Phylogenetic

Molecular Phylogenetics An introduction to computational methods and tools for analyzing evolutionary relationships Karen Dowell Math 500 Fall 2008 Molecular Phylogenetics Karen Dowell 1 Abstract Molecular phylogenetics applies a combination of molecular and statistical techniques to infer evolutionary relationships among organisms or genes.This review paper provides a general introduction to phylogenetics and phylogenetic trees, describes some of the most common computational methods used to infer phylogenetic information from molecular data, and provides an overview of some of the many different online tools available for phylogenetic analysis. In addition, several phylogenetic case studies are summarized to illustrate how researchers in different biological disciplines are applying molecular phylogenetics in their work. Introduction to Molecular PhylogeneticsThe similarity of biological functions and molecular mechanisms in living organisms strongly suggests that species descended from a common ancestor. Molecular phylogenetics uses the structure and function of molecules and how they change over time to infer these evolutionary relationships. This branch of study emerged in the early 20th century but didn’t begin in earnest until the 1960s, with the advent of protein sequencing, PCR, electrophoresis, and other molecular biology techniques.Over the past 30 years, as computers have become more powerful and more generally accessible, and computer algorithms more sophisticated, researchers have been able to tackle the immensely complicated stochastic and probabilistic problems that define evolution at the molecular level more effectively. Within past decade, this field has been further reenergized and redefined as whole genome sequencing for complex organisms has become faster and less expensive. As mounds of genomic data becomes publically available, molecular phylogenetics is continuing to grow and find new applications. 4, 10, 17, 20, 22] The primary objective of molecular phylogenetic studies is to recover the order of evolutionary events and represent them in evolutionary trees that graphically depict relationships among species or genes over time. This is an extremely complex process, further complicated by the fact that there is no one right way to approach all phylogenetic problems. Phylogenetic data sets can consist of hundreds of different species, each of which may have varying mutation rates and patterns that influence evolutionary change.Consequently, there are numerous different evolutionary models and stochastic methods available. The optimal methods for a phylogenetic analysis depend on the nature of the study and data used. [5, 19, 20] Molecular Evolution: Beyond Darwin Evolution is a process by which the traits of a population change from one generation to another. In On the Origin of Species by Means of Natural Selection, Darwin proposed that, given overwhelming evidence from his extensive comparative analysis of living specimens and fossils, all living organisms descended from a common ancestor.The book’s only illustration (see Figure 1) is a tree-like structure that suggests how slow and successive modifications could lead to the extreme variations seen in species today. [11, 27] Molecular Phylogenetics Karen Dowell 2 Figure 1. Evolution Defined Graphically. The sole illustration in Darwin’s Origin of the Species uses a tree-like structure to describe evolution. This drawing shows ancestors at the limbs and branches of the tree, more recent ancestors at its twigs, and contemporary organisms at its buds. [34] Darwin’s theory of evolution is based on three underlying principles: ariation in traits exist among individuals within a population, these variations can be passed from one generation to the next via inheritance, and that some forms of inherited traits provide individuals a higher chance of survival and reproduction than others. [11] Although Darwin developed his theory of evolution without any knowledge of the molecular basis of life, it has since been determined that evolution is actually a molecular process based on genetic information, encoded in DNA, RNA, and proteins. At a molecular level, evolution is driven by the same types of mechanisms Darwin observed at the species level.One molecule undergoes diversification into many variations. One or more of those variants can be selected to be reproduced or amplified throughout a population over many generations. Such variations at the molecular level can be caused by mutations, such as deletions, insertions, inversions, or substitutions at the nucleotide level, which in turn affect protein structure and biological function. [11, 22] What is a Phylogeny? According to modern evolutionary theory, all organisms on earth have descended from a common ancestor, which means that any set of species, extant or extinct, is related.This relationship is called a phylogeny, and is represented by phyloge netic trees, which graphically represent the evolutionary history related to the species of interest (see Figure 2). Phylogenetics infers trees from observations about existing organisms using morphological, physiological, and molecular characteristics. Figure 2. Phylogeny of Mammalia. This phylogenetic tree shows the evolutionary relationships among six orders of Mammalian species (taxa). Taxa listed in grey are extinct. The â€Å"tree of life† represents a phylogeny of all organisms, living and extinct.Other, more specialized species and molecular phylogenies are used to support comparative studies, test biogeographic hypotheses, evaluate mode and timing of speciation, infer amino acid sequence of extinct proteins, track the evolution of diseases, and even provide evidence in criminal cases. [19] Molecular Phylogenetics Karen Dowell 3 Understanding Phylogenetic Trees Before exploring statistical and bioinformatic methods for estimating phylogenetic trees from molecular data , it’s important to have a basic familiarity of the terms and elements common to these types of trees. See Figure 3. ) Figure 3. Basic elements of a phylogenetic tree. Phylogenetic trees are composed of branches, also known as edges, that connect and terminate at nodes. Branches and nodes can be internal or external (terminal). The terminal nodes at the tips of trees represent operational taxonomic units (OTUs). OTUs correspond to the molecular sequences or taxa (species) from which the tree was inferred. Internal nodes represent the last common ancestor (LCA) to all nodes that arise from that point.Trees can be made of a single gene from many taxa (a species tree) or multi-gene families (gene trees). [1, 10] A tree is considered to be â€Å"rooted† if there is a particular node or outgroup (an external point of reference) from which all OTUs in the tree arises. The root is the oldest point in the tree and the common ancestor of all taxa in the analysis. In the absence of a known outgroup, the root can be placed in the middle of the tree or a rootless tree may be generated. Branches of a tree can be grouped together in different ways. (See Figure 4. ) Figure 4.Groups and associations of taxonomical units in trees. A monophyletic group consists of an internal LCA node and all OTUs arising from it. All members within the group are derived from a common ancestor and have inherited a set of unique common traits. A paraphyletic group excludes some of its descendents (for examples all mammals, except the marsupialia Molecular Phylogenetics Karen Dowell 4 taxa). And a polyphyletic group can be a collection of distantly related OTUs that are associated by a similar characteristic or phenotype, but are not directly descended from a common ancestor. 1, 17] Trees and Homology Evolution is shaped by homology, which refers to any similarity due to common ancestry. Similarly, phylogenetic trees are defined by homologous relationships. Paralogs are homologous s equences separated by a gene duplication event. Orthologs are homologous sequences separated by a speciation event (when one species diverges into two). Homologs can be either paralogs or orthologs. [1, 11, 22] Molecular phylogenetic trees are drawn so that branch length corresponds to amount of evolution (the percent difference in molecular sequences) between nodes. 1, 19] Figure 5. Understanding paralogs and orthologs. Paralogs are created by gene duplication events. (See Figure 5. ) Once a gene has been duplicated, all subsequent species in the phylogeny will inherit both copies of the gene, creating orthologs. Interestingly, evolutionary divergence of different species may result in many variations of a protein, all with similar structures and functions, but with very different amino acid sequences. Phylogenetic studies can trace the origin of such proteins to an ancestral protein family or gene. [1, 22] Figure 6. Mirror Phylogenies.Gene A and Gene A1 are paralogs, whereas all i nstances of Gene A are orthologs of each other in different Canid species. One way to ensure that paralogs and orthologs are appropriately referenced in a phylogenetic tree, and guard against misrepresentation due to missing or incomplete taxonomic information is to generate mirror phylogenies (see Figure 6) in which paralogs serve as each other’s outgroup. [1, 4, 19, 22] Estimating Molecular Phylogenetic Trees Molecular phylogenetic trees are generated from character datasets that provides evolutionary content and context.Character data may consist of biomolecular sequence alignments of DNA, RNA, or amino acids, molecular markers, such as single nucleotide polymorphisms (SNPs) or restriction fragment length polymorphisms (RFLPs), morphology data, or information on gene order and content. Evolution is modeled as a process that changes the state of a character, such as the type of nucleotide (AGTC) at a Molecular Phylogenetics Karen Dowell 5 specific location in a DNA sequence ; each character is a function that maps a set of taxa to distinct states. 1, 19] Note that most of the examples in this paper use DNA sequences as character data, but trees can be accurately estimated from many different types of molecular data. Figure 7. Evolution of a DNA Sequence Figure 7 illustrates how a molecular sequence might evolve over time as a result of multiple mutations that results small, but evolutionarily important changes in a nucleotide sequence. At the protein level, these changes may not initially affect protein structure or function, but over time, they may eventually shape a new purpose for a protein within divergent species. 10, 19, 22] OTUs can be used to build an unrooted phylogenetic tree that clearly depicts a path of evolutionary change. Steps in Phylogenetic Analysis Although the nature and scope of phylogenetic studies may vary significantly and require different datasets and computational methods, the basic steps in any phylogenetic analysis remain t he same: assemble and align a dataset, build (estimate) phylogenetic trees from sequences using computational methods and stochastic models, and statistically test and assess the estimated trees. 4, 19, 20] Assemble and Align Datasets The first step is to identify a protein or DNA sequence of interest and assemble a dataset consisting of other related sequences. For example, to explore relationships among different members of the Notch family of proteins, one might select DNA sequences for Notch1 through Notch4, in different species, such as human, dog, rat, and mouse, then perform a multiple sequence alignment to identify homologies. [1, 10, 13, 19, 20] There are a number of free, online tools available to simplify and streamline this process. DNA sequences of interest can be retrieved using NCBI BLAST or similar search tools.When evaluating a set of related sequences retrieved in a BLAST search, pay close attention to the score and E-value. A high score indicates the subject seque nce retrieved with closely related to the sequence used to initiate the query. The smaller the E-value, the higher the probability that the homology reflects a true evolutionary relationship, as opposed to sequence similarity due to chance. As a general rule, sequences with E-values less than 10-5 are homologs of a query sequence. [10] Once sequences are selected and retrieved, multiple sequence alignment is created.This involves arranging a set of sequences in a matrix to identify regions of homology. Typically, gaps (one or more spaces in the alignment) are introduced in one or more sequences to represent insertions or deletions in the molecular code that may have occurred over time. Effective multiple sequence alignment hinged on gap analysis—determining where to insert gaps and how large to make them. There are many websites and software programs, such as ClustalW, MSA, MAFFT, and T-Coffee, designed to perform multiple sequence on a given set of molecular data. ClustalW i s currently the most mature and most widely used. 1, 10. 19] Molecular Phylogenetics Karen Dowell 6 Building Phylogenetic Trees To build phylogenetic trees, statistical methods are applied to determine the tree topology and calculate the branch lengths that best describe the phylogenetic relationships of the aligned sequences in a dataset. Many different methods for building trees exist and no single method performs well for all types of trees and datasets. The most common computational methods applied include distance-matrix methods, and discrete data methods, such as maximum parsimony and maximum likelihood. 4, 17, 20] There are several software packages, such as Paup*, PAML, PHYLIP, that apply most popular methods. [4] Paup* is a commercially available program that implements a wide variety of methods for phylogenetic inference, including maximum likelihood analysis for DNA data using different models. Paup* also includes a set of exact and heuristic methods for searching optimal trees. PAML (Phylogenetic Analysis by Maximum Likelihood) is open-access set of programs for phylogenetic analysis and evolutionary model comparison.PAML includes many advanced models—DNA- and AAbased models as well as codon-based models that can be used to detect positive selection. Many of the programs in PAML can model heterogeneity of evolutionary rates among sequence sites using ? distributions, and evolutionary dynamics of different sequence regions (concatenated gene sequences). PHYLIP is another large suite of open-access programs for phylogenetic inference that estimates trees using numerous methods, including pairwise distance, maximum parsimony, and maximum likelihood.The maximum likelihood programs can handle a few simple stochastic models and have good tree searching capabilities. PHYLIP is generally considered good educational software for novice phylogeneticists. Distance-Matrix Methods Distance matrix methods compute a matrix of pairwise â€Å"distances† between sequences that approximate evolutionary distance. Distance-based methods tend to be in polynomial time and are quite fast in practice. These methods use clustering techniques to compute evolutionary distances, such as the number of nucleotide or amino acid substitutions between sequences, for all pairs of taxa.They then construct phylogenetic trees using algorithms based on functional relationships among distance values. There are several different distance-matrix methods, including the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA), which uses a sequential clustering algorithm; the Transformed Distance Method, which uses an outgroup as a reference, then applies UPGMA; the Neighbor-Relations Method, which applies 4point condition to adjust the distance matrix, then applies UPGMA; and the Neighbor-Joining Method, which arranges OTUs in a star, the finds neighbors sequentially to minimize total length of tree. 4, 17] The following section on the UPGMA method prov ides a more detailed example of how distance-matrix methods work. UPGMA Method UPGMA produces rooted trees for which the edge lengths can be viewed as times measured by a molecular clock with a constant rate. This method uses a sequential clustering algorithm to identify two OTUs that are most similar (meaning they have the shortest evolutionary distance and are most similar in sequence) and treat them as a single new composite OTU. This process is repeated iteratively until only two OTUs remain.The algorithm defines the distance (d) between two clusters Ci and Cj as the average distance between pairs of sequences from each cluster: Molecular Phylogenetics Karen Dowell 7 Where |Ci| and |Cj| are the number of sequences in clusters i and j. This sequential clustering process is visually described in Figure 8. In this example, the two most homologous sequences are 1 and 2. They are clustered into a new composite parent node (6), and the branch lengths (t1 and t2) are defined as 1/2d1,2 . The next step is to search for the closest pair among remaining sequences and node 6.Pair 4 and 5 are identified and clustered into a new parent node (7), and the branch length for t4 and t5 is calculated. [4, 17] Figure 8. Sequential clustering of sequences using the UPGMA method. [17] In this interactive process, parent node 8 is created from pairs 7 and 3, and parent node 9 is created by clustering nodes 6 and 8. [4, 17] Thus, all sequences are clustered into a single evolutionary tree. The total time (t9) can be calculated as: D6,8 = 1/6 (d1,3 + d1,4 + d1,5 + d2,3 + d2,4 +d2,5)Discrete Data Methods Discrete data methods examine each column of a multiple sequence alignment dataset separately and search for the tree that best represents all this information. Although distance-based methods tend to be much faster than discrete data methods, they typically yield little information beyond the basic tree structure. Discrete data analyses, on the other hand, are information rich. The se methods produce a separate tree for each column in the alignment, so it is possible to trace the evolution for specific elements within a given sequence, such as catalytic sites or regulatory regions. 10, 17, 19, 20) Commonly used discrete data methods include maximum parsimony, which searches for the most parsimonious tree that requires the least number of evolutionary changes to explain differences observed, maximum likelihood, which requires a probabilistic model for the process of nucleotide substitution, and Bayesian MCMC, which also requires a stochastic model of evolution, but creates a probability distribution on a set of trees or aspects of evolutionary history. [17, 19, 20] Discrete data methods are generally considered to produce the best estimates of evolutionary history.However, these methods can be computationally expensive, and it can take weeks or months to obtain a reasonable level of accuracy for moderate to large datasets with 100 or more OTUs. [19] Molecular P hylogenetics Maximum Parsimony Karen Dowell 8 Among the most widely used tree-estimation techniques, maximum parsimony applies a set of algorithms to search for the tree that requires the minimum number of evolutionary changes observed among the OTUs in the study. For example, Figure 9 lists four sample sequences from which phylogenetic trees could be inferred using maximum parsimony.Site Seq 1 2 3 4 1 A A A A 2 A G G G 3 G C A A 4 A C T G 5 G G A A 6 T T T T 7 G G C C 8 C C C C 9 A G A G Figure 9. Sample sequences for a maximum parsimony study [17] Maximum parsimony algorithms identify phylogenetically informative sites, meaning the site favors some trees over others. Consider the sequences in Figure 9: Site 1 is not informative, because all sequences at that site (in column 1) are A (Adenine), and no change in state is required to match any one sequence (1-4) to another.Similarly, Site 2 is not informative because all three trees require one change and there is no reason to favor one tree over another. Site 3 is not informative because all three trees require two changes. (See Figure 10). Figure 10. Site 3 trees all require one evolutionary change. [17] Site 4 is not informative because all three trees require three changes. No one tree can be identified as parsimonious. (See Figure 10 Figure 11. Site 4 trees all require three evolutionary changes. [17] Site 5 is informative because one tree requires only one nucleotide change, whereas the other two trees require 2 changes.In Figure 12, the first tree on the left, which requires only one nucleotide change, is identified as the maximum parsimony tree. Figure 12. Site 5 trees vary in the number of evolutionary changes required. [17] Molecular Phylogenetics Maximum Likelihood Karen Dowell 9 The maximum likelihood method requires a probabalistic model of evolution for estimating nucleotide substitution. This method evaluates competing hypotheses (trees and parameters) by selecting those with the highest likeliho od, meaning those that render the observed data most plausible. The ikelihood of a hypothesis is defined as the probability of the data given that hypothesis. In phylogeny reconstruction, the hypotheses are the evolutionary tree (its topology and branch lengths) and any other parameters of the evolutionary model. [17, 20] The likelihood calculations required for evolutionary trees are far from straightforward and usually require complex computations that must allow for all possible unobserved sequences at the LCA nodes of hypothesized trees. This method specifies the transition probability from one nucleotide state to another in a time interval in each branch.For example, for a one-parameter model with rate of substitution ? per site per unit time, the probability that the nucleotide at time t is i is: The probability that the nucleotide at time t is j is: To set up a likelihood function, given x as the ancestral node and y and z as internal nodes, the probability of observing nucle otides i, j, k, l at the tips of the tree is computed as: Pxl(t1+t2+t3)Pxy(t1)Pyk(t2+t3)Pyz(t2)Pzi(t3)Pzj(t3) For the ancestral node (root) x, the probability of having nucleotide l in sequence 4 is calculated as: Pxl(t1+t2+t3)Because x, y, and z can be any one of four nucleotides (ACGT), it is necessary to sum over all possibilities to obtain the probability of observing the configuration of nucleotides i, j, k, l, in sequences 1, 2, 3, 4, for a given hypothetical tree (see Figure 13. ). This likelihood probability is calculated as: h(I,j,k,l)= [? gxPxl(t1+t2+t3)] [? Pxy(t1)Pyk(t2+t3)] [? Pyz(t2)Pzi(t3) Pzj(t3)] The appropriate likelihood function depends on the hypothetical tree and the evolutionary model used. (See Figure 13. ) [17] Figure 13. Different types of model trees for the derivation of the maximum likelihood function. 17] Molecular Phylogenetics Stochastic Models of Evolution Karen Dowell 10 Evolutionary changes in molecular sequences result from mutations, some of whic h occur by chance, others by natural selection. Rates of change can also differ among OTUs, depending on several factors ranging from GC content to genome size. To accurately estimate phylogenetic trees, assumptions must be made about the substitution process and those assumptions must be stated in the form of a stochastic evolutionary model. These probabilistic models are used to rank trees according to likelihood: P(data|tree).From a Bayesian perspective, they rank trees according to a posterior probability: P(tree|data). [17, 20] The objective of probabilistic models is to find likelihood or posterior probability of a particular taxonomic feature, then define and compute: P(x? |T,t ? ) Where x ? is xj for j=1†¦n, T is a tree with n leaves with sequence j at leaf j, and t ? are tree edge lengths. [17] A few popular stochastic models of evolution include the single parameter Jukes-Cantor (JC) method, Kimura 2-parameter (K2P), Hasegawa-Kishino-Yano (HKY), and Equal-Input.Some s oftware programs, such as Paup*, will automatically use a default model for the tree estimation method chosen. The JC method is the easiest one to comprehend, because it assumes that if a site changes its state, it changes with equal probability to the other states. This is not very realistic, however, as some sites are known to evolve more rapidly than others, and some sites may be invariable and not allowed to change at all. Determining how best to select the appropriate model is a topic of another paper (or papers) as there is no one model that incorporates all mutation rules and patterns across different species and macromolecules. 4, 17, 20] Hidden Markov Models Profile hidden Markov models (HMMs) are a form of Bayesian network that provides statistical models of the consensus structure of a sequence family. Gary Churchill at The Jackson Lab was the first evolutionary geneticist to propose using profile HMMs to model rates of evolution. Many software packages and web services n ow apply HMMs to estimate phylogenetic relationships. [8] In the HMM format, each position in the model corresponds to a site in the sequence alignment. For each position, there are a number of possible states, each of which corresponds to a different rate of evolution.In addition, transitions between all possible rate-states at adjacent positions. Transition probabilities capture any tendency for patterns of rates to occur in successive sites. [2, 4] Assessing Trees Tree estimating algorithms generate one or more optimal trees. This set of possible trees is subjected to a series of statistical tests to evaluate whether one tree is better than another – and if the proposed phylogeny is reasonable. Common methods for assessing trees include the Bootstrap and Jackknife Resampling methods, and analytical methods, such as parsimony, distance, and likelihood.To illustrate how these methods are used, consider the steps involved in a bootstrap analysis. Bootstrap Analysis A bootstra p is a statistical method for assessing trees that takes its name from the fact that it can â€Å"pull itself up by its bootstraps† and generate meaningful statistical distributions from almost nothing. Using bootstrap analysis, distributions that would otherwise be difficult to calculate exactly are estimated by repeated creation and analysis of artificial datasets. In a Non-parametric bootstrap, artificial datasets Molecular Phylogenetics Karen Dowell 11 generated by resampling from original data.In a parametric bootstrap, data is simulated according to hypothesis tested. The objective of any bootstrap analysis is to test whether the whole dataset supports the tree. [1, 4, 17] Figure 14 illustrates the basic steps in any bootstrap analysis. Sample datasets are automatically generated from an original dataset. Trees are then estimated from each sample dataset. The results are compiled and compared to determine a bootstrap consensus tree. Figure 14. Steps in a phylogenetic tr ee bootstrap analysis. [1] Phylogenetic Analysis Tools There are several good online tools and databases that can be used for phylogenetic analysis.These include PANTHER, P-Pod, PFam, TreeFam, and the PhyloFacts structural phylogenomic encyclopedia. Each of these databases uses different algorithms and draws on different sources for sequence information, and therefore the trees estimated by PANTHER, for example, may differ significantly from those generated by P-Pod or PFam. As with all bioinformatics tools of this type, it is important to test different methods, compare the results, then determine which database works best (according to consensus results, not researcher bias) for studies involving different types of datasets.In addition, to the phylogenetic programs already mentioned in this paper, a comprehensive list of more than 350 software packages, web-services, and other resources can be found here: http://evolution. genetics. washington. edu/phylip/software. html. PANTHER ( pantherdb. org) Protein ANalysis Through Evolutionary Relationships, known by its acronym PANTHER, is a library of protein families and subfamilies indexed by function. Panther version 6. 1 contains 5547 protein families. Molecular Phylogenetics Karen Dowell 12It categorizes proteins by evolutionary related proteins (families) and related proteins with same function (subfamilies). [8, 21, 26] PANTHER is composed of both a library and index. The library is a collection of â€Å"books† that represent a protein family as a collection of multiple sequence alignments, HMMs, and a family phylogenetic tree. Functional divergence within the tree is represented by dividing the parent tree into child trees and HMMs based on shared functions. These subfamilies enable database curators to more accurately capture functional divergence of protein sequences as inferred from genomic DNA. 25, 26] PANTHER database entries are annotated to molecular function, biological process and pathway with a proprietary PANTHER/X ontology system, which is supposed to be easier to understand than the more global standard Gene Ontology (GO). Database entries in PANTHER are generated through clustering of UniProt database using a BLAST-based similarity score. Trees are automatically generated based on multiple sequence alignments and parameters of the protein family HMMs using the Tree Inferred from Profile Score (TIPS) clustering algorithm.Scientific curators review all family trees, annotate each tree, and determine how best to divide them into subtrees using a tree-attribute viewer that tabulates annotations for sequences in a tree. In addition, trees and subfamilies are manually cross-checked and validated by curators. [25, 26] P-POD (ortholog. princeton. edu) The Princeton Protein Orthology Database (P-POD) combines results from multiple comparative methods with curated information culled from the literature.Designed to be a resource for experimental biologists seeking evolutionary information on genes on interest, P-POD employs a modular architecture, based on their Generic Model Organism Database (GMOD). P-POD can be accessed from their web service or downloaded to run on local computer systems. [12] P-POD accepts FASTA-formatted protein sequences as input, and performs comparative genomic analyses on those sequences using OrthoMCL and Jaccard clustering methods. The P-POD database contains both phylogenetic information and manually curated experimental results.The site also provides many links to sites rich in human disease and gene information. This tool may be particularly helpful for bioinformaticists and statisticians developing comparative genomic database tools and resources. Pfam (pfam. sanger. ac. uk/) PFam is a collection of protein families represented by multiple sequence alignments and HMMs. It contains models of protein clans, families, domains, and motifs, and uses HMMs representing conserved functional and structural domains. It is a large, widely used, actively curated mature database that has been available online since 1995.Pfam can be used to retrieve the domain architectures for a specific protein by conducting a search using a protein sequence against the Pfam library of HMMs. This database is also helpful for proteomes and protein domain architecture analysis. [6, 8, 24] There are two versions of the Pfam database: Pfam–B is generated automatically from ProDom, using PsiBLAST, an open access bioinformatics tool available through NCBI for identifying weak, but biologically relevant sequence similarities. Pfam-A is hand-curated from custom multiple sequence alignments. Pfam protein domain families are clustered with Mkdom2, and aligned with ProDomAlign.ProDom is a comprehensive set of protein domain families automatically generated from the SWISSPROT and TrEMBL sequence databases. Mkdom2 is a ProDom program used to make ProDom family clusters. Protein domain families in ProDom were aligned using an improved parallelized program called Molecular Phylogenetics Karen Dowell 13 ProDomAlign, developed in C++ using OpenMP. ProDomAlign is based on MultAlign, a program well suited for aligning very large sequence families with thousands of associated sequences. As of early 2008, Pfam matched 72 percent of known proteins sequences, and 95 percent of proteins for which there is a known structure.Within the Pfam database, 75 percent of sequences will have one match to Pfam-A, 19 percent to Pfam-B. There are also two versions of Pfam-A and Pfam-B. Pfam-ls handles global alignments, and Pfam-fs is optimized for local alignments. Interestingly, Pfam entries can be classified as â€Å"unknown,† but that doesn’t mean the protein is undocumented. Unknown entries can be proteins for which some information is known, but it has not been fully researched or cannot be adequately annotated. For example, Pfam entry PFO1816 is a LeucineRich Repeat Variant (LRV), which has a known structure (1LRV ) available in the Protein Databank (pdb. rg). LRV repeat regions, which are found in many different proteins, are often involved in cell adhesion, DNA repair, and hormone reception—but identification of an LRV within a sequence encoding a protein doesn’t specifically reveal the protein’s function. For studies involving a large number of protein searches, it may be more convenient to run Pfam locally on a client machine. The standalone Pfam system requires the HMMER2 software, the Pfam HMM libraries and a couple of additional files from the Pfam website to be installed on the client machine. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. ) Once the initial search is complete, researchers can go to the Pfam website to further analyze select number of sequences using additional features on website. [6, 8, 24] TreeFam (TreeFam. org) TreeFam is a curated database of phylogenetic trees and orthology predictions f or all animal gene families that focuses on gene sets from animals with completely sequenced genomes. Orthologs and paralogs are inferred from phylogenetic tree of gene family.Release 4 contains curated trees for 1314 families and automatically generated trees for another 14351 families. [16, 23] Like Pfam, TreeFam is a two-part database: TreeFam-B contains automatically generated trees, and TreeFam-A consists of manually curated trees. To automatically generate trees, an algorithm selects clusters of genes to create TreeFam-B â€Å"seeds† from core species with high-quality reference genome sequences, first using BLAST to rapidly assemble an initial list of possible matches, then HMMER to expand and filter probable sequence matches for each TreeFam B seed family.The filtered alignment is fed into a neighbor-joining algorithm and a tree is constructed based on amino acid mismatch distances. For TreeFam version 4, the most current release, five â€Å"clean† family trees were built for each TreeFam B seed, two using a maximum likelihood tree generated using PHYML (one based on the protein alignment, the other on codon alignment), three using a neighbor joining tree, using different distance measurements based on codon alignments. 16, 23] Scientific curators then manually any correct errors (based on information in the literature) in automatically generated TreeFam-B trees. Curated TreeFam-B trees then become seeds for TreeFam-A trees. Clean TreeFam-A trees are build using three merging algorithms and bootstrapping to find the consensus tree of seven trees: two constrained maximum likelihood trees based on protein and codon alignment, and five unconstrained neighbor-joining trees generated using different distance measurements based on codon alignments.For both TreeFam-B and TreeFam-A families, orthologs and paralogs are inferred only from clean trees using Duplication/Loss Inference (DLI) algorithm that requires a species tree (NCBI taxonomy tree). [16, 23] Molecular Phylogenetics PhyloFacts (phylogenomics. berkeley. edu/phylofacts) Karen Dowell 14 PhyloFacts is an online phylogenomic encyclopedia for protein functional and structural classification. It contains more than 57,000 â€Å"books† for protein superfamilies and structural domains.Each book contains heterogenous data for protein families, including multiple sequence alignments, one or more phylogenetic trees, predicted 3-D protein structures, predicted functional subfamilies, taxonomic distributions, GO annotations, and PFAM domains. HMMs constructed for each family and subfamily permit novel sequences to be classified to different functional classes. [14] Unlike other databases mentioned in this paper, PhyloFacts seeks to correct and clarify annotation errors associated with computational methods for predicting protein function based on sequence homology.It uses a consensus approach that integrates many different prediction methods and sources of experimental data over an evolutionary tree. By applying evolutionary and structural clustering of proteins, PhyloFacts is able to analyze disparate datasets using multiple methods, identify potential errors in database annotations, and provide a mechanism for improving the accuracy of functional annotation in general. [14] PhyloFacts can be used to search for protein structure prediction or functional classification for a particular protein sequence.Researchers may also browse through protein family books and multiple sequence alignments, phylogenetic trees, HMMs and other pertinent information for proteins of interest. This webservice also provides many links to literature and other information sources. [14] Applied Molecular Phylogenetics Molecular phylogenetic studies have many diverse applications. As the amount of publically available molecular sequence data grows and methods for modeling evolution become more sophisticated and accessible, more and more biologists are incorporating phylog enetic analyses into their research trategy. Here’s a sampling of how molecular phylogenetics might be applied. Tracing the evolution of man In one case study, molecular phylogenetic techniques were used to compare and analyze variation in DNA sequences using modern human and Neanderthal mitochondrial DNA (mtDNA). For this study, 206 modern human mtDNAs and parts of two Neanderthal mtDNAs sequences derived from skeletal remains were used to generate an initial dataset. Genetic distance was first estimated using the Jukes-Cantor single parameter model.Then the Kimura 2-Parameter model was used to distinguish between transition (replacement of one purine with another purine or one pyrimidine with another pyrimidine) and transversion (replacement of one purine with a pyrimidine or vice versa) probabilities with Kimura 2parameter model. A phylogenetic tree representing primate evolution was generated using pairwise genetic distances between primate Hypervariable regions I and II of mtDNA. [3] Chasing an epidemic: SARS Using publically available genomic data, it is possible to reconstruct the progression of the SARS epidemic over time and geographically.To conduct this phylogenetic analysis, researchers used the neighborjoining method to construct a phylogenetic tree of spike proteins in various coronaviruses and identify the viral host (a Himalyan palm civet). They then obtained 13 SARs genome sequences with documented information on the date and location of the sample. The neighbor-joining method and a distance matrix based on Jukes-Cantor model, were used to generate an epidemic tree, from which it was possible to identify the origin (date and location) of the virus by observing progression of mutations over time. 3] Molecular Phylogenetics Barking up the right tree Karen Dowell 15 Phylogenetics is increasingly incorporated into biological and biomedical research papers. When the canine genome was published, researchers used sequence data to estimate a co mprehensive phylogeny of the canid family. Figure 15. Phylogenetic Tree of the Canid family This canid family phylogenetic tree is based on 15 kb of exon and intron sequence. It was constructed using the maximum parsimony method and represents the single most parsimonious tree.A good example of how phylogenies are referenced in the literature, this tree includes bootstrap values and Bayesian posterior probability values listed above and below internodes, respectively. Dashes indicate bootstrap values below 50%. In addition, divergence time in millions of years (Myr) is indicated for three nodes. [18] Seeing the Forest from the Trees Molecular phylogenetics is a broad, diverse field with many applications, supported by multiple computational and statistical methods. The sheer volumes of genomic data currently available (and rapidly growing) render molecular phylogenetics a key component of much biological research.Genome-scale studies on gene content, conserved gene order, gene expre ssion, regulatory networks, metabolic pathways, functional genome annotation can all be enriched by evolutionary studies based on phylogenetic statistical analyses. [19, 25 27] Molecular phylogenies have fast become an integral part of biological research, pharmaceutical drug design, and bioinformatics techniques for protein structure prediction and multiple sequence alignment. Although not all molecular biologists and bioinformaticians may be familiar with the techniques describedMolecular Phylogenetics Karen Dowell 16 in this paper, this is a rapidly growing and expanding field and there is ongoing need for novel algorithms to solve complex phylogeny reconstruction problems. References 1. Baldauf, SL (2003) â€Å"Phylogeny for the faint of heart: a tutorial. † Trends in Genetics, 19(6):345-351. 2. Brown, D, K Sjolander (2006) â€Å"Functional Classification Using Phylogenomic Inference. † PLos Computational Biology, 2(6):0479-0483. 3. Cristianini, N, and M Hahn (2007 ) Introduction to Computational Genomics: A Case Studies Approach.Cambridge University Press: Cambridge. 4. Durbin, R, S Eddy, A Krogh, G Mitchison (1998) Biological Sequence Analysis. Cambridge University Press: Cambridge. 5. Ewens, WJ, R Grant (2005) Statistical Methods in Bioinformatics. Springer Science and Business Media: New York. 6. Finn, RD, J Tate, J Mistry, PC Coggill, SJ Sammut, HR Hotz, G Ceric, K Forslund, SR Eddy, ELL Sonnhammer, A Bateman (2008) â€Å"The Pfam protein families database. † Nucleic Acids Research, 36:D281288. 7. Gabaldon, T (2008) â€Å"Large-scale assignment of orthology: back to phylogenetics? Genome Biology, 9:235. 1-235. 6. 8. Gollery, M. (2008) Handbook of Hidden Markov Models in Bioinformatics. CRC Press, Taylor & Francis Group: London. 9. Goodstadt, L, CP Ponting (2006) â€Å"Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human. † PLoS Computational Biology, 2(9):1134-1150. 10. Hall, BG. (2004 ) Phylogenetic Trees Made Easy: A How-To Manual, 2nd ed. Sinauer Associates, Inc. : Sunderland, MA. 11. Hartwell, LH, L Hood, ML Goldberg, AE Reynolds, LM Silver, RC Veres (2008) Genetics: From Genes to Genomes, 3rd Ed.McGraw-Hill: New York. 12. Heinicke, S, MS Livstone, C Lu, R Oughtred, F Kang, SV Angiuoli, O White, D Botstein, K Dolinski (2007) â€Å"The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists. † PLoS ONE, 8:e766. 1-15. 13. Kortschak, RD, R Tamme (2001) â€Å"Evolutionary analysis of vertebrate Notch genes. † Dev Genes Evol, 211:350-354. 14. Krishnamurthy, N, DP Brown, D Kirshner, K Sjolander (2006) â€Å"PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. † Genome Biology, 7:R83. -13. 15. Kuzniar, A, RCHJ van Ham, S Pongor, JAM Leunissen (2008) â€Å"The quest for orthologs: finding the corresponding gene across genomes. † Trends in G enetics, 24(11):539-551. Molecular Phylogenetics Karen Dowell 17 16. Li, H, A Coghlan, J Ruan, LJ Coin, JK Heriche, L Osmotherly, R Li, T Liu, Z Zhang, L Bolund, GKS Wong, W Zheng, P Dehal, J Wang, R Durbin (2006) â€Å"TreeFam: a curated database of phylgenetic trees of animal gene families. † Nucleic Acids Research, 34:D573-580. 17. Li, WH (1997) Molecular Evolution. Sinauer Associates: Sunderland, MA. 18.Lindblad-Toh, K, CM Wade, TS Mikkelsen, EK Karlsson, DB Jaffe, M Kamal, M Clamp, JL Chang, EJ Kulbokas III, MC Zody, E Mauceli, X Xie, M Breen, RK Wayne, EA Ostrander, CP Ponting, F Galibert, DR Smith, PJ deJong, E Kirkness, P Alvarez, T Biagi, W Brockman, J Butler, C Chin, A Cook, J Cuff, MJ Daly, D DeCaprio, S Gnerre, M Grabherr, M Kellis, M Kleber, C Bardeleben, L Goodstadt, A Heger, C Hitte, L Kim, KP Koepfli, HG Parker, JP Pollinger, SMJ Searle, NB Sutter, R Thomas, C Webber, ES Lander (2005) â€Å"Genome Sequence, Comparative Analysis and Haplotype Structure of the Domestic Dog.Nature, 438:803-819. 19. Linder, CR, T Warnow (2005) â€Å"An overview of phylogeny reconstruction. † In the Handbook of Computational Molecular Biology, Chapman and Hall/CRC Computer & Information Science. 20. Lio, P, N Goldman (1998) â€Å"Models of Molecular Evolution and Phylogeny. † Genome Research, 8:12331244. 21. Mi, H, N Guo, A Kejariwal, PD Thomas (2007) â€Å"PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Research, 35:D247-252. 22. Patthy, Laszlo. (1999) Protein Evolution. Blackwell Science, Ltd: Malden, MA. 23. Ruan, J, H Li Z Chen, A Coghlan, LJM Coin, Y Guo, JK Heriche, Y Hu, K Kristiansen, R Li, T Liu, A Mose, J Qin, S Vang, AJ Vilella, A Ureta-Vidal, L Bolund, J Wang, R Durbin (2008) â€Å"TreeFam: 2008 Update. † Nucleic Acids Research, 36:D735-740. 24. Sammut, SJ, RD Finn, A Bateman (2008) â€Å"Pfam 10 years on: 10000 families and still growing. â €  Briefings in Bioinformatics, 9(3):210-219. 5. Thomas, PD, A Kejariwal, N Guo, H Mi, MJ Campbell, A Muruganujan, B Lazareva-Ulitsky (2006) â€Å"Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. † Nucleic Acids Research, 34:W645-650. 26. Thomas, PD, MJ Campbell, A Kejariwal, H Mi, B Karlak, R Daverman, K Diemer, A Muruganujan, A Narechania. â€Å"PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. † Genome Research, 13:2129-2141. 27.Warnow, T (2004) â€Å"Computational Methods in Phylogenetics† Computational Systems Biology Conference, Stanford, CA 28. Whelan, S, P Lio, N Goldman (2001) â€Å"Molecular phylogenetics: state of the art methods for looking into the past. † Trends in Genetics, 17(5):262-272. Molecular Phylogenetics Karen Dowell 18 Appendix Website Resources Phylogeny Programs. A University of Washington site formerly supported by the National Science Foundation. http://www. evolution. genetics. washington. edu/phylip/software. tml TreeFam Tree Families Database. http://wwww. treefam. org Protein Analysis Through Evolutionary Relationships (PANTHER) Classification System. http://www. pantherdb. org. 29. Pfam Database of Protein Families. http://pfam. sanger. ac. uk 30. Princeton Protein Orthology Database (P-POD). http://ppod. princeton. edu 31. Wikipedia. http://en. wikipedia. org/wiki/Tree_of_life(science) Cover Page The cover image is from a phylogeny of canid species that appeared in Lindblad-Toh et al, 2005. [18]

Economic exploitation in America Essay

As a historian, James Blaut became so popular because of his criticism with the idea of Eurocentrism. From the word itself, Eurocentrism promotes the idea that European civilizations are superior to others and they have a lot of advantages compared to other civilization in Asia and Africa. In his book entitled 1492: The Debate on Colonialism, Eurocentrism, and History, Blaut argued with some of the famous philosopher and authors who are known for their Eurocentric ideas. Blaut tried to weaken their arguments and show to this modern world that our idea that Europeans have superior culture is only a delusion. Why 1492? According to the author, that year is the start of cultural evolution in Europe that brought them so much success in terms of dominating the world. According to Blaut, Europe is not ahead of Asia and Africa in terms of development and even the precondition of development. Europe just take advantage of the situation which is opposite to the beliefs of the proponents of Eurocentric idea that it has something to do with their superior culture. The year just inaugurated a set of historical process the helped the Europeans to develop their economy. One good example is their triumph over feudalism which was later on replaced by capitalism. We can say that Blaut was able to give good arguments and strong evidences that disprove the arguments presented by famous Eurocentric author such as Karl Marx and strengthen his theory that Europe’s exploitation of America paves their way to world domination. His arguments are the following: (page 2) 1. â€Å"Europeans had no advantage over Africa and Asia prior to 1492. Indeed, we cannot say that European culture is superior to those of Africa and Asia for the later two regions has their own economic and cultural advantages. † As oppose to the idea of Eurocentric theory which says that their weak culture resulted to their weak civilization, African and Asian civilization has their own cultural strengths that helped their economy to flourish. 2. â€Å"Colonialism is inevitable, it will happen even if there is no capitalism in Europe. † It is oppose the Eurocentric idea that the success of capitalism in Europe is the reason for their colonial expansion in different parts of the world. It is a very Eurocentric idea because it implies that colonialism starts in Europe as capitalism birthed in that region. Blaut argues that even if capitalism didn’t develop in Europe, powerful countries will still colonize other regions of the world. The birth of colonialism is a destiny for human civilization and an inevitable product of the natural characteristic of human society. 3. â€Å"Economic exploitation in America in 16th and 17th century was vastly intensive. † It is the main reason and explanation why Europe dominates the world not the rise of capitalism in Europe. Thus, the transformation of European society is just a mere product of major historical events and Europe just grabbed the opportunity. It contrasts the Eurocentric idea that the superiority of European culture and the weakness of others is the cause of their cultural transformation. 4. â€Å"There was no transition from feudalism to capitalism, rather a sharp break, a historical unconformity between medieval Europe and the Europe of bourgeoisie revolution. † Blaut disprove the belief that Europe experienced a social transformation which they triumph over the medieval feudalism. The idea of this social transformation implies that Europe of capable of transforming its society which can be attributed to their cultural superiority. Blaut theory vs. Eurocentric diffusionism For a long time, Eurocentric diffusionism is the dominant belief of the Europeans as well as other historians. It implies that the diffusion of Europe’s superior culture has brought progress throughout the world and caused worldwide social revolution. Eurocentric diffusionism believes that there is no need to look at other cultures which are lesser than those of the Europeans. Instead, historian believes in tunnel history as a source of historical reasoning. â€Å"Historical reasoning thus looks back the tunnel of time for causes of important changes in their history†. ( Blaut, p. 8). Because they see themselves as superior, they use their own history to interpret their society and disregard the contribution of the lesser civilization. The only exemption to this kind of social reasoning is when those lesser civilization caused so much decivilizing change such as barbarian invasion, plagues, and heresies. This reflects how the Europeans see the outside world. The significance of the outside culture is based on their effect on the ethnocentric Europeans. Another doctrine which is part of Eurocentric diffusinism is the outward diffusion of European intellect and spirituality that brought social evolution to the outside world of Europe. Actually, we cannot separate European intellect from spirituality for European intellect was shaped by Christian faith. As written by Blaut: â€Å"Two centuries ago it was axiomatic that God and his church were the fountainhead of progress. A Christian God ofcourse will put ideas in the heads of Christians particularly those Christians who worship him the right way and he will lead his people toward civilization. Gradually this explicit doctrine became implicit and Christians Europeans were themselves seen as the source of innovative ideas and hence evolutionary change for reasons not usually grounded in faith. †

Attitude, Legislation, and Litigation on Special Education Essay

Attitude, Legislation, and Litigation on Special Education - Essay Example The thrust of the special education movement has been to give students with disabilities access to a general education, remove the stigma of being labeled, and create methods to monitor and measure the success of these programs. The 1975 act was originally known as the Education for the Handicapped Act (EHA) and was designed to give students with disabilities a free education in the least restrictive environment possible (Special education laws, 2005). Subsequent amendments have been aimed at broadening the definition of disabled to include visual impairment and making provisions for including these students in regular classes when possible. Physical and mental challenges have historically been stigmatized and labeling has often been used as a detrimental tool to exclude students from normal activities. The 1975 Act was passed to reduce these social consequences and provide a system that was more fair in its treatment of the disabled. Prior to any legislation regarding special education, disabilities were generally viewed as a negative and the students were often shunted to areas outside the mainstream school system. One of the issues that have framed the special education debate in the last 30 years is the move towards inclusion. ... "outright denial of disability in some cases, illustrated by the contention that disability exists only in attitudes" (Kauffman, McGee, & Brigham, 2004, p.615). This has had the counter-productive effect of making a disability seem as something that does not matter. While this has had the positive effect of making regular classrooms more accessible to students, it has also minimized the challenge that faces these students. In many cases the past 30 years have seen attitudes change from discriminatory to indifference. The long-term outlook for special education in its current form could produce results that are the opposite of what it hopes to accomplish. Pratts (2000) states that " race and social class are being related to levels of academic achievement". This is only logical as we see poverty and family history placing many students at a disadvantage. This impacts the makeup of special education classes because "academic achievement is a strong predictor of referral and eventual placement in special education" (Hosp & Reschly, 2004, p.187). This has the potential to place a disproportionate number of students into special education based on socio-economic class. If the current movement of inclusion creates an environment of indifference, these students may become isolated and neglected. Public awareness of the realities of being disabled needs to be continually addressed. Without creating a proper public attitude towards special education, we may create a system that is less restrictive and mor e fair, but we also may cultivate an atmosphere of injustice. Feelings of awkwardness have often been a part of my own personal reaction to students with disabilities. In the past I was uncomfortable confronting their disabilities due to my confusion about whether or not they

Ballard Part 2 Research Paper Example | Topics and Well Written Essays - 750 words

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Surveillance and intelligence Term Paper Example | Topics and Well Written Essays - 1000 words

Surveillance and intelligence - Term Paper Example Festinger in his analysis of the cognitive dissonance theory gave the analogy of a fearful person, who could not find commensurate cause for his fear. The person’s knowledge that he is fearful is incompatible with his knowledge that there is nothing to fear. (Wicklund and Brehm1). Cognition or elements of knowledge refer to knowledge one has concerning the environment or himself (Wicklund and Brehm 3). Critical thinkers need to understand the cognitive dissonance and how it impacts on our response to domestic and international developments. According to Festinger, it is this uncertainty in knowledge that culminates in a psychological state known as cognitive dissonance. Cognition also varies in extent to which it has resistance to knowledge. For example, a person’s knowledge of the greenness of grass is immensely resistant to change; a person with normal vision would find it difficult to visualize grass as being any other color than green. Generally, there are two disti nct sources of resistance to change. The first source of resistance to change is difficulty in altering events cognized. What is commonly referred to as facts, for example, the grass is green, those worldly aspects that give us firm and clear cognitions. On the other hand, highly ambiguous events, for example, what will be the quality of life on earth a century from now?, is not clear. The second source of resistance to change is the clarity of reality presented by cognition. Cognitions concerning historical events are immensely resistant to change. On the other hand, contemporaneous events and cognitions related to them are easier to change. For example, if one finds that the air conditioner is too noisy, he or she can simply decide to turn it off. The original statement of Festinger’s cognitive dissonance theory thus notably proposed resistance to change of cognitions and proportion of cognitions that are dissonant. Inclusion of the latter proposition distinguishes cognitiv e dissonance theory from other theories of cognitive balance, and makes it a fertile source of research. Cognitive dissonance theory however overlooks some aspects that characterize it from other theories of cognitive balance (Wicklund and Brehm 3). 2. Go into either â€Å"Factcheck.org† or â€Å"Politifact.com† and checkout one of the â€Å"Pants on fire† presentations. Write a short note why the original claim cannot be substantiated (30 points). The United States of America Congress financial services committee chairman in a house of congress floor speech commented that â€Å"members of Congress†¦Ã¢â‚¬ ¦are going to be the only people in America to get subsidies in the Obamacare exchanges† (â€Å"GOP rep. Jeb Hensarling Assails,† politifact.com). Obama and his allies created a system in which most Americans who have insurance remain on their existing health insurance plans. The marketplaces were created for Americans who lacked insurance en tirely. Subsidies in Obamacare were rolled out in October 1st, 2013; the same day the shutdown began. Any American with a specified income range and who purchases insurance on the Obamacare market place will be eligible for subsidies in the form of tax credits. Staffers and legislators do not qualify for the stipulated subsidies or tax credits, since their income is very high. Instead they qualify for employer-cost sharing; that is, employer sponsored health insurance plans that long preceded the Obama care health system. Obamacare is

Legal Regulation Essay Example | Topics and Well Written Essays - 1250 words

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BUSINESS ANALYTICS METHOD AND SOFTWARE Coursework

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Development in the Hardware and Software Industries Tapped by GIS Appl Assignment

Development in the Hardware and Software Industries Tapped by GIS Applications - Assignment Example Hardware and software industries have catered to the needs of various areas defined in the marketplace. Software that is used to integrate geographical information with people and events, help in producing knowledge useful in the industrial operations and a basis of research outcomes. Examples are the GIS software and hardware used for libraries, museums, and schools that facilitate management, demographic/market analysis, asset mapping and inventories (Educational License Options n.d.).   Specific applications include ArcGIS for Desktop, Explorer, Mapping, Server, Server Image Extension and many others. In the case of Botanical Gardens and Zoological Parks, a software was developed specifically designed as a data model for mapping facilities and plant collections. It is called ArcGIS Public Garden Data Model. The hardware developments kept up with the industry standard or what was required for efficient data capture of GIS components. The digitizing tablets allowed the operator to record coordinates and scanners which convert analog source documents into digital raster form (Jackson and Woodsword 2012). GIS has been integrated into social networking. Ushahidi, for example, is a software that is used to collect information from multiple channels such as text messages, email, and Twitter (Dumbill 2010). It has been found useful in reporting disasters such as floods and aggregating reports from citizen journalists. The trend analysis provided by GIS in a combination of social data resulted in quick and effective disaster management. It has used information from social networking as sensors of the pending disaster, enabling the authorities to respond accordingly.

Australia Essay Example | Topics and Well Written Essays - 1250 words

Australia - Essay Example They were thought to have arrived here from the South East Asia during the last ice age. The belief is that the aboriginals numbered at least one million and scatter across 300 clans with at least 250 languages and 700 dialects between them. Due to the relatively dry environment of the country, the aboriginals were forced to become nomadic tribes traveling on a quest of trade, finding water, and food. Australia was founded in unforgiving territory. Stemming from the outback desserts, tropical rain forests, and snow capped mountains, the early aboriginals believe in the myth that the totemic spirits ancestors are all connected to nature, the past, present, and future (â€Å"Australias History†). This was the state of Australia before the British colonized the land for their own means. It was Captain James Cook who in the 17th century chartered the east coast in the name of Britain. When he first landed on Australian soil, the continent was recognized by most sailors as New Holland. Britain was more than happy to claim the land because its location made it perfect to use as a penal colony. As a new outpost, the penal colony came into being on January 26 1788 with the first British inhabitants alighting in Australia. A fleet of 11 ships carried 1.500 people with more than half of them being convicts. By 1868 it is believed that at least 160,000 men and women had settled in Australia as convicts being punished or banished by Britain. Of course life was different for the free settlers who came in during the 1790s. The convicts were constant under threat of losing their lives in the harsh conditions and even harsher treatment from the officers of the colony. Suffering alongside the convicts were the aboriginals who were displaced, their lands, stolen, and their tradit ional lifestyle and practices no longer fitting into the new world of Australia as

Hitler and the Munich Beer Hall Putsch (1923) Term Paper

Hitler and the Munich Beer Hall Putsch (1923) - Term Paper Example After the failed attempt of Munich Beer Hall Putsch, Hitler was sentenced to fie years in prison while being convicted of treason. During the following one year, he dictated his autobiography. Called â€Å" Mein Kampf†, based on his political career. While he did not spend more than one year in prison, the event made him a national hero, as he pursued the fresh attempts to rebuild the Nazi party within the given legal framework. After the heavy loss in World War I and very unfavorable terms of Versailles treaty, the nation had been facing many economic hurdles. The years following this witnessed national instability with veterans and rebellious youths swelling the membership of both the right and left wing parties with the aim of overthrowing the government through armed struggle. The successful â€Å"March to Rome† by Mussolini that gave power to fascists in Rome during October 1922 provided inspiration for the youths who had joined Hitler’s Nazi party to carry out such an attempt in Germany. As Nazis prepared for the coup attempt, the membership of this party had exceeded almost 50,000. Accordingly, Hitler planned to start a â€Å"March on Berlin† movement for taking over the national government. During this time, many responsible authorities of Bavarian state government were agitating against the federal policies on the issue of resistance to Franco-Belgian occupation troops. This resulted in their preparation for a coup against the Berlin rule. Accordingly, they discussed the strategy for such action on the evening of 8 November 1923, while meeting at a hall in the eastern part of Munich. In the meanwhile all nationalist and radical forces had formed a coalition called â€Å"Kampfbund† to give it a shape of a combat league. However, as Hitler was not invited to the Bavarian meeting of November 8, the rivalry of Hitler and Bavarian President Kahr resulted in the deposition of Bavarian government. Accordingly, the

Hamburger and Wendy Essay Example for Free

Hamburger and Wendy Essay Executive Summary Wendys offers a variety of fast food. The food selection ranges from hamburgers, French fries, salads, chicken, potatoes, and chili. Wendys income is based on the sale of fast food. The demand of Wendys service is highly elastic. A change in price will affect demand for products. Wendys market structure is an oligopoly and has two main competitors; McDonalds and Burger King. In an oligopoly, the market is dominated by a few large producers of a homogeneous or differentiated product. Because of their fewness, oligopolies have considerable control over their prices, but each must consider the possible reaction of rivals to its own pricing, output, and advertising decisions (McConnell Brue, 2005). Since there are many substitutes, Wendys has to be willing to keep their prices and quality of food relative to competitors. McDonalds and Burger King offer substitutes to Wendys food. Advertising and promotional offers can help Wendys stay competitive. Wendys also has to be observant of economic trends. Raises in inflation and food costs will affect the demand for fast food. However, inflation and food costs should also affect McDonalds and Burger King. Therefore, Wendys market share should not be affected if they raise prices collectively with McDonalds and Burger King. In the future, there is a chance for a healthy fast food restaurant to enter the market. Society is leaning towards a more health conscience population and the fast food industry will have to adjust. Wendys and its competitors currently offer salads. Wendys should consider offering healthier menu items and increase advertising to gain market share. Investing in advanced technology will also keep Wendys competitive. More technology will result in higher productivity and lower average total cost. Description of Utility of the Good or Service Wendys is a fast food restaurant that provides an alternative to home cooked meals. The convenience of their products is not a necessity but can be considered as a luxury. In the past, women were not in the work force and stayed home to tend to household chores. Chores included tending to the children, cooking and cleaning. In the twentieth century, women had begun working outside of the home. In addition, there has been an increase with single-parent homes. The work day has also increased in hours. These factors have increased the demand for an alternative to home cooked meals. Wendys offers fast food at an affordable rate. Time that would have been spent in the kitchen can now be spent with family or running errands. Fast food also serves as an alternative to traditional restaurants that seat customers and offer full course meals. The meals offered at traditional establishments are priced higher than fast food restaurants. In addition, the time spent at a traditional restaurant is significantly more than time spent getting food at a fast food restaurant. For added convenience, most fast food restaurants offer seating for customers who wish to dine-in. Description of Substitutes and/or Complementary Products Wendys competes in local, regional, national, and international markets. Wendys mainly competes with Burger King and McDonalds on all market levels. Burger King and McDonalds offer the same types of foods as Wendys. Each fast food chain, however, offers something that the others do not. For instance, Burger King and McDonalds sell fish sandwiches all year, while Wendys only sells fish during Lent. On the other hand, Wendys offers chili while Burger King and McDonalds only sell chili in certain markets, or not at all. Wendys doesnt offer many complimentary items. Items sold at Wendys can be eaten alone or with other products. French fries usually complement sandwiches but can be eaten alone. Wendys offer a combination meal that includes a sandwich, fries and a drink since the items are usually purchased together. With the change in culture to a more health conscience environment, Wendys allows side salads as a substitute for French fries. In the immediate future, there may be a chance for a healthy fast food restaurant to enter the market. In general, the oligopolies in the food industry have large marketing budgets that hinder others from entering into the market. In addition, the members of the oligopoly can begin a price war to deter other entrants into the industry. However, it is conceivable that a healthy fast food restaurant may emerge in the near future. The fast food industry may have difficulties advertising against a healthy fast food restaurant, since the current culture is health conscience. Price Elasticity of Demand The price elasticity of demand is relatively elastic. If McDonalds and Burger King have promotional sales and Wendys does not follow suit, the demand curve for Wendys food will shift to the left, reflecting a decrease in demand. Due to the decrease in demand, Wendys will have more supply than usual. The supply curve will shift to the right. On the other hand, if Wendys raised the price on their food and other competitor prices remain the same, demand for Wendys food will decrease. Another factor of demand for Wendys food comes from a healthier culture. The shift in society has been to a more health conscience population. Demand for fast food had decreased as a result of high fat content in many of the foods. Wendys can adjust to a decrease in demand by increasing promotions and advertising. Having a promotional low-fat sandwich and extensive advertising will result in the demand curve shifting to the right. Another method to counteract a decrease in demand is to offer reduced prices for popular selling items. For example, Wendys could offer fifty cent junior cheeseburgers for a two week period. This type of promotion will get consumers back into Wendys and should boost the sell of French fries, since the two are usually sold together. To counteract the demand for a healthy fast food restaurant, Wendys will have to promote healthy items. Wendys has taken steps to include nutritional facts on their website and offer healthy menu items. They have increased their selection of salads and have collaborated with the American Diabetes Association to help familys select menu items for a healthier lifestyle (www. wendys. com). Advertising healthier menu items is an important part of countering restaurants that offer health food. Issues that Affect Consumer Demand and Price. Oligopolies are affected by the price competitors charge for similar products. The market share should remain constant if oligopolies collectively increase or decrease prices for similar products. Issues that affect consumer demand for fast food include changes in national, regional, and local economic conditions, consumer preferences and spending patterns, demographic trends, consumer perceptions of food safety, weather, traffic patterns, the type, number and location of competing restaurants (www. wendys-invest. com). For instance, fast food on highways and toll roads are priced higher than residential areas. The higher price can be charged on the roads and will not affect demand because travelers have few substitutes and will pay the higher price. Residents, on the other hand, can cook at home and have more substitutes than a traveler. The same is true for demographics. A restaurant in a metro area with a higher cost of living will have prices higher than a restaurant that is not located in a metro area. Demand for the higher priced items will not decrease because the cost of living is higher. The location of competitors will greatly affect price and demand. If there are many substitutes available, consumers will not buy an expensive product. In an oligopoly, a company has to be aware of competitors prices and predict what impact their own prices will have on competitors. The previously mentioned issues will continue to affect Wendys in the future. Wendys should remain competitive if their prices remain relative to their competitors. Wendys has to remain aware of the location of immediate competitors and competitors prices. Cost Component Factors such as inflation, food costs, legal claims, labor costs and benefit costs, affect administrative expenses (www. wendys-invest. com). Labor and Benefit costs are minimal expenses for Wendys compared to other industries. Wendys usually pays minimum wage and the majority of its employees are part-time. Therefore, benefits costs are low. Wendys is affected by inflation and food costs. However, the benefit that an oligopoly affords Wendys is they can expect competitors to react to increase inflation and food costs, as well. Increased prices should be realized by all competitors. Technology and productivity are indirectly proportional to average total cost. By increasing technology, productivity will increase. For example, a large grill will allow multiple hamburger orders to be processed at one time. Productivity increases for hamburgers. As a result, the average total cost to process on sandwich decreases. Wendys also has incorporated an automatic coin changer. This allows the coin portion of a customers change to be automatically dispensed by the register. Cashiers no longer have to count out someones change. This reduces processing time and allows for more customers to be served. In the future, inflation, food costs, legal claims, labor costs and benefit costs will continue to be a cost for the fast food industry. Advanced technology can aide in faster processing of customers and free up monies allocated for labor. For example, robotic arms can process all orders for fries. The culture has evolved into a ? get rich quick society. Frivolous law suits can pose as an added expense in the future, as well. The time and effort to investigate and disprove claims can be expensive. Wendys was recently involved in a severed finger scandal. Wendys official state that Wendys quarterly earnings fell nearly $2 million dollars after the scam (www. money. cnn. com). Market Structure Component. Wendys is an oligopoly. An oligopoly is a market structure that contains few large sellers. Most likely, there are barriers to enter the industry. The sellers have interdependence in pricing and output decisions. Oligopolies consider responses of rivals in pricing decisions. Strategies for pricing and output decisions include retaliatory pricing and advertising (McConnell Brue, 2005). Retaliatory pricing is one strategy that may govern how Wendys reacts to anothers price and output decision. Wendys can sale their sandwiches for a lower price than McDonalds and Burger King. However, Wendys could lose money by slashing prices and may have to raise prices or layoff employees to compensate for lost monies. Price slashing may work as an immediate competition tool, but should not be a long term solution for competing. Advertising is another strategy that governs how Wendys can compete with anothers price and output decision. Advertising can be more effective than price matching. By providing information about competing goods, advertising diminishes monopoly power and results in greater economic efficiency. Successful advertising can boost demand, lower long run average total cost due to increased output, and enable firms to enjoy economies of scale, (Muryn, n. d. ). Successful advertising campaigns may also raise the cost of entry to potential competitors. In the future, Wendys has to be more health conscience. McDonalds and Burger King are making advances towards healthier menu items. To stay competitive, Wendys should make more strides to display healthy menu items. Some of the advertising budget has to be directed toward health conscience consumers. Promotional campaigns should introduce the public to healthier items offered by Wendys. The market share for Wendys should remain competitive with the introduction of healthy menu items. Conclusion Wendys is an oligopoly that competes with McDonalds and Burger King. Demand is relatively elastic. To stay competitive, Wendys must stay aware of the competitions prices, location and menu items. Wendys should also know what current economic trends, costs, and societal shifts affect demand for their product. Wendys should use increased advertising as a long term tool to stay competitive. References CNN (2005). Wendys Frosty, Retrieved May 15, 2005 from http://www. money. cnn. com/2005/05/10/news/midcaps/wendys_frosty McConnell R. C. , Brue S. L. (2005). Economics principles, problems, and policies, 16th ed. New York: McGraw-Hill/Irwin. Muryn, Jack (n. d. ). ch25. ECO 204, Retrieved May 26, 2005, from http://www. washington. uwc. edu Wendys (2005). Eating Better Together, Retrieved May 30, 2005 from http://www. wendys. com/food/US_nutrition_topics. jsp Wendys-invest (2005). Safe Harbor Statement, Retrieved May 30, 2005 from http://www. wendys-invest. com/safeharbor.

Dream Of Becoming An Engineer English Language Essay

Dream Of Becoming An Engineer English Language Essay The man-made world which consists of machines and devices aroused my curiosity since I was a child. I used to always keep wondering of how a machine operates and how every part of a machine compliment with each other to function well. As a child, I thought that the creators of these machines must have been magicians who are able to command supernatural powers to make a machinery works. And the reason grows along my age. Despite this, I still believe that engineers are magicians; they are the last remaining practitioners of this art in an increasingly modernised world. They continue to amaze and captivate the world with their creations. And they never seemed to be running out of tricks from their sleeves. The thought of how great the profession of engineering keeps lingering in my mind, and I think it will be the same for everyone. [1]Take a glimpse look around you; can you jot down anything that is not relying to certain degree on the work of engineers? I bet anyone would struggle on it. Because of that particular reason I chose to be on this lane, to serve community with a better technology that will shape the century and change the world. However, it was the entire previous story because right now I have been on the platform of the sound tertiary education that will provide me with the best experience the embryonic engineer can have. Only one problem remains; how to grab this chance to make the dream of becoming an engineer come to reality. Time is said to be precious because it is irreversible. Others said that it is eternal. But the main point here is what is done today is not tomorrow, and what is in the past cannot be in the present because time moves. You cannot predict what will happen today or in the future because it is yet to come but you experienced yesterdays event however it is not in your jurisdiction to change that occurrence. That is why it is said that time resembles gold caused by its preciousness. This principle goes well with engineers life. Time management is not something that you can let it happen by itself, it needs a proper planning. Even though people said that time changes things but, actually we have to change them ourselves. Professional engineer is someone who knows how to juggle many things at one time. They work to enhance welfare, health and safety of all and make professional commitments to boost the wellbeing of society through the exploitation of knowledge and the management of creati ve terms. But, frankly speaking, I was a student who practised procrastination in my study. I kept saving all the works given on the eleventh hour this was during the high school era, and in the early life as a university student. However, the hectic life of first year student with assignments and tests educates me that engineers will not just be an idle person but need to devote themselves in acquiring and cramming a brand new technology in physical world. However, what happens if I keep saving all the work till the last minute? Will I be able to prepare myself then to discover some new knowledge? These kind of thoughts that kept wandering in my mind, helped me to get a picture that no matter how eventful my life with works is, I need to get them done once I got assigned. So I decided to make an improvement to my study style. I made a to-do list bright and early, as the first task of the commencement of my day; on a clear white paper to prevent me from wasting any time worrying ab out anything that I might forget. Therefore my whole activities throughout the day tend to follow this list without even a second being wasted. This forces me not to make a group meeting turns to a worthless chat, or whenever I bump into someone it will not become a reunion party because every single second counts. Thus, sometimes I need to say no for a certain matter although it is a very hard thing to do for most people but I believe that it has a tremendous reward. Normally my whole night is filled with either twittering, facebooking or watching drama (since I am a drama enthusiast), however, the to-do list that I made has replaced those times with something beneficial to my study; either preparing for laboratories, tests, or make a quick revision for the next lectures. For instance, assignment given to SESM1015 Professional Engineering students (absolutely this essay) makes my night more meaningful. 30 minutes watching drama has been replaced by 15 minutes essay writing even t hough at first it was a bit hard to get used to. Engineers are meant to not just please themselves but also others since they are the one who will succour people towards better life. So in order to do that they need to know what they are working on or objectives of the job they are doing at the moment. [2]But my problem is how to adapt to the transition between school and university environment. The way on how the teaching goes on is totally different; you need to do everything on your own, without having any teacher attends you personally to make sure that you understand what you have learned, or keep an eye on your attendance to every class it is totally on you. Since my secondary school, I have heard about this tittle-tattle and that scared me a bit. However, I am very indebted to the existing university student there at that time who gave me a clear grasp about how a university environment is; and get me prepared earlier. Even though the nervousness of a fresher in a new situation is still there but I need to get up and help myself first so that I will familiarise with the university atmosphere quicker. Thus, the way how I confronted this problem for the past three month is that I keep preparing myself for the next lecture with a quick revision. At least I need to know the objectives of my learning for the next lectures, so that I can groom my understandings about that topic in the class. To get to know the topic in detail, my friends and I made a study group, and we discuss certain problematic topics because I need to know my subject well so that I can relate the subject with the current application in the world. Whenever we have come to a conclusion we will verify it with a lecturer or senior students so that our discussions will not go wrong. Before that, I need to discipline myself with this new lifestyle as this is how a professional engineer should become, because sometimes I am bombarded with so many distractions that will disrupt my mood and concentration. Sometimes when I was indulged in a dist raction, it will drag up to 1 hour period (unfortunately it is normally caused by watching drama). Most importantly is how you change those distractions into actions [3]. I need to restrain myself from all unnecessary matters by considering which activities will benefit me more; giving some rates to those actions before doing it is the best selection for now. Besides that I need to constantly learn new things as technology is always changing [4]. Just look at the gap between the release of the two phones by the worlds third-largest mobile phone maker after Samsung and Nokia; Apple it is not even a year after the release of iPhone 4s, they have already released iPhone 5. Maybe because of the rapid civilisation, proponents of technological determinisms make a strong case for letting self-accelerating technologies to follow their own life cycle. So as an engineer-to-be, I need to keep myself up-to-date with the current technologies since an engineer needs to have accuracy and vigour. Hopefully, by watching documentaries or educational channels in the television, for instance Mythbuster and Top Gear, they deepen my understandings on how the situation is on the current world. Being an engineer needs me to work not only with machines but with people too. There are a lot of surveys made by different kind of companies reveal that apart from a flying colours result, employers are looking for someone who does well on communicate articulately on both writing and verbal forms or sometime is called as interpersonal skills. [5]The ability to communicate effectively, builds rapport, persuade people of your position or ideas without alienating them, get along with a wide variety of people, be an effective contributor on teams, and leads team to achieve exceptional results this is what the term soft skills or interpersonal skills mean. Engineer is not someone who only stuffing their life with machines but they need to know how to deal with people. But, seems like at first this was the hardest things to do communicate with local student with British slang is easier said than done. Truthfully, to seize the understandings given by the lecturer in a class need me to s pare some great efforts. So I take same actions by watching same British TV Shows to improve my capability in listening and conveying messages to others. Yet, it is still in the to-do list, the time spent for watching TV shows is fixed (normally when I am having my lunch or dinner). Furthermore, I am actively involved in Table Tennis Club which predominantly by local student; so sometimes I initiated a simple conversation to practise my communication skills. As for social skills I am grateful that I was able to improve my interpersonal skills when I was in a Board of Prefect in my secondary school. I learned how to deal with personal problems, anger and dissatisfaction within the student ranks; plus within a team environment I acquired the skills to lead others and motivate them when they are in their dead end or discouraged for I know that each individual is a component in the machinery of an organization. One deficient component creates an inefficient machine. To sum up, all the confusions about how to become a decent engineer might be resolved if I kept practicing all the steps; whether in communicating with others, time management or continuous learning. The most importing thing for me is not to rush things because even if I am not following all the advices there is no one who will correct them for me. I am not an individual who will only serving the consumers only, but also the government, firms, industries and global environment. The 4 years in university life must be spent wisely so that the result would be great. The dream to become an engineer can be achieve with a proper practical on every days matter.

Religion Essays Feminist Theology

Religion Essays Feminist Theology It has been argued that alternative spirituality movements and alternative religions offer contemporary women greater possibilities of participation in religion and of expression oftheir religiosity. All feminist scholars of religionhighlight the wrongs which have been done to women through the neglect offemale religious experience. They subject misogynistic views of womens natureand their place in the world to critical examination. Feminist theologians therefore, seek to address the injustices whichthey perceive in patriarchal religious traditions, and to offset theirandrocentric bias by making a specific feminist contribution to the study ofreligious traditions. It is this critique of patriarchy and patriarchal religious traditions that has opened the way for the alternative spirituality movements and alternative religions that for some women, provides new and radically different ways for women to express their spirituality. These take vary forms and include the Wiccan movement, the most extreme element of which rejects any forms of patriarchal discourse and any involvement of women in religious practices that involve male participation, the Goddess movement and Eco-spirituality. Thispaper will investigate the view that the development of what has been callednew age religion and alternative spirituality movements offer contemporarywomen greater participation in religion and in expressing their religiositywith examples from the Goddess movement and from the Eco-feminist movement. Feminisms influence on the Emergence of Different Spiritualities Fromthe late 1960s onwards what became known as feminist theology emerged. Womencriticised what they saw as the male-centred theology of patriarchal religionand this led feminist theologian Rosemary Radford-Ruether to write: The uniqueness of feminist theology lies not inits use of the criteria of experience but rather in its use of womensexperience, which has been almost entirely shut out of theological reflectionin the past. The use of womens experience in feminist theology, therefore,explodes as a critical force, exposing classical theology, including itscodified traditions, as based on male experience rather than on universal humanexperience (Ruether, 1992:13). Thiswas an expression of what these feminists had been saying for years, that womenneeded to find ways in which they could speak of their own religiousexperiences and as women express their spirituality in terms that feltcomfortable for them. For many women this meant a complete rejection oftraditional religion and a move towards specifically women-centredspiritualities eg Carol Christs 1986 Womenspirit Rising. Goddess Movements Hanegraff(1996) contends that new spiritualities such as the Goddess Movement are rootedin the ancient pagan traditions of occultism and witchcraft. He contends thatthis has influenced the development of New Age womens spiritualities ingeneral, although he regards the term spiritualities as diffuse. He claims thatwomens spirituality, Goddess movements and Wicca tend to blend in together,although it could be argued that there may be some women who own a goddessspirituality who may not subscribe to Wiccan views. This is particularly thecase with the womens spirituality movement that lies within theJudaeo-Christian tradition (see for example Plaskow, 1989). This movement isalso evident in other traditions such as Islam and Hinduism and the idea is todiscover neglected elements within the tradition that express womens religiousexperience. Some women say that these elements have been deliberately neglectedor covered up by the male interpreters of patriarchal religions (see SchusslerFioren za 1984, Mernissi, 1991 and Gupta 1991). While they emphasise thattranscendence can be seen as goddess rather than a god and worshipped as suchthey do not equate this with pagan Goddess worship (Hanegraff, 1996). However,Hanegraff contends that the boundaries between these things are extremelyblurred and that in some cases in the historical traditions there is so muchemphasis on the primacy of experience that the result is no concrete idea ofwho or what the goddess that is being worshipped and in some areas the experientialnature can take extreme forms. Thus he argues: spiritual growth leads to connection with a Higher Power-theGod/Goddess within and without, Christ, Allah, Buddah and All-That-is. Thistheology easily assimilates all personal perspectives on God as equallyvalid.prominence over others is rejected as reflecting a limitedconsiousness..and is lacking in authentic religious experience (Hanegraff, 1996:185). Hanegraff contends that this reflects a view thatsays that those who hold it are not sure who or what God is. However, this maybe a reaction to the reification of God concepts that takes place inpatriarchal thinking, most particularly within the Judaeo-Christian tradition(Daly, 1982). Yet Goddess worshippers within the traditions are conscious ofthe importance of symbolism. Feminists say that it needs to berecognised that symbolism is important to women because they themselves havebeen symbolised. As Daly argues women have been presented with masculineconcepts of themselves which are symbolic of mens fear of the feminine. Thisis evident in maternal and virginal representations in Christianity, and in thedistorted images of Kali in Hinduism (Gupta, 1991). Women do need to find theirown way of relating to the religious symbolic and perhaps this means that theyare nervous of committing the same mistakes as patriarchal tradition andreducing transcendence to an object. King (1995 contends that although symbolscan be male, female, or androgynous, most of the worlds religious traditionshave taken the male as normative and used the symbolism to uphold maledominance in the religious and social structure. In the same way Carol Christ(1980) has argued that masculine symbolism has been so damaging for women thatthe only response women can make is to adopt purely feminine symbols and toworship the Goddess. It is her view that this is the only way that women canassert their own gendered identity in a patriarchal society. Thus she writes, Religioncentered on the worship of a male God creates moods and motivations thatkeep women in a state of psychological dependence on men and male authority,while at the same time legitimating the political and social authority offathers and sons in the institute of society (1980:275). Goddessworshippers Hanegraff (1996) argues are concerned to express the fact that thewhole of reality is permeated by the Goddess while at the same timeinvestigating the historical roots of Goddess worship both with and without thetraditions. King (1995) maintains that along with the Goddess movement there isalso a lot of work in the area of ecology, or eco-feminism, particularlyRuethers 1992 work, Gaia and God. Eco-Feminism The work ofeco-feminists such as (Mcfague, 1987, Ruether, 1992 et al) stems from a newconcern for global issues and the way in which human beings have treated theearth. Ruether uses the Gaia principle taken from science, and takes theposition that the earth is our sacred mother we come from it and return to ityet throughout history humankind have damaged the earth and other forms of lifethat exist here. Sallie McFague 1987 has argued that patriarchal the religionsthat have oppressed women have also dominated the earth. They have taken thebiblical saying that man should have dominion over the earth and all that is init so literally that they have come close to destroying Gods gifts. McFaguerefers in her work to the earth as Gods body, the earth, she maintains is ametaphor for the body of God. In Models of God (1987)McFague argues that the metaphor of the world as Gods body would not just helpto repair the relationship that human beings have with the earth, but wouldalso help to dispel some of the hierarchical images of God that exist withinthe Christian tradition. Thus she writes, The metaphor of the world asGods body puts God at risk (McFague, 1987:73). God is seen asvulnerable when God is such an intimate part of creation. The earth, therefore,is among the oppressed. It suffers with us and if the world is seen as the bodyof God, then God may be seen as suffering with Gods people. McFagues Modelsof God are metaphors that allow both the transcendental as well asthe ethical nature of God to emerge. Hanegraff (1996) maintains that: The ecological crisis has beencreated by a society based on fundamentally flawed presuppositions. Humanityhas to change its way of thinking perceiving and acting, and then it willhopefully still be possible to heal the world (Hanegraaf, 1996:118). Conclusion Clearlyalternative spiritualities seem to be the way forward for many women to expresstheir religiosity, nevertheless, there are still women who, despite patriarchaloppression, remain with their inherited faith traditions and struggle to freeit from patriarchal restraint. It would seem to me that there has always beensome concern for the female in religious imagery e.g. the person of Mary inCatholicism and the many Goddesses of Hinduism. In a sense there have alwaysbeen these alternatives and I would say that the emergence of second wavefeminism in the late 1960s and their critique of all things patriarchal is whathas brought these alternatives to the fore. The higher profile of thesespiritualities is necessary so that all women feel able to choose how theyexpress their spiritual experiences. Bibliography Christ,C (1980) DivingDeep and Surfacing, Women Writers on a Spiritual Crest, Beacon Press,Boston Daly, M (1982) BeyondGod The Father, 2nd EditionThe Womens Press, London Fiorenza, E(1984) In Memory of Her, SPCK, London Gupta, L (1991)Kali the Saviour, in Cooey, P, Eakin, W, McDaniel, J (eds.) (1991) AfterPatriarchy: Feminist Transformationsof World Religions,Orbis, New York Hanegraaff (1996) New AgeReligion and Western Culture New York, Brill. King, U (ed.)(1994) Feminist Theology From the Third World, SPCK, London McFague, S(1987) Models of God, SPCK, London Plaskow, J(1993) We are also your sisters: The development of womens studies inreligion, Womens Studies Quarterly, XXI, 12 p. 9-21 Ruether, R(1992} Gaia and God, SCM, London