Genetic Code

A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the redundancy distribution of codons in the genetic code obeys MD minimization principle; 2, the hydrophilic-hydrophobic distribution of amino acids on the code table is global MD (GMD) minimal; 3, the standard genetic code can be deduced from the adaptive minimization of GMD; 4, the variants of the standard genetic code can be explained quantitatively by use of GMD formalism and the general trend of the evolution is GMD non-increasing which reflects the selection on the code. We have demonstrated that the redundancy distribution of codons and the hydrophobic-hydrophilic (H-P) distribution of amino acids are robust in the code relative to the mutational parameter, and indicated that the GMD can be looked as a non-fitness function on the adaptive landscape. Finally, an important aspect on the symmetry of the code construction, the Yin-Yang duality is investigated. The Yin-Yang duality among codons affords a sound basis for understanding the H-P structure in the genetic code.

q-bio.OT↗

arXiv2009

Coherent and Noncoherent Photonic Communications in Biological Systems

The possible mechanisms of communications between distant bio-systems by means of optical and UV photons are studied. It is argued that their main production mechanism is owed to the biochemical reactions, occurring during the cell division.. In the proposed model the bio-systems perform such communications, radiating the photons in form of short periodic bursts, which were observed experimentally for fish and frog eggs1. For experimentally measured photon rates the communication algorithm is supposedly similar to the exchange of binary encoded data in computer net via optical channels

q-bio.OT↗

arXiv2009

Multiple positive steady states in subnetworks defined by stoichiometric generators

In Systems Biology there is a growing interest in the question, whether or not a given mathematical model can admit more than one steady state. As parameter values are often unknown or subject to a very high uncertainty, one is often interested in the question, whether or not a given mathematical model can, for some conceivable parameter vector, exhibit multistationarity at all. A partial answer to this question is given in Feinberg's deficiency one algorithm. This algorithm can decide about multistationarity by analyzing systems of linear inequalities that are independent of parameter values. However, the deficiency one algorithm is limited to what its author calls regular deficiency one networks. Many realistic networks have a deficiency higher than one, thus the algorithm cannot be applied directly. In a previous publication it was suggested to analyze certain well defined subnetworks that are guaranteed to be of deficiency one. Realistic reaction networks, however, often lead to subnetworks that are irregular, especially if metabolic networks are considered. Here the special structure of the subnetworks is used to derive conditions for multistationarity. These conditions are independent of the regularity conditions required by the deficiency one algorithm. Thus, in particular, these conditions are applicable to irregular subnetworks.

q-bio.OT↗

arXiv2009

Scaling of human body mass with height: the Body Mass Index revisited

We adapt a biomechanical argument of Rashevsky, which places limits on the stress experienced by a torso supported by the legs, to deduce that body mass $m$ of growing children should scale as the $p$th power of height $h$ with $7/3<p<8/3$. Further arguments based on stability and heat loss suggest that $p$ should be close to 8/3. The arguments are extended to suggest that waist circumference $w$ should scale as $h^q$ with $q$ near the lower end of $2/3\leq q \leq 1$. Data from Hong Kong and British children are consistent with these hypotheses.

physics.bio-ph↗

arXiv2009

Differential Operator in Seizure Detection

Differential operators can detect significant changes in signals. This has been utilized to enhance the contrast of the seizure signatures in depth EEG or ECoG. We have actually taken normalized exponential of absolute value of single or double derivative of epileptic ECoG. Variance operation has been performed to automatically detect seizures. A novel method for determining the duration of seizure has also been proposed. Since all operations take only linear time, the whole method is extremely fast. Seven novel parameters have been introduced whose patient specific thresholding brings down the rate of false detection to a bare minimum. Results of implementation on the ECoG data of four epileptic patients have been reported with an ROC curve analysis. High value of the area under the ROC curve indicates excellent detection performance.

q-bio.QM↗

arXiv2009

Accelerating the pace of discovery by changing the peer review algorithm

The number of scientific publications is constantly rising, increasing the strain on the review process. The number of submissions is actually higher, as each manuscript is often reviewed several times before publication. To face the deluge of submissions, top journals reject a considerable fraction of manuscripts without review, potentially declining manuscripts with merit. The situation is frustrating for authors, reviewers and editors alike. Recently, several editors wrote about the ``tragedy of the reviewer commons', advocating for urgent corrections to the system. Almost every scientist has ideas on how to improve the system, but it is very difficult, if not impossible, to perform experiments to test which measures would be most effective. Surprisingly, relatively few attempts have been made to model peer review. Here I implement a simulation framework in which ideas on peer review can be quantitatively tested. I incorporate authors, reviewers, manuscripts and journals into an agent-based model and a peer review system emerges from their interactions. As a proof-of-concept, I contrast an implementation of the current system, in which authors decide the journal for their submissions, with a system in which journals bid on manuscripts for publication. I show that, all other things being equal, this latter system solves most of the problems currently associated with the peer review process. Manuscripts' evaluation is faster, authors publish more and in better journals, and reviewers' effort is optimally utilized. However, more work is required from editors. This modeling framework can be used to test other solutions for peer review, leading the way for an improvement of how science is disseminated.

cs.DL↗

arXiv2009

Biological Computing Fundamentals and Futures

The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored to discuss the possibilities of a new computing paradigm. We assume the reader to possess a basic knowledge of Biology and Computer Science

cs.CE↗

arXiv2009

Genetic Code and Number Theory

Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures. This article contains an introductory brief review of genetic information, its coding and translation of genes to proteins through the genetic code. Some theoretical approaches to the modelling of the genetic code are presented. In particular, connection of the genetic code with number theory is considered and the role of $p$-adic numbers is underlined.

q-bio.OT↗

arXiv2011

Are mental properties supervenient on brain properties?

The "mind-brain supervenience" conjecture suggests that all mental properties are derived from the physical properties of the brain. To address the question of whether the mind supervenes on the brain, we frame a supervenience hypothesis in rigorous statistical terms. Specifically, we propose a modified version of supervenience (called epsilon-supervenience) that is amenable to experimental investigation and statistical analysis. To illustrate this approach, we perform a thought experiment that illustrates how the probabilistic theory of pattern recognition can be used to make a one-sided determination of epsilon-supervenience. The physical property of the brain employed in this analysis is the graph describing brain connectivity (i.e., the brain-graph or connectome). epsilon-supervenience allows us to determine whether a particular mental property can be inferred from one's connectome to within any given positive misclassification rate, regardless of the relationship between the two. This may provide motivation for cross-disciplinary research between neuroscientists and statisticians.

q-bio.OT↗

arXiv2009

VirusPKT: A Search Tool For Assimilating Assorted Acquaintance For Viruses

Viruses utilize various means to circumvent the immune detection in the biological systems. Several mathematical models have been investigated for the description of viral dynamics in the biological system of human and various other species. One common strategy for evasion and recognition of viruses is, through acquaintance in the systems by means of search engines. In this perspective a search tool have been developed to provide a wider comprehension about the structure and other details on viruses which have been narrated in this paper. This provides an adequate knowledge in evolution and building of viruses, its functions through information extraction from various websites. Apart from this, tool aim to automate the activities associated with it in a self-maintainable, self-sustainable, proactive one which has been evaluated through analysis made and have been discussed in this paper.

cs.IR↗

arXiv2009

Data management in Systems biology II - Outlook towards the semantic web

The benefit of using ontologies, defined by the respective data standards, is shown. It is presented how ontologies can be used for the semantic enrichment of data and how this can contribute to the vision of the semantic web to become true. The problems existing today on the way to a true semantic web are pinpointed, different semantic web standards, tools and development frameworks are overlooked and an outlook towards artificial intelligence and agents for searching and mining the data in the semantic web are given, paving the way from data management to information and in the end true knowledge management systems.

cs.DB↗

arXiv2010

Optimization of Production Protocol of Alkaline Protease by Streptomyces pulvereceus

Extra cellular alkaline protease producing species is an isolate from soil which was characterized and identified as Streptomyces pulvereceus MTCC 8374. Studies on submerged fermentation revealed that maximum level of enzyme production was during early stationary phase. Optimum pH, inoculum and temperature were 9.0, 3 percent and 33 C respectively. Among carbon sources 0.3 peccent starch gave a maximum production followed by maltose, xylose and fructose. High yield of protease production was reported with 1.0 percent casein followed by soybean meal, yeast extract and malt extract. Further, it was optimized with 0.5 percent, 1.0 percentand 1.5 percent of NaCl among which 1 percent NaCl resulted in maximum level of protease. The protease profile of the isolate shows its potential as a good source for industrial application.

q-bio.OT↗

arXiv2010

The shade avoidance syndrome: a non-markovian stochastic growth model

Plants at high population density compete for light, showing a series of physiological responses known as the shade avoidance syndrome. These responses are controlled by the synthesis of the hormone auxin, which is regulated by two signals, an environmental one and an internal one. Considering that the auxin signal induces plant growth after a time lag, this work shows that plant growth can be modelled in terms of an energy-like function extremization, provided that the Markov property is not applied. The simulated height distributions are bimodal and right skewed, as in real community of plants. In the case of isolated plants, the theoretical expressions for the growth dynamics and the growth speed excellently fit experimental data for Arabidopsis thaliana. Moreover, the growth dynamics of this model is shown to be consistent with the biomass production function of an independent model. These results suggest that memory effects play a non-negligible role in plant growth processes.

q-bio.OT↗

arXiv2010

Complete Human Mitochondrial Genome Construction Using L-systems

Recently, scientists from The Craig J. Venter Institute reported construction of very long DNA molecules using a variety of experimental procedures adopting a number of working hypotheses. Finding a mathematical rule for generation of such a long sequence would revolutionize our thinking on various advanced areas of biology, viz. evolution of long DNA chains in chromosomes, reasons for existence of long stretches of non-coding regions as well as would usher automated methods for long DNA chains preparation for chromosome engineering. However, this mathematical principle must have room for editing / correcting DNA sequences locally in those areas of genomes where mutation and / or DNA polymerase has introduced errors over millions of years. In this paper, we report the basics and applications of L-system (a mathematical principle) which could answer all the aforesaid issues. At the end, we present the whole human mitochondrial genome which has been generated using this mathematical principle using PC computation power. We can claim now that we can make any stretch of DNA, be it 936 bp of olfactory receptor, with or without introns, mitochondrial DNA to 3 x 109 bp DNA sequences of the whole human genome with even a PC computation power.

q-bio.OT↗

arXiv2010

The genome is software and evolution is a software developer

The genome is software because it a set of verbal instructions for a programmable computer, the ribosome. The theory of evolution now reads: evolution is the software developer responsible for the existence of the genome. We claim that this setting, whose official name is genetic programming, is necessary and sufficient to discuss all important questions about evolution. A great effort has been made to pass from wording to science, i.e., from naive theories to robust models to predictions to testing for falsification.

q-bio.OT↗

arXiv2010

Semi-Circular Canals Anomalies//Idiopathic Scoliosis

Thanks to a novel modelling programme to detect anomalies in the membranous semi circular canals (SSC) of idiopathic scoliosis (IS) we found severe anomalies mainly located in lateral SCC devoted to trunk rotation and lateral deviations. We also found a specific communication between the lateral and posterior canal involving the utricular chamber which is also highly suspected in scoliosis. Key points: - Membranous semi circular canals (SCC) modelling based on MRI revealed significant anomalies in IS patients compared to normal subjects. - Frequent aplasias located in the lateral canal were found in IS. - We also discovered a, never described, abnormal communication between lateral and posterior canal. - Lateral SCC is involved in trunk rotation and lateral deviation: these movements are frequently abnormal in IS. Supports: Fondation Yves Cotrel pour la recherche en pathologie rachidienne. Institut de France, Paris. SHFJ/CEA Orsay in the frame of the cooperation through IFR 49 INSERM/CNRS France.

q-bio.NC↗

arXiv2010

A stem-cell ageing hypothesis on the origin of Parkinson's disease

A transcriptome-wide blood expression dataset of Parkinson's disease (PD) patients and controls was analyzed under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem cell/differentiation process expression program defect and suggest this research direction deserves further investigation.

q-bio.CB↗

arXiv2010

Active Matter

The term active matter describes diverse systems, spanning macroscopic (e.g. shoals of fish and flocks of birds) to microscopic scales (e.g. migrating cells, motile bacteria and gels formed through the interaction of nanoscale molecular motors with cytoskeletal filaments within cells). Such systems are often idealizable in terms of collections of individual units, referred to as active particles or self-propelled particles, which take energy from an internal replenishable energy depot or ambient medium and transduce it into useful work performed on the environment, in addition to dissipating a fraction of this energy into heat. These individual units may interact both directly as well as through disturbances propagated via the medium in which they are immersed. Active particles can exhibit remarkable collective behaviour as a consequence of these interactions, including non-equilibrium phase transitions between novel dynamical phases, large fluctuations violating expectations from the central limit theorem and substantial robustness against the disordering effects of thermal fluctuations. In this chapter, following a brief summary of experimental systems which may be classified as examples of active matter, I describe some of the principles which underlie the modeling of such systems.

cond-mat.soft↗