scispace - formally typeset
Search or ask a question
Journal ArticleDOI

Metabolic stability and epigenesis in randomly constructed genetic nets

TL;DR: The hypothesis that contemporary organisms are also randomly constructed molecular automata is examined by modeling the gene as a binary (on-off) device and studying the behavior of large, randomly constructed nets of these binary “genes”.
About: This article is published in Journal of Theoretical Biology.The article was published on 1969-03-01. It has received 4250 citations till now.
Citations
More filters
Journal ArticleDOI
04 Jun 1998-Nature
TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Abstract: Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

39,297 citations

Journal ArticleDOI
TL;DR: Developments in this field are reviewed, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.
Abstract: Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

17,647 citations

Journal ArticleDOI
08 Mar 2001-Nature
TL;DR: This work aims to understand how an enormous network of interacting dynamical systems — be they neurons, power stations or lasers — will behave collectively, given their individual dynamics and coupling architecture.
Abstract: The study of networks pervades all of science, from neurobiology to statistical physics. The most basic issues are structural: how does one characterize the wiring diagram of a food web or the Internet or the metabolic network of the bacterium Escherichia coli? Are there any unifying principles underlying their topology? From the perspective of nonlinear dynamics, we would also like to understand how an enormous network of interacting dynamical systems-be they neurons, power stations or lasers-will behave collectively, given their individual dynamics and coupling architecture. Researchers are only now beginning to unravel the structure and dynamics of complex networks.

7,665 citations


Cites background from "Metabolic stability and epigenesis ..."

  • ...They have also served as idealized coupling architectures for dynamical models of gene networks, ecosystems and the spread of infectious diseases and computer viruse...

    [...]

Journal ArticleDOI
TL;DR: A hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O (md log n) where d is the depth of the dendrogram describing the community structure.
Abstract: The discovery and analysis of community structure in networks is a topic of considerable recent interest within the physics community, but most methods proposed so far are unsuitable for very large networks because of their computational cost. Here we present a hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O (md log n) where d is the depth of the dendrogram describing the community structure. Many real-world networks are sparse and hierarchical, with m approximately n and d approximately log n, in which case our algorithm runs in essentially linear time, O (n log(2) n). As an example of the application of this algorithm we use it to analyze a network of items for sale on the web site of a large on-line retailer, items in the network being linked if they are frequently purchased by the same buyer. The network has more than 400 000 vertices and 2 x 10(6) edges. We show that our algorithm can extract meaningful communities from this network, revealing large-scale patterns present in the purchasing habits of customers.

6,599 citations

Journal ArticleDOI
TL;DR: The recent rapid progress in the statistical physics of evolving networks is reviewed, and how growing networks self-organize into scale-free structures is discussed, and the role of the mechanism of preferential linking is investigated.
Abstract: We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

3,368 citations


Cites background from "Metabolic stability and epigenesis ..."

  • ..., collaboration networks [11, 12, 13, 14, 15], public relations nets [16, 17, 18, 19, 20], citations of scienti®c papers [21, 22, 23, 24, 25, 26, 27], some industrial networks [11, 12, 28], transportation networks [29, 30], nets of relations between enterprises and agents in ®nancial markets [31], telephone call graphs [32], many biological networks [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], food and ecological webs [46, 47, 48, 49, 50, 51, 52], etc....

    [...]

  • ...Networks of metabolic reactions The valuable example of a biological network with the extremely rich topological structure is provided by the network of metabolic reactions [33, 34, 67]....

    [...]

References
More filters
Book
01 Jan 1944

2,603 citations


"Metabolic stability and epigenesis ..." refers background in this paper

  • ...Schrodinger (1944) noted that high molecular specificity, guaranteed by quantum stabilization, is required for the precision of biosynthesis in living things....

    [...]

Book
01 Jan 1970
TL;DR: The long-awaited Fifth Edition of James D. Watson's classic text, Molecular Biology of the Gene, has been thoroughly revised and is published to coincide with the 50th anniversary of Watson and Crick's paper on the structure of the DNA double-helix as discussed by the authors.
Abstract: The long-awaited Fifth Edition of James D. Watson's classic text, Molecular Biology of the Gene, has been thoroughly revised and is published to coincide with the 50th anniversary of Watson and Crick's paper on the structure of the DNA double-helix. Though completely updated, the new edition retains the distinctive character of earlier editions that made it the most widely used book in molecular biology. Twenty-one concise chapters, co-authored by five highly respected molecular biologists, provide current, authoritative coverage of a fast-changing discipline. The completely new art is printed in full color for the first time. Divided into five parts, the first (Chemistry and Genetics) begins with an overview of molecular biology, placing the discipline in historical context and introducing the basic chemical concepts that underpin our description of molecular biology today. The second and third parts (Maintenance of the Genome and Expression of the Genome) form the heart of the book, describing in detail the basic mechanisms of DNA replication, transcription and translation. The fourth part of the book (Regulation) deals with how gene expression is regulated - from the examination of basic mechanisms that regulate gene expression in bacterial and eukaryotic systems, to a description of how regulation of gene expression lies at the heart of the process of development. Recent findings from sequencing whole genomes of several animals have revealed that they all share essentially the same genes. The last chapter in the regulation section looks at how changes in gene regulation can account for how different animals can be made up of the same genes. The final part of the book (Methods) deals with the techniques and methods used in molecular biology.

2,520 citations

Journal Article
TL;DR: Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages, not only for you, but for the other peoples with those meaningful benefits.
Abstract: No wonder you activities are, reading will be always needed. It is not only to fulfil the duties that you need to finish in deadline time. Reading will encourage your mind and thoughts. Of course, reading will greatly develop your experiences about everything. Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages. The advantages are not only for you, but for the other peoples with those meaningful benefits.

718 citations


"Metabolic stability and epigenesis ..." refers background or methods in this paper

  • ...…Pisum sativutn Tradescantia paludosa Tulipa kaufmanniam Helianthus annuus Trillium erectwn Aspergillus nidulans Saccharomyces cervesiae DNA per cell Watson (1965) Nanney & Rudzinska (1960) Sparrow & Evans (1961) Vendrely (1955) Vendrely (1955) Vendrely (1955) Vendrely (1955) Vendrely (1955)…...

    [...]

  • ...I) number of genes per cell was estimated by comparison of its DNA per cell with that of Escherichiu coli, which Watson (1965) has estimated to have about 2000 genes....

    [...]

  • ...Macklin (1968) Watson (1965) Macklin (1968) t The DNA per cell in hydra presumably lies between sponge and jellyfish. logarithm of the estimated number of genes per cell in each organism, in Fig....

    [...]

Book
01 Jan 1967

589 citations

Book
01 Jan 1963

448 citations


"Metabolic stability and epigenesis ..." refers background in this paper

  • ...In biology, a gene specifies a protein, and the t Present address: Cincinnati General Hospital, Cincinnati, Ohio, U.S.A. 437...

    [...]

  • ...Goodwin (1963) has treated the gene as a continuously oscillating biochemical element whose output of mRNA is repressed by the protein specified....

    [...]

  • ...To study the behavior of nets with arbitrarily complex couplings requires us to abandon the effort to obtain an integral of motion for the system (Goodwin, 1963)....

    [...]

  • ...Estimates of the time required to switch a gene on or off lie between 5 and 90 seconds (Goodwin, 1963)....

    [...]