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On Programs and Genomes

Werner, Eric
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 24/10/2011
Relevância na Pesquisa
55.47%
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from control genes or cenes. Cenes are interpreted and executed by the cell and, thereby, direct cell actions including communication, growth, division, differentiation and multi-cellular development. The cenome is the global developmental control network in the genome. The cenome is also a cene that consists of interlinked sub-cenes that guide the ontogeny of the organism. The complexity of organisms is linked to the complexity of the cenome. The relevance to ontogeny and evolution is mentioned. We introduce the concept of a universal cell and a universal genome.; Comment: This a slightly extended version of Part I of a position paper distributed on November 18, 2007 to the participants of our Balliol Seminar on the Conceptual Foundations of Systems Biology. It presented my ideas on the global control architecture of genomes. Denis Noble and myself started the seminar in the Michaelmas term in the autumn of 2006 at Balliol College, University of Oxford

The genome is software and evolution is a software developer

Rodriguez, Jose
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 02/03/2010
Relevância na Pesquisa
55.49%
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.; Comment: 53 pages, 1 figure

Comparative study of non-invasive force and stress inference methods in tissue

Ishihara, S.; Sugimura, K.; Cox, S. J.; Bonnet, I.; Bellaiche, Y.; Graner, F.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 18/01/2013
Relevância na Pesquisa
65.43%
In the course of animal development, the shape of tissue emerges in part from mechanical and biochemical interactions between cells. Measuring stress in tissue is essential for studying morphogenesis and its physical constraints. Experimental measurements of stress reported thus far have been invasive, indirect, or local. One theoretical approach is force inference from cell shapes and connectivity, which is non-invasive, can provide a space-time map of stress and relies on prefactors. Here, to validate force- inference methods, we performed a comparative study of them. Three force-inference methods, which differ in their approach of treating indefiniteness in an inverse problem between cell shapes and forces, were tested by using two artificial and two experimental data sets. Our results using different datasets consistently indicate that our Bayesian force inference, by which cell-junction tensions and cell pressures are simultaneously estimated, performs best in terms of accuracy and robustness. Moreover, by measuring the stress anisotropy and relaxation, we cross-validated the force inference and the global annular ablation of tissue, each of which relies on different prefactors. A practical choice of force-inference methods in distinct systems of interest is discussed.; Comment: 12 pages...

The Dynamic Evolution of the Power Exponent in a Universal Growth Model of Tumors

Guiot, Caterina; Delsanto, Pier Paolo; Carpinteri, Alberto; Mansury, Nicola Pugno Yuri; Deisboeck, Thomas S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 01/02/2005
Relevância na Pesquisa
55.5%
We have previously reported that a universal growth law, as proposed by West and collaborators for all living organisms, appears to be able to describe also the growth of tumors in vivo. In contrast to the assumption of a fixed power exponent p (assumed by West et al. to be equal to 3/4), we show in this paper the dynamic evolution of p from 2/3 to 1, using experimental data from the cancer literature and in analogy with results obtained by applying scaling laws to the study of fragmentation of solids. The dynamic behaviour of p is related to the evolution of the fractal topology of neoplastic vascular systems and might be applied for diagnostic purposes to mark the emergence of a functionally sufficient (or effective) neo-angiogenetic structure.

Studies on the Origin and Evolution of Codon Bias

Biro, Jan C
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 24/07/2008
Relevância na Pesquisa
65.5%
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias. Results: Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 +/- 1.1% (S.E.M, n=113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues. Conclusions: The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.; Comment: 24 pages including 10 figures and 4 tables

Finite volume and asymptotic methods for stochastic neuron models with correlated inputs

Rosenbaum, Robert; Ma, Jianfu; Marpeau, Fabien; Barua, Aditya; Josic, Kresimir
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
55.47%
We consider a pair of stochastic integrate and fire neurons receiving correlated stochastic inputs. The evolution of this system can be described by the corresponding Fokker-Planck equation with non-trivial boundary conditions resulting from the refractory period and firing threshold. We propose a finite volume method that is orders of magnitude faster than the Monte Carlo methods traditionally used to model such systems. The resulting numerical approximations are proved to be accurate, nonnegative and integrate to 1. We also approximate the transient evolution of the system using an Ornstein--Uhlenbeck process, and use the result to examine the properties of the joint output of cell pairs. The results suggests that the joint output of a cell pair is most sensitive to changes in input variance, and less sensitive to changes in input mean and correlation.

A Unified Theory on Construction and Evolution of the Genetic Code

Luo, Liaofu
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/08/2009
Relevância na Pesquisa
55.53%
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.; Comment: 40 pages; 7 figures

Mozart Effect, Cognitive Dissonance, and the Pleasure of Music

Perlovsky, Leonid; Cabanac, Arnaud; Bonniot-Cabanac, Marie-Claude; Cabanac, Michel
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 15/09/2012
Relevância na Pesquisa
65.36%
The Mozart effect refers to scientific data on short-term improvement on certain mental tasks after listening to Mozart, and also to its popularized version that listening to Mozart makes you smarter (Tomatis, 1991; Wikipedia, 2012). Does Mozart effect point to a fundamental cognitive function of music? Would such an effect of music be due to the hedonicity, a fundamental dimension of mental experience? The present paper explores a recent hypothesis that music helps to tolerate cognitive dissonances and thus enabled accumulation of knowledge and human cultural evolution (Perlovsky, 2010, 2012). We studied whether the influence of music is related to its hedonicity and whether pleasant or unpleasant music would influence scholarly test performance and cognitive dissonance. Specific hypotheses evaluated here are that during a test students experience contradictory cognitions that cause cognitive dissonances. If some music helps to tolerate cognitive dissonances, then first, this music should increase the duration during which participants can tolerate stressful conditions while evaluating test choices. Second, this should result in improved performance. These hypotheses are tentatively confirmed in the reported experiments as the agreeable music was correlated with better performance above that under indifferent or unpleasant music. It follows that music likely performs a fundamental cognitive function explaining the origin and evolution of musical ability considered previously a mystery.; Comment: 11 pages

Atomic Biology, Electrostatics, and Ionic Channels

Eisenberg, R. S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
55.5%
I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology. Electrodiffusion in the open channel. Electrodiffusion in mixed electrolytes. Models of permeation. State Models of Permeation are Inconsistent with the Electric Field. Making models in atomic biology. Molecular dynamics. Temporal Limitations; Spatial Limitations; Periodic boundary conditions. Hierarchy of models of the open channel. Stochastic Motion of the Channel. Langevin Dynamics. Simulations of the Reaction Path: the Permion. Chemical reactions. What was wrong? Back to the hierarchy: Occam's razor can slit your throat. Poisson-Nernst-Planck PNP Models Flux Ratios; Pumping by Field Coupling. Gating in channels of one conformation. Gating by Field Switching; Gating Current; Gating in Branched Channels; Blocking. Back to the hierarchy: Linking levels. Is there a theory? At what level will the adaptation be found? Simplicity, evolution, and natural function.; Comment: This is a submission without substantive change of a chapter in the hard to find book, "New Developments and Theoretical Studies of Proteins" World Scientific Publishing Philadelphia...

Local stability and evolution of the genetic code

Chechetkin, V. R.; Lobzin, V. V.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 24/09/2009
Relevância na Pesquisa
55.47%
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function, the negative variations of which correspond to a more robust code. The fraction of more robust codes obtained under small modifications appeared to be unexpectedly high, ranged from 0.1 to 0.4 depending on the choice of stability function and code modifications, yet significantly lower than the corresponding fraction in the random codes (about a half). In this sense the standard code ought to be considered distinctly non-random in accordance with previous observations. The distribution of the negative variations of stability function revealed very abrupt drop beyond one standard deviation, much sharper than for Gaussian distribution or for the random codes with the same number of codons in the sets coding for amino acids or stop-codons. This behavior holds for both the standard code as a whole and its binary NRN-NYN, NWN-NSN, and NMN-NKN blocks. Previously, it has been proved that such binary block structure is necessary for the robustness of a code and is inherent to the standard genetic code. The modifications of the standard code corresponding to more robust coding may be related to the different variants of the code. These effects may also contribute to the rates of replacements of amino acids. The observed features demonstrate the joint impact of random factors and natural selection during evolution of the genetic code.; Comment: 16 pages...

A rate-distortion scenario for the emergence and evolution of noisy molecular codes

Tlusty, Tsvi
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 23/07/2010
Relevância na Pesquisa
65.37%
We discuss, in terms of rate-distortion theory, the fitness of molecular codes as the problem of designing an optimal information channel. The fitness is governed by an interplay between the cost and quality of the channel, which induces smoothness in the code. By incorporating this code fitness into population dynamics models, we suggest that the emergence and evolution of molecular codes may be explained by simple channel design considerations.; Comment: PACS numbers: 87.10.+e, 87.14.Gg, 87.14.Ee

On Pattern and Evolution

Cummings, Frederick W.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
65.46%
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss curvature'K'enters. The model suggests a novel point-like placement for organs such as eyes, antennae, limbs, and wings. In the case of plant patterns, 'leaf' outgrowths from a stem are predicted to be under the control of a yet to be discovered "master regulatiory gene", analogous to the animal case, when various outgrowths from the animal body are generally accompanied by activation of the 'distal-less' (Dll) gene.; Comment: 38 pages, seven figures

Interrelationship Between Protein Electrostatics and Evolution in HCV and HIV Replicative Proteins

Frenz, Christopher M.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 10/10/2008
Relevância na Pesquisa
65.41%
Protein electrostatics have been demonstrated to play a vital role in protein functionality, with many functionally important amino acid residues exhibiting an electrostatic state that is altered from that of a normal amino acid residue. Residues with altered electrostatic states can be identified by the presence of a pKa value that is perturbed by 2 or more pK units, and such residues have been demonstrated to play critical roles in catalysis, ligand binding, and protein stability. Within the HCV helicase and polymerase, as well as the HIV reverse transcriptase, highly conserved regions were demonstrated to possess a greater number and magnitude of perturbations than lesser conserved regions, suggesting that there is an interrelationship present between protein electrostatics and evolution.; Comment: Published in the Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2007). Pages 91-97

Dynamical Systems Basis of Metamorphosis: Diversity and Plasticity of Cellular States in Reaction Diffusion Network

Takagi, Hiroaki; Kaneko, Kunihiko
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/11/2003
Relevância na Pesquisa
65.41%
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with considering the division and death of cells, developmental process from a single cell is studied. Cell differentiation process is found to occur through instability in transient dynamics and cell-cell interaction. In a long time behavior, extinction of multiple cells is repeated, which leads to itinerancy over successive quasi-stable multi-cellular states consisting of different types of cells. By defining the plasticity of a cellular state, it is shown that the plasticity of cells decreases before the large extinction, from which diversity and plasticity are recovered. After this switching, decrease of plasticity again occurs, leading to the next extinction of multiple cells. This cycle of diversification and extinction is repeated. Relevance of our results to the development and evolution is briefly discussed.; Comment: 26 pages, 15 figures, submitted to Jour. Theor. Biol

Material forces in the context of biotissue remodelling

Garikipati, K.; Narayanan, H.; Arruda, E. M.; Grosh, K.; Calve, S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 29/11/2003
Relevância na Pesquisa
55.5%
Remodelling of biological tissue, due to changes in microstructure, is treated in the continuum mechanical setting. Microstructural change is expressed as an evolution of the reference configuration. This evolution is expressed as a point-to-point map from the reference configuration to a remodelled configuration. A ``preferred'' change in configuration is considered in the form of a globally incompatible tangent map. This field could be experimentally determined, or specified from other insight. Issues of global compatibility and evolution equations for the resulting configurations are addressed. It is hypothesized that the tissue reaches local equilibrium with respect to changes in microstructure. A governing differential equation and boundary conditions are obtained for the microstructural changes by posing the problem in a variational setting. The Eshelby stress tensor, a separate configurational stress, and thermodynamic driving (material) forces arise in this formulation, which is recognized as describing a process of self-assembly. An example is presented to illustrate the theoretical framework.; Comment: 6 pages, 3 figures, to appear in ``Mechanics of Material Forces'' edited by P. Steinmann and G. A. Maugin, Kluwer Academic Publishers

Beauty and Art. Cognitive Function, Evolution, and Mathematical Models of the Mind

Perlovsky, Leonid
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/12/2010
Relevância na Pesquisa
65.36%
The paper discusses relationships between aesthetics theory and mathematical models of mind. Mathematical theory describes abilities for concepts, emotions, instincts, imagination, adaptation, learning, cognition, language, approximate hierarchy of the mind and evolution of these abilities. The knowledge instinct is the foundation of higher mental abilities and aesthetic emotions. Aesthetic emotions are present in every act of perception and cognition, and at the top of the mind hierarchy they become emotions of the beautiful. The learning ability is essential to everyday perception and cognition as well as to the historical development of understanding of the meaning of life. I discuss a controversy surrounding this issue. Conclusions based on cognitive and mathematical models confirm that judgments of taste are at once subjective and objective, and I discuss what it means. The paper relates cognitive and mathematical concepts to those of philosophy and aesthetics, from Plato to our days, clarifies cognitive mechanisms and functions of the beautiful, and resolves many difficulties of contemporary aesthetics.

Physics of the mind: Concepts, emotions, language, cognition, consciousness, beauty, music, and symbolic culture

Perlovsky, Leonid
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/12/2010
Relevância na Pesquisa
65.36%
Mathematical approaches to modeling the mind since the 1950s are reviewed. Difficulties faced by these approaches are related to the fundamental incompleteness of logic discovered by K. G\"odel. A recent mathematical advancement, dynamic logic (DL) overcame these past difficulties. DL is described conceptually and related to neuroscience, psychology, cognitive science, and philosophy. DL models higher cognitive functions: concepts, emotions, instincts, understanding, imagination, intuition, consciousness. DL is related to the knowledge instinct that drives our understanding of the world and serves as a foundation for higher cognitive functions. Aesthetic emotions and perception of beauty are related to 'everyday' functioning of the mind. The article reviews mechanisms of human symbolic ability, language and cognition, joint evolution of the mind, consciousness, and cultures. It touches on a manifold of aesthetic emotions in music, their cognitive function, origin, and evolution. The article concentrates on elucidating the first principles and reviews aspects of the theory proven in laboratory research.

Matrix genetics, part 3: the evolution of the genetic code from the viewpoint of the genetic octave Yin-Yang-algebra

Petoukhov, Sergey V.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 30/05/2008
Relevância na Pesquisa
55.51%
The set of known dialects of the genetic code (GC) is analyzed from the viewpoint of the genetic octave Yin-Yang-algebra. This algebra was described in the previous author's publications. The algebra was discovered on the basis of structural features of the GC in the matrix form of its presentation ("matrix genetics"). The octave Yin-Yang-algebra is considered as the pre-code or as the model of the GC. From the viewpoint of this algebraic model, for example, the sets of 20 amino acids and of 64 triplets consist of sub-sets of "male", "female" and "androgynous" molecules, etc. This algebra permits to reveal hidden peculiarities of the structure and evolution of the GC and to propose the conception of "sexual" relationships among genetic molecules. The first results of the analysis of the GC systems from such algebraic viewpoint say about the close connection between evolution of the GC and this algebra. They include 8 evolutionary rules of the dialects of the GC. The evolution of the GC is appeared as the struggle between male and female beginnings. The hypothesis about new biophysical factor of "sexual" interactions among genetic molecules is put forward. The matrix forms of presentation of elements of the genetic octave Yin-Yang-algebra are connected with Hadamard matrices by means of the simple U-algorithm. Hadamard matrices play a significant role in the theory of quantum computers...

The Origin, Evolution and Development of Bilateral Symmetry in Multicellular Organisms

Werner, Eric
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 13/07/2012
Relevância na Pesquisa
65.38%
A computational theory and model of the ontogeny and development of bilateral symmetry in multicellular organisms is presented. Understanding the origin and evolution of bilateral organisms requires an understanding of how bilateral symmetry develops, starting from a single cell. Bilateral symmetric growth of a multicellular organism from a single starter cell is explained as resulting from the opposite handedness and orientation along one axis in two daughter founder cells that are in equivalent developmental control network states. Several methods of establishing the initial orientation of the daughter cells (including oriented cell division and cell signaling) are discussed. The orientation states of the daughter cells are epigenetically inherited by their progeny. This results in mirror development with the two founding daughter cells generating complementary mirror image multicellular morphologies. The end product is a bilateral symmetric organism. The theory gives a unified explanation of diverse phenomena including symmetry breaking, situs inversus, gynandromorphs, inside-out growth, bilaterally symmetric cancers, and the rapid, punctuated evolution of bilaterally symmetric organisms in the Cambrian Explosion. The theory is supported by experimental results on early embryonic development. The theory makes precise testable predications.; Comment: 29 pages

How to Grow an Organism Inside-Out: Evolution of an internal skeleton from an external skeleton in bilateral organisms

Werner, Eric
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/07/2012
Relevância na Pesquisa
55.52%
An intriguing unanswered question about the evolution of bilateral animals with internal skeletons is how an internal skeleton evolved in the first place. Computational modeling of the development of bilateral symmetric organisms suggests an answer to this question. Our hypothesis is that an internal skeleton may have evolved from a bilaterally symmetric ancestor with an external skeleton. By growing the organism inside-out an external skeleton becomes an internal skeleton. Our hypothesis is supported by a computational theory of bilateral symmetry that allows us to model and simulate this process. Inside-out development is achieved by an orientation switch. Given the development of two bilateral founder cells that generate a bilateral organism, a mutation that reverses the internal mirror orientation of those bilateral founder cells leads to inside-out development. The new orientation is epigenetically inherited by all progeny. A key insight is that each cell contained in the newly evolved organism with the internal skeleton develops according to the very same downstream developmental control network that directs the development of its exoskeletal ancestor. The networks and their genomes are are identical, but the interpretation is different because of the cell's inverted orientation. The result is inside-out bilateral symmetric development generating an inside-out organism with an internal skeleton.; Comment: 9 pages. Key Words: Metazoan evolution...