Rise and Fall of Nazi Officer Franz Stangl

Franz Stangl, nicknamed The White Death, was an Austrian Nazi who served as director of the Treblinka and Sobibor death camps in Poland during World War II. Under his co-direction, it is estimated that more than 1 million people were gassed and buried in mass graves. After the war, Stangl fled Europe, first to Syria and then to Brazil. In 1967, he was tracked down by Nazi hunter Simon Wiesenthal and extradited to Germany, where he was tried and sentenced to life imprisonment. He died from a heart attack in prison in 1971. Stangl as a Youth Franz Stangl was born in Altmuenster, Austria, on March 26, 1908. As a young man, he worked in textile factories, which would help him find employment later while on the run. He joined two organizations: the Nazi party and the Austrian police. When Germany annexed Austria in 1938, the ambitious young policeman joined the Gestapo and soon impressed his superiors with his cold efficiency and willingness to follow orders. Stangl and Aktion T4 In 1940, Stangl was assigned to Aktion T4, a Nazi program designed to improve the Aryan master race gene pool by weeding out the infirm. Stangl was assigned to the Hartheim Euthanasia Center near Linz, Austria. Germans and Austrian citizens who were deemed unworthy were euthanized, including those born with birth defects, the mentally ill, alcoholics, those with Down’s syndrome and other illnesses. The prevailing theory was that those with defects were draining the resources from society and polluting the Aryan race. At Hartheim, Stangl proved that he had the proper combination of attention to detail, organizational skill and absolute indifference to the suffering of those he deemed inferior. Aktion T4 was eventually suspended after indignation from German and Austrian citizens. Stangl at Sobibor Death Camp After Germany had invaded Poland, the Nazis had to figure out what to do with the millions of Polish Jews, who were considered subhuman according to the racial policy of Nazi Germany. The Nazis built three death camps in eastern Poland: Sobibor, Treblinka, and Belzec. Stangl was assigned as chief administrator of the Sobibor death camp, which was inaugurated in May 1942. Stangl served as camp director until his transfer in August. Trains carrying Jews from all over Eastern Europe arrived at the camp. Train passengers arrived, were systematically stripped, shaved and sent to the gas chambers to die. It is estimated in the three months that Stangl was at Sobibor, 100,000 Jews died under Stangl’s watch. Stangl at Treblinka Death Camp Sobibor was running very smoothly and efficiently, but the Treblinka death camp was not. Stangl was reassigned to Treblinka to make it more efficient. As the Nazi hierarchy had hoped, Stangl turned the inefficient camp around. When he arrived, he found corpses strewn about, little discipline among the soldiers and inefficient killing methods. He ordered the place cleaned up and made the train station attractive so that incoming Jewish passengers would not realize what was going to happen to them until it was too late. He ordered the construction of new, larger gas chambers and raised the killing capacity of Treblinka to an estimated 22,000 per day. He was so good at his job that he was awarded the honor â€Å"Best Camp Commandant in Poland† and awarded the Iron Cross, one of the highest Nazi honors. Stangl Assigned to Italy and Return to Austria Stangl was so efficient at administrating the death camps that he put himself out of work. By the middle of 1943, most of the Jews in Poland were either dead or hiding. The death camps were no longer needed. Anticipating the international outrage to the death camps, the Nazis bulldozed the camps and tried to hide the evidence as best they could. Stangl and other camp leaders like him were sent to the Italian front in 1943; it was hypothesized that it may have been a way to try and kill them off. Stangl survived the battles in  Italy and returned to Austria in 1945, where he stayed until the war ended. Flight to Brazil As an SS officer, the genocidal terror squad of the Nazi Party, Stangl attracted the attention of the Allies after the war and spent two years in an American internment camp. The Americans did not seem to realize who he was. When Austria began to show interest in him in 1947, it was due to his involvement in Aktion T4, not for the horrors that took place in Sobibor and Treblinka. He escaped in 1948 and made his way to Rome, where pro-Nazi bishop Alois Hudal helped him and his friend Gustav Wagner escape. Stangl first went to Damascus, Syria, where he easily found work in a textile factory. He prospered and was able to send for his wife and daughters. In 1951, the family moved to Brazil and settled in Sà £o Paulo. Turning up the Heat on Stangl Throughout his travels, Stangl did little to hide his identity. He never used an alias and even registered with the Austrian embassy in Brazil. By the early 1960s, although he felt safe in Brazil, it had to have been clear to Stangl that he was a wanted man. Fellow Nazi Adolf Eichmann was snatched off a Buenos Aires street in 1960 before being taken to Israel, tried and executed. In 1963, Gerhard Bohne, another former officer associated with Aktion T4, was indicted in Germany; he would eventually be extradited from Argentina. In 1964, 11 men who had worked for Stangl at Treblinka were tried and convicted. One of them was Kurt Franz, who had succeeded Stangl as commander of the camp.   Nazi Hunter Wiesenthal on the Chase Simon Wiesenthal, the well-known concentration camp survivor, and Nazi hunter had a long list of Nazi war criminals he  wanted to be brought  to justice, and Stangl’s name was near the top of the list. In 1964, Wiesenthal got a tip  that Stangl was living in Brazil and working at a Volkswagen factory in Sà £o Paulo. According to Wiesenthal, one of the tips came from a former Gestapo officer, who demanded to be paid one penny for every Jew killed at Treblinka and Sobibor. Wiesenthal estimated that 700,000 Jews had died in those camps, so the total for the tip came to $7,000, payable if and when Stangl was captured. Wiesenthal eventually paid the informant. Another tip to Wiesenthal concerning Stangl’s whereabouts may have come from Stangl’s former son-in-law. Arrest and Extradition Wiesenthal pressured Germany to issue a request to Brazil for the arrest and extradition of Stangl. On February 28, 1967, the ex-Nazi was arrested in Brazil as he returned from a bar with his adult daughter. In June, Brazilian courts ruled that he should be extradited and shortly thereafter he was put on a plane for West Germany. It took German authorities three years to bring him to trial. He was charged with the deaths of 1.2 million people. Trial and Death Stangl’s trial began on May 13, 1970. The prosecution’s case was well-documented and Stangl did not contest most of the accusations. He instead relied on the same line prosecutors had been hearing since the Nuremberg Trials, that he was only â€Å"following orders.† He was convicted on December 22, 1970, of complicity in the deaths of 900,000 people and sentenced to life in prison. He died of a heart attack in prison on June 28, 1971, about six months after his conviction. Before he died, he gave a long interview to Austrian writer Gitta Sereny. The interview sheds some light on how Stangl was able to commit the atrocities he did. He repeatedly said that his conscience was clear because he had come to see the endless train cars of Jews as nothing more than cargo. He said he did not hate Jews personally but was proud of the organizational work he had done in the camps. In the same interview, he mentioned that his former colleague Gustav Wagner was hiding in Brazil. Later, Wiesenthal would track Wagner down and have him arrested, but the Brazilian government never extradited him.   Unlike some of the other Nazis, Stangl did not appear to relish the killing he oversaw. There are no accounts of him ever murdering anyone personally like fellow camp commander Josef Schwammberger or Auschwitz â€Å"Angel of Death† Josef Mengele. He wore a whip while at the camps, which he apparently seldom used it, although there were very few eyewitnesses who survived the Sobibor and Treblinka camps to verify it. There is no doubt, however, that Stangl’s institutionalized slaughter ended the lives of hundreds of thousands of people. Wiesenthal claimed to have brought 1,100 former Nazis to justice. Stangl was by far the â€Å"biggest fish† that the famous Nazi hunter ever caught. Sources Simon Wiesenthal Archive. Franz Stangl. Walters, Guy. Hunting Evil: the Nazi War Criminals Who Escaped and the Quest to Bring them to Justice. 2010: Broadway Books.

Personalities of Hamlet in William Shakespeare´s Play by...

â€Å"A man does what he must — in spite of personal consequences, in spite of obstacles and dangers, and pressures — and that is the basis of all human morality,† John F. Kennedy once stated. In the tragedy, Hamlet, William Shakespeare presents Hamlet as one of the most distinguishable characters due his quest to avenge his father’s death. Hamlet Throughout the play, he is given various voices: as an avenger, as a moralist, and as a philosopher. In this essay, I will be explaining these personalities of Hamlet in depth. The voice of Hamlet as an avenger is observed across the play after the ghost of old king Hamlet reveals that Claudius is the individual who murdered him. Hamlet commences his quest to kill Claudius by initially, acting†¦show more content†¦Instead of killing the king immediately, he follows his morals by first seeking to learn if what the ghost said is true. While giving much thought to his situation, Hamlet comes up with a plan called the â€Å"Mousetrap† in which the actors will reenact the death of old King Hamlet. If Claudius reacts nervous due to this play, Hamlet will know that the ghost can be trusted Hamlet can lastly be seen as a philosophical figure across many instances in this play. He enjoys thinking about complex questions that he himself cannot answer without any doubts. Hamlet primarily questions himself about existence and death questions, pondering about what happens after a body dies, suicide, and in addition, the afterlife. For example, in Act 5, Scene 1, Hamlet states â€Å"Alexander died, Alexander was buried, Alexander returned to dust, the dust is dirt, and dirt makes mud we use to stop up holes.† In this quote, Hamlet can be observed as a philosopher since he emphasizes that everyone faces the same fate of death regardless if that certain individual is an impoverished person or a wealthy person. 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In order to clarify Hamlet’s personality and behaviour, I will provide some aspects of the historical context in which Shakespeare was inspired to write this play, and aRead MoreSurface, Depth, And A Reflected World Of Hamlet1830 Words   |  8 PagesWorld of Hamlet Although dynamic characters typically develop through solely personal obstacles, William Shakespeare uses the character of Hamlet as a contradiction by illustrating his growth through other characters. In Hamlet, Prince of Denmark, Shakespeare strategically uses Laertes and Fortinbras in order to foil the character of Hamlet. An extended metaphor of a pond is created and through tangled family ties, internal conflict concerning perfection, and the pursuit of justice, Shakespeare is ableRead MoreThe Problem with â€Å"Hamlet and His Problems†1862 Words   |  8 Pagesespecially William Shakespeare, have created some of the most stirring and thought provoking stories to be performed on stage. 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A characteristic of Hamlet s personality is to make broad, sweeping generalizations andRead MoreThe First Act Of Hamlet By William Shakespeare1447 Words   |  6 PagesHamlet Throughout the first act of Hamlet, by William Shakespeare, clothing imagery is used to illustrate the common theme of â€Å"is versus seems.† The clothing references made with Laertes, son of Polonius, Gertrude, the queen of Denmark, and Hamlet, the protagonist of the play, come to either reflect the character’s true feelings, or highlight the differences between what the character feels and what emotion they display. Before leaving to France, Polonius, counselor to the king, advises his sonRead More Soliloquy Term Paper: Hamlet’s Soliloquies3192 Words   |  13 PagesReading Shakespeare’s Hamlet, it seems that at every other turn in the narrative the prince is alone and uttering another soliloquy. What is the nature of his various soliloquies? How many are there? What are their contexts? This essay will answer these questions and more. John Russell Brown in â€Å"Soliloquies and Other Wordplay Let the Audience Share Some of Hamlet’s Thoughts† explains that soliloquies are but one form of wordplay Hamlet uses: By any reckoning Hamlet is one of the most complexRead More Shakespeares Hamlet - Hamlet’s Villain, King Claudius Essay3285 Words   |  14 PagesHamlet’s Villain, King Claudius      Ã‚  Ã‚   In the drama Hamlet Shakespeare has concocted a multi-dimensional character in the person of King Claudius. It is the intent of this essay to analyze and probe all the various aspects of this curious personality.    Ward and Trent in The Cambridge History of English and American Literature consider Shakespeare’s options in designing the character of Claudius:    There were at least two ways in which an ordinary, or rather more than ordinaryRead MoreWilliam Shakespeare s Hamlet And Tom Stoppard s Rosencrantz And Guildenstern Are Dead2522 Words   |  11 PagesA Play Interpreted In The Eyes of Two Fools William Shakespeare’s Hamlet and Tom Stoppard’s Rosencrantz and Guildenstern Are Dead, are contrasting plays with a variety of similarities. Shakespeare’s Hamlet was written between the years 1599 to 1602 and is a play about tragedy set in the Kingdom of Denmark. Hamlet is about the young prince of Denmark, Hamlet, seeking revenge against his uncle, Claudius, for succeeding the throne after murdering his father, King Hamlet, and immediately marrying hisRead More Sexuality and Aggression in Hamlet Essay1998 Words   |  8 PagesSexuality and Aggression in Hamlet  Ã‚  Ã‚  Ã‚  Ã‚           Ã‚  Ã‚  Ã‚  Ã‚   In Man and Wife Is One Flesh: Hamlet and the Confrontation with the Maternal Body, Janet Adelman argues that the motivating force behind the plot action in Hamlet is the collapse of boundaries between relationships of individuals, sexes, and divisions of public (state) and private (love) life. The primary cause of the breakdown results from the bodily contamination spread through overt sexuality, specifically maternal sexuality. 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Phylogenetic Free Essays

string(36) " which all OTUs in the tree arises\." 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. We will write a custom essay sample on Phylogenetic or any similar topic only for you Order Now Introduction to Molecular Phylogenetics The 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 cons ist 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 sinc e 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 phylogenetic 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. You read "Phylogenetic" in category "Essay examples" 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 sequences 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 instances 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 prote in 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 the 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 specie s, 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 sequence 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 is 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 w ell 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 provides 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 th e 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. These 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, b ut 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 Phylogenetics 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 likelihood, 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 sequen ces 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 nucleotides 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 which 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 software 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 servi ces now 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 bootstrap 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 tree 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 12 It 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 for 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 co don 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 phylogenetic 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 comprehensive 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 expression, 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 described Molecular 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 Ass ociates, 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 Genetics, 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)  "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. † 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 i n Lindblad-Toh et al, 2005. [18] How to cite Phylogenetic, Essay examples

Marketing Mix of Toyota Motor Corporation-Samples for Students

Question: Where and how does the firm get its current financing?". In particular, assess current financing of TMC. How does the firm currently raise equity? Answer: Based on the financial statements of the company i.e. TMC for FY2017, it is apparent that majority of the incremental funding for the company comes from raising debt that too in particular long term debt. With regards to equity, the majority component of equity belongs to the retained earnings which stand at 17,601 trillion yen out of the total shareholder equity of 18,123 trillion yen. Further considering the debt and equity as on March 31, 2017, it is apparent that the debt equity ratio of company is quite healthy ( 0.75 ) which allows the company to raise additional debt financing (TMC, 2017). Equity One of the mechanisms to raise equity is through the issue of AA class shares. These were first issued in the year 2015 and the relevant details are summarised below (TMC, 2017). The company has not raised any incremental capital in the last three financial year through the issue of common stock as indicated from the table below (TMC, 2017). However, the company tends to raise some funding through the issue of treasury stock as indicated below (TMC, 2017). However, typically only a limited financing is done in this manner and also these shares are repurchased from time to time and also some are retired. Debt The short term debt for the company comprises of bank loans and also commercial paper, the details of which are as highlighted below (TMC, 2017). The long term debt for the company consists of the following (TMC, 2017). Unsecured loans from banks Secured loans from banks Medium term notes issued by consolidated subsidiaries Unsecured notes issued by the parent company Unsecured notes issued by consolidated subsidiaries Secured notes issued by consolidated subsidiaries Capital lease obligations (long term) The break-up of the long term debt is indicated below (TMC, 2017). It is also apparent from the above details that the debt is floating and not fixed which is apparent from the altering interest rate from year to year. The currency breakup of the long term debt as on March 31, 2017 is indicated below (TMC, 2017). US Dollars (51%) Japanese Yen (11%) Australian Dollar (10%) Euros (9%) Other Currency (19%) Additionally, the expected amount due for maturity in the next five years for the company is as highlighted below (TMC, 2017). Reference TMC (2017), SEC Filings- Form 20-F, TMC website, [Online] available at https://www.toyota-global.com/pages/contents/investors/ir_library/sec/pdf/20-F_201703_final.pdf [Accessed August 22, 2017]

Technology Changes free essay sample

Rapid technological change has shaped the world we live in today. Far from having a positive influence, living in a hi-tech world dependent on computers and mobile devices has distanced us from what is really important in life. There has been significant progress in many sectors, such as health, engineering, education etc. , with the advancing technology. Over and above, the fact that we can quickly reach any information we need in very short space of time has made our lives more practical and easier. But I shall argue that this is not the whole picture. Technology has also taken so much from our lives: health and social relationship. We start out with the first point: living in a hi-tech world can cause bad effect on our health. People firstly created technology to make our life easier, but in fact, people are busier and busier these days. Spending all day sitting in front of the computer and lacking of sport activities are the reason for some diseases such as dry and near-sighted eyes. We will write a custom essay sample on Technology Changes or any similar topic specifically for you Do Not WasteYour Time HIRE WRITER Only 13.90 / page Besides, there are also health complaints because of muscle and joint diseases such as pain in neck, shoulder, loins and even the damage of arm nerves due to the excessive time spent working on the computer. Moreover, the number of obesity cases has increased. It isnt just the inactivity that causes the obesity but the endless snacking on junk food while people are hanging out with their technology. Obesity is responsible for diseases such as diabetes and heart conditions.Then, we move on the second point: innovations in information technology have led to a decrease in social activities and relations in people’s lives. In today’s society, more and more people stay indoors, in front of their computers rather than going out and it leads to unsociable lives. Plus, people started to prefer talking on the internet or chatting by cell phones as it is the quickest and easiest way to communicate. Consequently, face-to-face relationships started to vanish and unrealistic relationships especially the ones which are built via the Internet started to be formed.As a result, we are living in a society where young people are not learning good social skills to well-prepare for their future. In conclusion, the technology breakthrough we have experienced in the recent years has dramatically changed the way we live. Far from having a positive influence, living in a high-tech world dependent on computers and mobile device has distanced us from our health and social relationships-what is really important in life. Therefore, we should make use of the benefits that the technology brings us but not depend on it too much.

Essay Sample on Indian Culture The Understanding of Values and Traditions

Essay Sample on Indian Culture The Understanding of Values and Traditions Human beings learn their cultural traditions and values from the inception of their lives. They acquire the cultural traditions and values through myths, legends, and fairy tales. Its great to know about ones own culture, but people should also attempt to inform themselves about other cultures for the sake of knowledge or to better understand each other. India is a beautiful country that shares different beliefs from other countries, which are what makes it unique. It has its own values, traditions and these are evident in the epic poems, fairy tales and famous people. The epic poems contain history and the beliefs that were passed down orally from generation to generation or a written down. The Mahabharata is one of the two most epic poems that embodies the essence of the Indian cultural heritage. The epic poem is an absorbing tale of a feud between two branches of a single Indian ruling family that culminates in a vast, cataclysmic battle. The two branches include the five Pandavas, the sons of the deceased Kind Pandu and the 100 Dhartarashtras, the sons of blind King Dhartarashtra. In a game of dice, the Dhartarashtras win and according the bet, the Pandavas live in wilderness for twelve years. After the Pandavas, fulfill their part of the bargain, the Dhartarashtras resist to restore half of the Kingdom to Pandavas. This dispute engenders the eighteen day battle between the two rival parties. In the end, Pandavas, with the help of God Vishnu in the form of Krishna, come out to be the victorious, but the victory was not easy because of the loss of beloved ones including Pandavas five sons by their only wife, Draupadi. The idea that The Mahabharata portrays is that good vs. evil, right vs. wrong always leads to the ascendancy of good over evil and right over wrong. Ramayana is the other great Indian epic that takes place in India around 1000 B.C.E. Rama, the main character, is born to a King of Aydohya, Dasaratha and being the oldest of the four sons, he is to become the ruler of Aydohya, but his stepmother wants her own son to be crowned as the next king. Remembering the the king once promised her any two wishes she desires, she demands to send Rama in exile for fourteen years and crown her son Bharata. Despite the kings relenting conscious, he asks his son to leave the kingdom. Rama who lives by the rules of dharma, accepts the order blithely. Rama accompanied with his wife, Sita, and his brother, Lakshma, leaves the palace immediately. Upon finding out what had happened, Bharata goes after Rama and begs him to come back, but Rama refuses to disobey his fathers order. During his journey in the forest, Rama faces many obstacles. He loses Sita when she is abducted by Ravana, the king of demons. With the help of a monkey named Hanuman, Rama successfully conquers Ravan and rescues Sita. The fourteen years expire and they return back to the palace where they receive warm welcome and Rama takes the places as a ruler. During this time, Sita proves to Rama her purity, but despite that Rama remains dubious of her fidelity, which leads to Sitas tragic end and departure from the earth. Besides that Ramayana is a story of love and jealously, separation and return, the moral reflects the idea of of dharma which is a duty that each person should fulfill and it also emphasizes ascendancy of good over evil. Famous people contributed and helped develop the Indian history. Mahatma Ghandi, born on Oct. 2, 1869, was known as the Father of the Nation. Throughout his life, Gandhi jis main mission was to fight against injustice. He devoted his entire life to diminish the oppression of the Indians by the whites. In order to accomplish his goal, he launched three significant movements serving one purpose freedom from the British rule. The first one was the Non-Cooperation Movement, the objective of which was to acquire independence by boycotting foreign goods, British courts and schools and go back to the Indian attire and values. The second was the Civil Disobedience Movement launched on April 6, 1930. It began the Dandi March. In order to oppose the British Salt Law, Gandhi ji, along with his followers, marched to Dandi to make their own salt. The third one was the Quit India Movement of 1942 resulting in the Quit India resolution urging the British to leave India. After all these year of stru ggling, India finally achieved its independence on August 15, 1947. All the protests that Ghandi ji initiated have one thing in common, which is the usage of peaceful and non-violent methods. It tells people that killing and committing atrocities is not the only way to resolve problems. Another person, Guru Nanak influenced and created a new religion called Sikhism. Since Guru Nanaks goal was to unify the Hindus and Muslims, he combined the both religions and created Sikhism. He taught people many lessons through his actions. He preferred to eat with the poor than the rich because when he squeezed poor mans bread, it oozed milk while rich mans bread oozed blood. Through this action, he taught that people should make honest living. Once at Mecca, he slept with his feet pointing to the holy book. An angry man outraged by this disgracefulness, shifted his feet and in whichever direction his feet were shifted, the Holy book also shifted. In this manner, he taught that God is ubiquitous. Guru Nanak believed that honest life would lead to salvation and freedom from the cycle of birth and death. A lesson one should learn is that its better to be poor and live honest life than be rich who is living off of peoples blood. Fairy tales play a great role in helping a child to develop the sense of its cultural traditions and moral values. The story Pigeon and the Crow is about a greedy crow. The crow sees that Pigeon lives in a household where there are all sorts of different food. In order to obtain delicious, savory food, he tells the pigeon that he wants to live with the pigeon to learn his sophisticated ways of eating. The pigeon agrees and they both head off in the wild to eat. Obviously, the crow pretends to observe pigeons ways and eats mostly worms. The next day, the cook is preparing fish for the household members and the crow determined to get some of the fish refuses to go along with the pigeon to eat in the wild. Upon his response, the pigeon leaves without the crow. The crow sits in the kitchen waiting for a chance for the cook to leave and when he does, the crow greedily eats the fish. The cook comes back and catches the crow red handed. In anger, he plucks crows feathers and applies a mixtu re of ginger and butter-milk. The moral that could be extracted out of this story is that one should not be greedy to take other peoples property because that only leads to chaos. The epic poems, famous people and the fairly tales play a great role in developing ones cultural understanding of the moral values and traditions. These elements help make a country unique and help bring the essence of the heritage. It is very important to read to the kids, so they can possess some knowledge about their own culture. It is great to know about ones culture, but its more interesting to learn about other peoples culture also.

Validity Essay Example | Topics and Well Written Essays - 250 words

Validity - Essay Example Validity can be face validity, criterion-related validity, formative validity and sampling validity (Klaus, Boyle and Simon, 13). Reliability and validity are related i.e. closely inter-dependent. Although validity cannot exist without reliability, the latter can exist without validity. Some of the systematic factors that affect both the reliability and validity of measurement include presence of unsystematic events, systematic inconsistency and the change in the event being measured. The unsystematic threats to reliability include subject reliability, situational reliability, observer reliability, instrument reliability and data processing reliability (Klaus, Boyle and Simon, 13). Some of the factors to consider in ensuring reliability and validity include time and money, difference in the measurement expected and reference to a previously validated measure. Some of the measures that can be applied in the improvement of the validity and reliability include ensuring that the goals ar e vividly defined and put into practice, matching the assessment measures to the set goals and objectives, presenting the tests for review to other interested parties, actively involving all participants in a measurement exercise, and comparing the measure with other measures that are

Health Promotion Research Paper Example | Topics and Well Written Essays - 2000 words - 1

Health Promotion - Research Paper Example Moreover, the consideration of the change programs and the various initiatives implemented to reduce these factors in a health promotion program. The health belief model (HBM) was developed in the 1950s by some social psychologists to explain why some individuals do not use health services such as screening and immunization. The theory has advanced to address newer concerns in detection and prevention (for instance influenza vaccines and mammography screening) as well as lifestyle mannerisms such as injury prevention and risk behaviors associated with sexual tendencies (Noar, Chabot & Zimmerman, 2008). The HBM hypothesizes that individuals beliefs on whether or not they are at risk for a health problem or disease, and their acumens on the benefits of taking action to avoid the risk, influences their willingness to take action. For instance, if an individual feels that their lifestyle may lead to diseases such as obesity, or diabetes, they may take the necessary actions such as eating healthier foods or becoming physically active to prevent those risks from occurring. The key concepts of the theory are: perceived severity and susceptibility, perceived benefits obtained from the action, perceived barriers to the action, cues to action and self-efficacy. HBM is often applied to asymptomatic and prevention-related health concerns such as the early detection of cancer and hypertension screening where opinions are as important as or more important than obvious symptoms. It is also relevant to interventions to lessen risk factors for cardiovascular disease. According to the theory therefore, people indulge in health programs only if the perceived risks and problems are severe. They then stop the health programs once the risks have reduced. The Trans-theoretical model (TTM) was developed from studies of the processes of change in psychotherapy and smoking cessation (De Vries & Mudde2008). The

Indivisual rights, health disparities and policy options Essay

Indivisual rights, health disparities and policy options - Essay Example According to surveys that have been conducted ranking health care provision in several areas of the United States, the state of Washington was found to have some of the region’s healthiest counties, and these counties included counties such as Montgomery and Fairfax. The research also showed that there happens to exist some pockets within the state that had relatively high levels of poor health. These counties included counties such as the Prince George’s County and Maryland County. Like most other poor counties in the United States, Maryland and Prince George counties of Washington have been found to be facing some major challenges in efforts aimed at trying to ensure that they provide quality health services to their residents. This has mainly been found to be as a direct result of crippling fiscal constraints as a direct result of the relatively poor income and high unemployment rates of the residents of these two areas (Rand Corporation 1). According to a report provided by the Center for Health Equity. Maryland County has been seen to be struggling with a variety of health care issues. The County has relatively high levels of smokers. While the current rate and goals that have been set by the CDC stand at 12 percent for adult smokers, Maryland County has an average adult smoker’s rate of over 17 percent. The state also spent about 1.5 billion dollars in treating ailments related to obesity (Avalere health 41). An estimated 80,000 of the adults living in prince George County were found to be uninsured. These levels were found to be more than twice of those in the neighboring County of Howard. The non-elderly Latino population in Maryland was also found to be more likely to be uninsured as compared to the whites in the County (Avalere health 41). Cancer has been found to be the second leading cause of death in Maryland County with lung cancer being the most common for both the women and men. In the

Our Religion Does Not Define Us Theology Religion Essay

Our Religion Does Not Define Us Theology Religion Essay Our religion does not define who we are regardless to popular belief. Our religion is only a part of who we are if we let it. Not everyone that practices a religion knows everything about it or even accepts it. Some people have a religion just because everyone else has one, and most people have a religion because they were brought up in it. The human mind is easily convinced to do and believe things when it is young and fragile. As a child, you listen to your parents, obey them and learn from most things they do we stand on the shoulders of others to get to the next level (Fraklin). Most people choose their religion based on the religion their parents practiced. Our religion could affects many aspects of our lives depending on how deeply we believe in it; this includes the way we see others, the way we act, and the way we influence those around us. Our faith in our religion can always be seen in the way we live our lives, nevertheless it does not define who we are. As humans, we learn everyday of our lives, introducing us to new things which indirectly change our point of view on certain things in our lives; we begin to see things in different ways and accept somethings we thought was wrong but some people still somehow let their religion come in the way of how they see these things, even though they have a different op inion on some matters they feel like they are obligated to believe whatever their religion asks of them. For those who accept this changes, it could bring about a big difference in their life. I believe no one can tell what religion is right or wrong because no one knows everything. Most people like to be right in most situations, so whenever they are asked what religion is right, it is quite normal for them to say theirs is right. Not everyone tries to realize that the same way they think their religion is right could be the way another person sees his as the right one The easy confidence with which I know another mans religion is folly teaches me to suspect that my own is also (Mark Twain). With what we know, religion might not even exist, which is why I believe that everyone should respect each others point of view on any situation God has no religion (Mahatma Gandhi), personally I think all that matters to God, if there is one, is the good and bad that people do. It is easy to t hink someone is wrong, when you think you are right even though you might be wrong. An example is the apology of Socrates. Socrates was a simple minded person who never thought himself to be more than he was. The fact that he acknowledge his ignorance makes him a wise person (Plato), most believers are ignorant of other religions, yet they believe their religion is the right one while others are not even though they do not know much of the one they criticize. Children learn most things from their parents and those around them. Growing up, children are taught what is right and wrong by their parent or guardian, and that helps them in deciding for themselves when they are adults. It is very common for a parent to take their children to where they worship, and as they grows they learn from their parents faith, making them believe in their religion. The reason why people rarely change their religion is because they grow in it and that makes it more of a lifestyle to them rather than something they learned. Most religions like Christianity has been made in a way that you are not allowed to question some of the things you might not agree with. Some of the stories and rules we learn from our religious books sometimes seem wrong and sometimes we might find some not quite sensible, but we have also learned that we have no right to question the things that happened in them, we just have accept it. The story of Job is one that should bring every Chr istian to question their God as to why he made a man go through so much, just to test his fate. Job was a faithful Christian, but he was tested by Satan with the permission of God; he lost everything he had and was terribly ill, with no help from anyone (The story of Job). Everything that happened to him is something no Christian would accept from any other person, it would not matter what reason they might have to do that, it will be considered bad, but when it is God that did this to a man just to test his faith, they are not allowed to question him. Even though Job went through a lot of things, he never questioned God. When believers feel angry towards God, most of them think it is a wrong feeling and they are not able to express themselves to other believers because they feel judged, guilty, and ashamed (julie and joshua). Every religious belief has its good and bad parts, some that we agree on and others that we dont, but the fear that has been put into us from when we were young is what makes us accept it even though we have other opinions. The fear of a god could make anyone do anything. The story of how Abraham is a great example. Abraham was willing to kill his only child because God asked him to do so, even though that was his only child and he knew he will never have any other child, he was still willing to kill his child And it happened after these things that God tested Abraham. And He said to him, Abraham! and he said, here I am. And he said, take, pray, your son, your only one, whom you love, Isaac, and go forth to the land of Moriah and offer him up as a burnt offering on one of the mountains which I shall say to you (Abraham and Isaac). Despite how deep our faith might be and how well we understand a religion, we still put in our own interpretation to it just to make it suit us. Lailak ask ed are we supposed to interpret the Bible in our own way?. Lone77star answered that we all have our own path to choose, he explained by saying he had his own interpretation and would not want anyone to follow it blindly (hubpages). Not every Christian that reads the Bible understands it, and not every Muslim that reads the Quran understands it. This is the reason there are pastors and Islamic leaders teaching their religion. Even though this people are seen as the holy ones, they also interpret the religion in a way they see fit. Religion is not just one thing, it is a way of life in which people design for themselves; everyone has their own unique religion because we all see and interpret things in different ways. Some people believe they are Christians because they go to the church. This is simply their interpretation of being a Christian Anyone who thinks sitting in a church can make you a Christian must also think sitting in a garage can make you a car (Garrison. goodread), it d oes not matter how much a person attends a church or pray, it is their heart towards things that defines them. The actions they take and how they deal with things. The most annoying people are those who try to get people into their religion; this is basically asking others to think like they do and see things from their own perspective. Christians believe that God created humans And God created the human in his image, in the image of God He created him, male and female He created them (Genesis). Christians accept and believe this theory. In some way this affects their way of living because they think they owe their existence to someone. They live most of their life trying to please someone they have never seen Religion has convinced people that theres an invisible man living in the sky. Who watches everything you do every minute of every day. And the invisible man has a list of ten specific things he doesnt want you to do. And if you do any of these things, he will send you to a special place, of burning and fire and smoke and torture and anguish for you to live forever, and suffer, and suffer, and burn, and scream, until the end of time. But he loves you. He loves you. He loves you and he needs money (George Carlin). The misinterpretation of religion could lead to disagreement, conflicts and even death. When people have different interpretation of what their religion says, it is very easy for them to disagree on most things. Some Muslims have been killing for years, and they believe what they are doing is right. They believe they can do anything as long as they ask for forgiveness. Religion has caused most of the wars the world has ever known. God says we should love our neighbors has we love ourselves. Anyone could interpret this the way they want, some would say it means to love your family, and others might think it means to love everyone love your fellow as yourself (livneh). Some people believe in God just so they have someone to blame when they are in trouble When people experience traumatic or highly stressful events, a common response is to blame God (Julie and Joshua), to these people God is just a figure they run to whenever they are in trouble or need someone to blame for their own fau lts and weaknesses. They do not fully understand the concept of God, but they feel that they need him. Our religion does not define who we are, what makes us who we are is what we accept our religion to be, our interpretation of it, and the choices we make through them. The Bible teaches about loving one another love your fellow as yourself (livneh), this is hard sometimes because some people are just hard to love. No matter how you try to get close to them, they still somehow do not accept you. Some Christians are this way, even though the bible says they should love one another. The bible also mentions not having hate towards a fellow human you shall not hate your kinsman in your heart (livneh), yet there are several Christians who have hate in their heart towards someone in their family, and people in the church. Even though the law of the bible ask them to love and never hate, this does not define them.

Origins Of Distrust Between Th :: essays research papers

The Arab world has been one of the most confusing areas known to the western world. Because of this confusion, the people of the Middle East have been made to suffer, not only at the hands of the west, but also by their own. Even though Arab and western world relations have been stabalizing, they are still long way off from achieving a lasting peace. â€Å"The roots of all these problems go back to the settlement imposed on the Middle East in 1918-1922†(Field 26). Since before the start of World War I, there was a great Western presence in the area we know today as the Arab world. Britsh and French forces occupied Northern Africa since 1882; British occupied Egypt, at the request of Sultan in Constantinople, and the region we today call the Mahgreb: Morocco, Tunisia, and Algeria. In addition, to its presence in Egypt, Britain also kept the Gulf states under her protection and held Aden as a colony. According to the â€Å"version of events one hears in the Middle East, is that British and French policy at the time was a straightforward betrayal of the Arabs†(Field 28). Because of the Ottoman rule in the Middle East, the Europeans began to persuade the Arab leaders to revolt by promising them their independence. But what was meant, was independence from Turkish rule with the aid, supervision and/or protection from Britain and France. In simple terms, the Europeans powers would be the new occupiers of the Middle East. The deception came in the form of two documents; one important to the Europeans powers, and the other to the Jews. The Sykes-Picot Agreement of February 1916, was the document that divided the Middle East between Britain and France. The agreement stated that Lebanon and Syria would be set aside as areas of French interests and the British were free to intervene in the Arab region in the South. Sykes-Picot remained a secret to the Arabs till 1917, when after the Bolshevik Revolution, Russia had published it. From 1918 the Europeans began to place monarchs in the countries(lands) they had established. Some remained in power for a short amount of time (Sherif Hussein) and others began a lineage (Abdullah in Transjordan). Nevertheless, the rulers that were placed by Britain, were deposed of due to the nationalistic ideas that were arising in the Middle East. The second form of deception was the Balfour Decleration, in which was stated that the British government favoured and supported â€Å"the establishment in Palestine of a natural home for the Jewish people†(Field 44).