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Dilema do prisioneiro evolucionário Darwiniano e Pavloviano no autômato celular unidimensional: uma nova representação e exploração exaustiva do espaço de parâmetros; Darwinian and Pavlovian Evolutionary Prisoner Dilemma in the One-Dimensional Cellular Automata: a new representation and exhaustive exploration of parameter space

Pereira, Marcelo Alves
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 11/04/2008 PT
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O Dilema do Prisioneiro (DP) é o jogo mais proeminente da Teoria dos Jogos devido à emergência da cooperação entre jogadores egoístas. O comportamento de cada jogador depende da estratégia que ele adotada e do seu ganho, que é determinado em função dos parâmetros do DP (T, R, P e S) e do número z de vizinhos com que ele joga. Portanto, a estrutura espacial dos jogadores não é relevante. Em nosso trabalho, utilizamos um autômato celular unidimensional onde cada jogador pode cooperar ou desertar ao interagir, simetricamente, com seus z vizinhos mais próximos. O sistema proposto nos permitiu realizar um estudo exaustivo do espaço de parâmetros para as estratégias evolucionárias Darwiniana (EED) e a Pavloviana (EEP) e compara-las. A geometria unidimensional nos possibilita obter os mesmos resultados dos sistemas em dimensionalidade arbitrária d, além de apresentar várias vantagens em relação a elas. No sistema que propomos os efeitos de borda são menores, exige menos tempo para a execução das simulações numéricas, permite variar o valor de z e é fácil obter uma representação visual da evolução temporal do sistema. Tal visualização simplifica a compreensão das interações entre os jogadores, pois surgem padrões nos agrupamentos de cooperadores/desertores...

Comparison of analytical models with cellular automata simulation of recrystallization in two dimensions

Rios,Paulo Rangel; Oliveira,Janaína Costa Pereira Torres de; Oliveira,Valmir Torres de; Castro,José Adilson de
Fonte: ABM, ABC, ABPol Publicador: ABM, ABC, ABPol
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/09/2005 EN
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Cellular automata simulation of recrystallization in two dimensions is carried out. The simulated microstrutural evolution is compared in detail with the predictions from mathematically exact analytical theories considering both kinetic and geometrical aspects. Very good agreement is observed between the cellular automata simulation and the theoretical results. Moreover, the simulated data is used to test new expressions recently derived to describe the evolution of the interfaces between recrystallized grains. This work focuses on recrystallization but its results are applicable to any nucleation and growth transformation.

Cellular automata simulation of site-saturated and constant nucleation rate transformations in three dimensions

Rios,Paulo Rangel; Oliveira,Valmir Torres de; Pereira,Luciana de Oliveira; Pereira,Maxwell Ruela; Castro,José Adilson de
Fonte: ABM, ABC, ABPol Publicador: ABM, ABC, ABPol
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/06/2006 EN
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Microstructural evolution in three dimensions of nucleation and growth transformations is simulated by means of cellular automata. Two types of nucleation are considered: site-saturated nucleation and constant nucleation rate. The simulated microstrutural evolution agrees very well with exact analytical expressions. The simulated data also gives very good agreement with expressions derived to describe the evolution of the interfaces between transformed grains.

On the evolution of cells

Woese, Carl R.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
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362.504%
A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the “Darwinian Threshold” for the reasons given.

Determining the Cellular Diversity of Hepatitis C Virus Quasispecies by Single-Cell Viral Sequencing

McWilliam Leitch, E. Carol; McLauchlan, John
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /12/2013 EN
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Single-cell genomics is emerging as an important tool in cellular biology. We describe for the first time a system to investigate RNA virus quasispecies diversity at the cellular level utilizing hepatitis C virus (HCV) replicons. A high-fidelity nested reverse transcription (RT)-PCR assay was developed, and validation using control transcripts of known copy number indicated a detection limit of 3 copies of viral RNA/reaction. This system was used to determine the cellular diversity of subgenomic JFH-1 HCV replicons constitutively expressed in Huh7 cells. Each cell contained a unique quasispecies that was much less diverse than the quasispecies of the bulk cell population from which the single cells were derived, suggesting the occurrence of independent evolution at the cellular level. An assessment of the replicative fitness of the predominant single-cell quasispecies variants indicated a modest reduction in fitness compared to the wild type. Real-time RT-PCR methods capable of determining single-cell viral loads were developed and indicated an average of 113 copies of replicon RNA per cell, correlating with calculated RNA copy numbers in the bulk cell population. This study introduces a single-cell RNA viral-sequencing method with numerous potential applications to explore host-virus interactions during infection. HCV quasispecies diversity varied greatly between cells in vitro...

FishFace: interactive atlas of zebrafish craniofacial development at cellular resolution

Eames, B Frank; DeLaurier, April; Ullmann, Bonnie; Huycke, Tyler R; Nichols, James T; Dowd, John; McFadden, Marcie; Sasaki, Mark M; Kimmel, Charles B
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
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Background: The vertebrate craniofacial skeleton may exhibit anatomical complexity and diversity, but its genesis and evolution can be understood through careful dissection of developmental programs at cellular resolution. Resources are lacking that include introductory overviews of skeletal anatomy coupled with descriptions of craniofacial development at cellular resolution. In addition to providing analytical guidelines for other studies, such an atlas would suggest cellular mechanisms underlying development. Description We present the Fish Face Atlas, an online, 3D-interactive atlas of craniofacial development in the zebrafish Danio rerio. Alizarin red-stained skulls scanned by fluorescent optical projection tomography and segmented into individual elements provide a resource for understanding the 3D structure of the zebrafish craniofacial skeleton. These data provide the user an anatomical entry point to confocal images of Alizarin red-stained zebrafish with transgenically-labelled pharyngeal arch ectomesenchyme, chondrocytes, and osteoblasts, which illustrate the appearance, morphogenesis, and growth of the mandibular and hyoid cartilages and bones, as viewed in live, anesthetized zebrafish during embryonic and larval development. Confocal image stacks at high magnification during the same stages provide cellular detail and suggest developmental and evolutionary hypotheses. Conclusion: The FishFace Atlas is a novel learning tool for understanding craniofacial skeletal development...

Using cellular evolution for diversification of the balance between accurate and interpretable fuzzy knowledge bases for classification

Ghandar, A.; Michalewicz, Z.
Fonte: IEEE; USA Publicador: IEEE; USA
Tipo: Conference paper
Publicado em //2011 EN
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Recent work combining population based heuristics and flexible models such as fuzzy rules, neural networks, and others, has led to novel and powerful approaches in many problem areas. This study tests an implementation of cellular evolution for fuzzy rule learning problems and compares the results with other related approaches. The paper also examines characteristics of the cellular evolutionary approach in generating more diverse solutions in a multiobjective specification of the learning task, and finds that solutions seem to have useful properties that could enable anticipating out of sample performance. We consider a bi-objective problem of learning fuzzy classifiers that balance accuracy and interpretability requirements.; http://cec2011.org/; Adam Ghandar, Zbigniew Michalewicz

The Ypt/Rab family and the evolution of trafficking in Fungi

Pereira-Leal, J.B.
Fonte: Wiley-Blackwell Publicador: Wiley-Blackwell
Tipo: Artigo de Revista Científica
Publicado em //2008 ENG
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The evolution of the eukaryotic endomembrane system and the transport pathways of their vesicular intermediates are poorly understood. A common set of organelles and pathways seems to be present in all free-living eukaryotes, but different branches of the tree of life have a variety of diverse, specialized organelles. Rab/Ypt proteins are small guanosine triphosphatases with tissue-specific and organelle-specific localization that emerged as markers for organelle diversity. Here, I characterize the Rab/Ypt family in the kingdom Fungi, a sister kingdom of Animals. I identify and annotate these proteins in 26 genomes representing near one billion years of evolution, multiple lifestyles and cellular types. Surprisingly, the minimal set of Rab/Ypt present in fungi is similar to, perhaps smaller than, the predicted eukaryotic ancestral set. This suggests that the saprophytic fungal lifestyle, multicellularity as well as the highly polarized secretion associated with hyphal growth did not require any major innovation in the molecular machinery that regulates protein trafficking. The Rab/Ypt and other protein traffic-related families are kept small, not paralleling increases in genome size, in contrast to the expansion of such components observed in other branches of the tree of life...

Impact of the Telecommunications Act of 1996 and spectrum allocation on cellular telephone technology

Glowacki, Jason P.
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
Tipo: Tese de Doutorado Formato: xiv, 83 p. : ill. ;
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Approved for public release; distribution in unlimited.; From 1983, when the first cellular network was established, to 1992, the wireless industry grew by ten million customers. From 1993 to 2000, the wireless industry grew by 90 million customers. Today, there are more than 149 million U.S. wireless subscribers. The phenomenal growth of the wireless industry can be traced to several factors. These factors are improvements in cellular technology, expansion of that technology and the allocation of spectrum by the federal government. This thesis analyzes the correlation between the Telecommunications Act of 1996 (the Act) and the rapid expansion of cellular technology that occurred after the Act became law. It also analyzes the impact of spectrum management and allocation on the evolution of cellular technology. To demonstrate how cellular technology has evolved over time, the history, standards, and generations of cellular technology will be reviewed. Research findings will be shown that validate the Act's impact on the expansion of cellular technology. Finally, the impact of spectrum management and allocation on the evolution of cellular technology in the United States, specifically in terms of implementation of third generation (3G) technology...

Plant MicroRNA Evolution and Mechanisms of Shape Change in Plants

Puzey, Joshua Robert
Fonte: Harvard University Publicador: Harvard University
Tipo: Thesis or Dissertation
EN_US
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Plant microRNAs have been shown to have important roles in regulating diverse processes ranging from reproductive development to stress response. In the first two chapters, I focus on miRNA diversity in Aquilegia studying both anciently evolved broadly conserved and rapidly evolving species specific miRNAs. In chapter one, I utilize Aquilegia's critical phylogenetic position between the well developed models Arabidopsis thaliana and Oryza sativa to study the evolution of ancient miRNAs across the angiosperms. In chapter two, I utilize smallRNA high-throughput sequencing to annotate Aquilegia specific miRNAs and, in the process, uncover the novel regulation of a floral homeotic gene by an Aquilegia-specific miRNA. In chapter three, I look at the tissue specific development of miRNA regulation in the bioenergetically relevant model organism Populus trichocarpa. High-throughput smallRNA sequencing from four diverse tissue sets including leaves, xylem, mechanically treated xylem, and pooled vegetative and reproductive tissues were analyzed, revealing a total of 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Expanding on my work with the petal identity pathway, I turned a broader analysis of Aquilegia petal spurs. Petal spurs are the distinguishing characteristic of Aquilegia and are argued to be a key innovation in the adaptive radiation of the genus. In the fourth chapter...

Cell evolution and Earth history: stasis and revolution

Cavalier-Smith, Thomas
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
EN
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360.27934%
This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (=Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this ‘chlorobacterial age’ of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic ‘age of cyanobacteria’ and, as the ozone layer grew, the rise of plankton; immensely later...

Carl Woese's vision of cellular evolution and the domains of life

Koonin, Eugene V
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
EN
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In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functionally distinct cellular systems are fundamentally different, with the information processing systems “crystallizing” earlier than operational systems. The advances of evolutionary genomics over the last decade vindicate major aspects of Woese’s vision. Despite the observations of pervasive horizontal gene transfer among bacteria and archaea, the ribosomal tree of life comes across as a central statistical trend in the “forest” of phylogenetic trees of individual genes, and hence, an appropriate scaffold for evolutionary reconstruction. The evolutionary stability of information processing systems, primarily translation, becomes ever more striking with the accumulation of comparative genomic data indicating that nearly allof the few universal genes encode translation system components. Woese’s view on the fundamental distinctions between the three domains of cellular life also withstand the test of comparative genomics...

Evolution: Life has Evolved to Evolve

Deem, Michael W.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 29/01/2014
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Jim Shapiro synthesizes a great many observations about the mechanisms of evolution to reach the remarkable conclusion that large-scale modification, exchange, and rearrangement of the genome are common and should be viewed as fundamental features of life. In other words, the genome should be viewed not as mostly read-only with a few rare mutations, but rather as a fully-fledged read-write library of genetic functions under continuous revision. Revision of the genome occurs during cellular replication, during multicellular development, and during evolution of a population of individuals. DNA formatting controls the timing and location of genetic rearrangements, gene expression, and genetic repair. Each of these events is under the control of precise cellular circuits. Shapiro reviews the toolbox of natural genetic engineering that provides the functionalities necessary for efficient long-term genome restructuring.; Comment: 3 pages

Unitarity in one dimensional nonlinear quantum cellular automata

Meyer, David A.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 15/05/1996
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Unitarity of the global evolution is an extremely stringent condition on finite state models in discrete spacetime. Quantum cellular automata, in particular, are tightly constrained. In previous work we proved a simple No-go Theorem which precludes nontrivial homogeneous evolution for linear quantum cellular automata. Here we carefully define general quantum cellular automata in order to investigate the possibility that there be nontrivial homogeneous unitary evolution when the local rule is nonlinear. Since the unitary global transition amplitudes are constructed from the product of local transition amplitudes, infinite lattices require different treatment than periodic ones. We prove Unitarity Theorems for both cases, expressing the equivalence in $1+1$ dimensions of global unitarity and certain sets of constraints on the local rule, and then show that these constraints can be solved to give a variety of multiparameter families of nonlinear quantum cellular automata. The Unitarity Theorems, together with a Surjectivity Theorem for the infinite case, also imply that unitarity is decidable for one dimensional cellular automata.; Comment: 32 pages, plain TeX, 3 PostScript figures included with epsf.tex (ignore the under/overfull \vbox error messages)

Flexible Time and the Evolution of One-Dimensional Cellular Automata

Redeker, Markus
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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Here I describe a view of the evolution of cellular automata that allows to operate on larger structures. Instead of calculating the next state of all cells in one step, the method here developed uses a time slice that can proceed at different places differently. This allows to "jump" over the evolution of known structures in a single step.; Comment: 13 pages, 1 figure. Corrected 2 typos of previous revision

Lempel-Ziv complexity analysis of one dimensional cellular automata

Estevez-Rams, E.; Serrano, R. Lora; Nunes, C. A. J.; Aragon-Fernandez, B.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 27/11/2015
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Cellular automata (CA) have long attracted attention as dynamical systems with local updating rules and yet can exhibit, for certain rules, complex, long space and time correlated patterns. This contrast with other rules which results in trivial patterns being homogeneous or periodic. In this article we approach CA from two related angles: we analyze the information transfer in the time evolution of CA driven sequences and; we revisit the sensibility of the initial configuration on sequence evolution. In order to do so, we borrow a recently reported information distance based on Kolmogorov algorithmic complexity. The normalized information distance has been used previously to find a hierarchical clustering of CA rules. What is different in our approach, is the temporal analysis of the sequence evolutions by correlating different calculated distances with entropy density. Entropy rate, is a length invariant measure of the amount of irreducible randomness in a dynamical process. In order to perform our analysis, we incorporate to the practical calculation of the entropy rate and the distance measure, the use of Lempel-Ziv complexity. Lempel-Ziv complexity carries a number of practical advantages while avoiding the uncomputable nature of Kolmogorov randomness. The reduction of entropy density during time evolution can be related to energy dissipation through Landauer principle. Related to the last fact...

On the decomposition of stochastic cellular automata

Bołt, Witold; Baetens, Jan M.; DeBaets, Bernard
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
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In this paper we present two interesting properties of stochastic cellular automata that can be helpful in analyzing the dynamical behavior of such automata. The first property allows for calculating cell-wise probability distributions over the state set of a stochastic cellular automaton, i.e. images that show the average state of each cell during the evolution of the stochastic cellular automaton. The second property shows that stochastic cellular automata are equivalent to so-called stochastic mixtures of deterministic cellular automata. Based on this property, any stochastic cellular automaton can be decomposed into a set of deterministic cellular automata, each of which contributes to the behavior of the stochastic cellular automaton.; Comment: Submitted to Journal of Computation Science, Special Issue on Cellular Automata Applications

Self-referencing cellular automata: A model of the evolution of information control in biological systems

Pavlic, Theodore P.; Adams, Alyssa M.; Davies, Paul C. W.; Walker, Sara Imari
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/05/2014
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Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial selection for function has recently become a powerful tool for understanding how evolution can innovate within its genetic rule space. However, conventional cellular automata lack the kind of state feedback that is surely present in natural evolving systems. Each new generation of a population leaves an indelible mark on its environment and thus affects the selective pressures that shape future generations of that population. To model this phenomenon, we have augmented traditional cellular automata with state-dependent feedback. Rather than generating automata executions from an initial condition and a static rule, we introduce mappings which generate iteration rules from the cellular automaton itself. We show that these new automata contain disconnected regions which locally act like conventional automata, thus encapsulating multiple functions into one structure. Consequently, we have provided a new model for processes like cell differentiation. Finally, by studying the size of these regions, we provide additional evidence that the dynamics of self-reference may be critical to understanding the evolution of natural language. In particular...

The Roles of Cellular Receptor Binding Avidity and Other Viral Phenotypes in the Antigenic Drift of Influenza

Yuan, Hsiang-Yu
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação
Publicado em //2013
Relevância na Pesquisa
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Despite high vaccination rates and effective adaptive immune responses from the part of infected individuals, influenza A viruses cause significant morbidity and mortality annually. This is due to influenza's rapid antigenic evolution, whereby continual mutations occurring in epitope regions of the virus's hemagglutinin protein result in the diminishment of long-term antibody recognition, in a process that has been termed `antigenic drift'. Although it is clear that antigenic drift enables previously infected individuals to become reinfected, the mechanism that is responsible for influenza's antigenic drift is still under debate. As recently as 2009, a new hypothesis of antigenic drift was put forward that argues that binding avidity changes in the viral hemagglutinin result in antigenic drift as a side effect. This hypothesis stands in contrast to the traditionally accepted hypothesis that mutations in epitope regions are positively selected for their ability to evade immune recognition. This thesis focuses on the use of epidemiological models and empirical data analysis to explore different hypotheses of antigenic drift.

In the first chapter, I am asking what effects on antigenic drift rate would be produced under the new hypothesis. I mathematically formulate the hypothesis that antigenic drift is simply a side effect of cellular receptor binding avidity changes that occur as the virus is transmitted between individuals of different immune status levels. I then use this formulation to explore how influenza's rate of antigenic drift depends on different epidemiological factors...

The Origin and Evolution of Viruses as Molecular Organisms

Claudiu I. Bandea
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
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363.38113%
Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for their origin from parasitic cellular species that fused with their host cells. By losing their membrane and cellular structure within the host cell, these new types of parasitic species gained full access to precursors for the synthesis of their specific molecules and to the host’s information processing machineries, such as translation, which created unique parasitic and evolutionary opportunities. To identify viruses during their intracellular stage of their life cycle, in which their specific molecules are free or dispersed within the host cell...