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Did God make pathogenic viruses?Jerry Bergman, Ph.D.bySummaryA review of the structure, function, and role of viruses in ecology is presented. It is concluded that viruses are non-living entities, similar to seeds and spores whose functions include carrying genes from one plant or animal to another. Viruses are a part of a system that helps to produce the variety that is critical for life and, importantly, they carry resistance to disease from one organism to another. Most viruses live in their host without causing problems. Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.IntroductionA major line of reasoning used to argue against the creationist worldview is ‘why a benevolent God would create pathogenic organisms whose sole function seems to be to cause disease and suffering?’ The account of Noah and the flood is often criticised by the claim that God must have wanted pathogenic viruses in the world: because they exist today, God must have brought them on the ark.1One evolutionist summarised this view as follows:Fig. 1. Model of an adenovirus showing icosahedral capsid with 20 triangular faces, 12 vertices and 30 edges (after Luria et al.).63‘ Although there is enormous beauty to be found in the plants and animals of this world, as well as in the physical planet itself, there is also much ugliness. Beauty and ugliness are, of course, human perceptions, but then so is the belief that an intelligent Creator is necessary to explain the existence and nature of the world. Innumerable examples could be cited of rather nasty biological realities which are perfectly understandable in terms of evolution, but which make no sense whatever in terms of design by an infinitely intelligent, wise, and compassionate Creator. Every living creature, including plants, must contend with the ravages of diseases and parasites. Most disease-causing bacteria and viruses, which exist in encyclopedic profusion, serve no useful “purpose” whatever except to infect other creatures and to make their lives more difficult or shorter.’2The word ‘virus’ elicits memories of virus plagues such as the 1918 influenza plague that killed up to an estimated 20 million people.3The common public perception is that the onlyfunction of viruses is to cause disease. Among the many common diseases caused by viruses are cold sores, hepatitis B, herpes, yellow fever, viral meningitis, chicken pox, colds, mononucleosis, mumps, rabies, polio, shingles, smallpox, warts, viral pneumonia, AIDS and some cancers.Viruses can also produce health problems by influencing the immune system to attack the body.Viruses can also produce health problems by influencing the immune system to attack the body, resulting in auto–immune diseases such as diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. Viruses can cause auto–immune diseases by leaving parts of their DNA in their host which may cause their protein–immune fingerprint to become embedded in the hosts’ cell membranes. When these cells reproduce, the daughter cells also possess these unique markings. White blood cells may mislabel these self-cells as foreign and inappropriately attack them. In Hepatitis B infections, more liver damage may be caused by the immune system’s attack on the infested liver cells than by the actual virus. Viruses have even been implicated in causing some cancers such as leukaemia and are also a scourge of farmers, infecting both livestock and their crops.Although viruses were discovered only at the turn of this century, research has now found a substantial amount of evidence that they serve several major roles in ecology and are actually essential for life. Without viruses, the genetic revolution we are now experiencing would be impossible. They also serve numerous beneficial functions that we are just beginning to research and understand.The discovery of virusesFig. 2. Diagrammatical representation of human immunodeficiency virus (HIV). GP120 and GP41 are two components of the glycoprotein studding the lipid membrane. The membrane envelope and protein envelope are made up of proteins P24 and P18, respectively (from Gallo).9Scientists first discovered and studied this mysterious form of ‘life’ at the turn of the century. Researchers found that if the fluid extract from certain diseased animals and plants was dissolved in a solvent and passed through the finest filter known then (unglazed ceramic plates were often used) the filtrate still caused disease.4Russian Scientist Dmitri Ivanovski found the filtrate from a section of a tobacco mosaic disease infected leaf would infect healthy plants.5Dutch botanist Martinus Bijerinck called this infectious fluid contagium vivum fluidum. This fluid contained agents that are now known as viruses, the Latin word for ‘poison’. At first, many researchers assumed that toxins must have caused the disease. Bijerinck disproved this theory when he showed that the sap could successively transmit the fully virulent disease through a large number of plant generations. This indicated that the disease agent was multiplying in the plant, otherwise it would have become successively weaker as it spread to each new plant generation. Others speculated that bacterial spores far smaller than those that had been discovered were the cause of the disease. It was eventually realised that the culprit was a non-cellular form of ‘life’ that could diffuse through the cell walls and membranes into the cell’s protoplasm.William Elford of the National Institute for Medical Research in London developed a new filter technology in 1931 which helped researchers to realise how extremely small viruses are.6We now know that comparing a virus to an animal cell is like comparing a basketball to the New York World Trade Center. It was only since the 1930s, with the invention of the electron microscope, that scientists could actually visualise viruses.In the middle 1930s, Wendell Stanley of the Rockefeller Institute mixed viruses in a solvent. He then allowed the solvent to evaporate and discovered that crystals formed. The fact that crystals formed meant that all the virus units have nearly identical shape, weight, charge, and chemical characteristics. Many viruses, including Reoviridae, Parvoviridae and Iridoviridae are regular icosahedrons having exactly 20 triangular faces, 12 vertices and 30 edges (Figure 1).7This is clear evidence that viruses are unlike any known living thing and are much more like inanimate than animate matter. Some viruses are isometric shaped, others resemble long round tubes, and still others give the appearance of miniature rocket ships. Debate as to whether viruses are living or nonliving ensued soon after Stanley’s discovery. Today we recognise that viruses are gene carriers just as lipoproteins are the cholesterol/fatty acid carriers of the body’s circulatory system.The construction of virusesFig. 3. The bacteriophage injection mechanism is an example of a complex accessory structure that enables viruses to bind to the host cell. a) virus attaches to host cell with sheath extended. b) sheath contracts injecting bacteriophage DNA into host cell (after Luria et al.).64Five basic morphological shapes of viruses exist: spherical, cylindrical, brick, bullet and tailed. Viruses are contained by a protein cover called a capsid that is often coated with an envelope made of carbohydrates or lipids—an icosahedral capsid is made up of 122 capsomers, of which 110 are hexameters and 12 are pentameters.8This coated capsid houses nucleic acid and other structures that facilitate preserving the genes they contain (Figure 2).9The nucleic acid may be either double or single stranded DNA or RNA. If RNA is used as the master code, the virus is called a retrovirus and requires the complex enzyme called reverse transcriptase to convert the RNA to DNA. Finally, all viruses contain proteins (called antigens) extending from their surface that can bind with specific receptors on the host cells.Some of the more complex viruses also have accessory structures that enable them to attach to selected organisms. These structures include a long tube-like sheath, several tail fibres, and an injector (Figure 3).10,11Each of these seemingly simple structures is enormously complex, and each has hundreds or thousands of parts. The research devoted to understanding them ‘will keep T-4 [a bacterial virus or bacteriophage] morphogenesis at the leading edge of molecular biology well into the next century.’12Viruses have none of the characteristics of life—they do not grow, they lack cells, and they come only in standard models with few, if any, variations of standard parts. They lack most of the cell enzymes and organelles needed to live, and consequently must exploit their host’s organelles. For this reason, viruses are called obligate intracellular parasites, and are ‘infectious particles’ rather than organisms. The complete infectious unit is called a virion.The few enzymes they possess (such as integrase) are usually related to the mechanisms they use to enter their host cell. They are usually only able to multiply in their specific host, and often in only a specific organ within the host (such as the liver). All members of one viral type are usually almost identical in every way except for the glycoprotein antigens on their protein coat.13It is this signal that can trigger an immune system response in a host.Once it was realised that viruses are gene carriers, the next step was to determine howthey carried genes to other cells and spliced them into these cells’ DNA. The contents of the gene package that allowed viruses to carry out their role was another research focus. As the role of viruses became better understood researchers began to try to exploit them for human uses. This gave rise to the genetic revolution, including recombinant DNA technology and gene therapy.Viral replicationViruses are the smallest infectious agents known and range from 200 nanometers for vaccinia to 20 nanometers for parvovirus. Compared to animal cells, viruses are extremely small—fully 50 million polioviruses can fit into the average human cell.14A typical bacterium is 1 micron in diameter, while a bacteriophage is one-fortieth of a micron long. The relation between viruses and their hosts is complex, and usually begins when a virus makes contact with a potential host cell. All known life forms can be ‘infected’ by viruses but some life forms appear to be less prone than others, for example, some species of arthropods and gymnosperms are known to be virus hosts.15Virus multiplication involves six basic steps:Attachment. Viruses and all animal cells contain projections, typically glycoproteins, that allow a virus and animal cell to make contact and to chemically and mechanically bond if compatibility exists. The protein coat (and lipid envelope, if present) thus must attach to the outer membrane of the host to infect it. To infect a cell, the antigens on the virus surface must fit into the cell’s receptor sites. If the fit is not precise, attachment cannot occur and penetration will not result. The fit is usually species-specific; thus a specific virus type will infect only a specific animal or plant type. However, some virus types such as rabies and influenza have a wide range of hosts.Penetration. Subsequent to attachment, most viruses are drawn into the cell by the cell membrane ‘closing in’. This process is called endocytosis and it is the same process the cell uses to take in nutrients. There are some virus types although, that can pass directly through the pores in the host’s cell membrane. There are also others such as bacteriophages which remain outside the cell but inject their DNA into the cells (Figure 3).Transfection. The viral DNA is spliced into a specific site on the host DNA by integrase. The enzyme does this by cutting the circular plasmid DNA, then splicing in the new DNA and repairing the two splice sites (see Figure 5).Replication and Synthesis. The viral DNA or RNA directs the host cell to produce copies of viral nucleic acids and proteins, including enzymes.Assembly. Once inside the cell, the virus can set up what might be likened to the biological equivalent of an assembly line (Figure 4)16. In one type of phage the tail is assembled by first constructing the protein scaffolding. Protein building blocks are then added one at a time. This process of addition stops when another protein acting as ‘measuring tape’ determines that the tail is the proper length. A signal is then produced indicating that the structure is complete and the scaffolding protein detaches to be used again in making other virus tails. Herpes and other viruses come with protein tool kits of their own. Most other viruses, such as the tobacco mosaic virus, have to rely almost totally upon the cell’s own tool kits.Release. The new viruses are released from the cell to infect other cells, spreading even more genes to other cells.17Retroviruses cannot damage cells until they use reverse transcriptase to convert their RNA to DNA. The host then may integrate the virus’ genes in its own DNA, thereby producing a copy of the virus whenever the cell replicates. In this state a phage genome is referred to as a prophage.The origin of all virusesSome evolutionists hypothesize that viruses ‘evolved’ from bacteria by natural selection. In this process, as they become parasites, they lost all the complex protein structures that bacteria require. Others hypothesize that viruses were the first form of life, and that bacteria evolved from them (as did all other life). The fatal problem with this theory is that viruses are not living, and in order to reproduce and to make ATP, they require all of the complex cellular machinery present in bacterial cells. Other scientists speculate that a reverse symbiosis occurred, and that viruses arose out of cell parts such as bacterial plasmids and other organelles, and eventually evolved into separate forms of life.18So far evidence is lacking for each of these theories. Both bacterial plasmids and viruses contain the nucleotide sequences required to initiate replication. While these structures are necessary for the function of each, this does not prove either’s phylogeny. Further, all ‘ancient’ viruses so far discovered in ‘ancient’ amber and other places are fully developed, functional viruses.The role of viruses in ecologyThe importance of viruses is closely related to the importance of bacteria. As Margulis notes, microorganisms have long been considered ‘tiny little beings [that] are primarily germs and pathogens.’19In contrast to this public image, bacteria are at the basis of our life-support system. They supply our fertile soil and atmospheric gases. They cleanse our water supply, play a role in stabilising the atmospheric nitrogen concentration, regulate the acidity or alkalinity of the soil environment, and thus generally ensure that our world is liveable.20The view now emerging of the normal relationship between viruses and genes is not so much a host/invader relationship, but a relationship more akin to bees carrying pollen from flower to flower, thus causing cross-fertilisation. Viruses carry not only their own genes, but also those of other creatures as well, especially those of bacteria.21Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important.22A critical role that viruses play relates to the fact that bacteria contain a constant, stable genetic system (the large replicon), but they function in the world by acquiring and exchanging a diverse set of variable genetic systems (several small replicons, including plasmids, viruses, and so forth). The small replicons are physically separated from the major bacterial DNA, called the genophore. New DNA can be inserted into the genophore; and it usually divides synchronously with it, but some is able to start self-replicating autonomously (Figure 5).Mathieu and Sonea claim that viruses convert all bacteria into one giant, global ‘superorganism’, and that viruses ‘possess a remarkable mechanism for the creation and exchange of genetic material’.23A major class of genes exchanged are antibiotic-resistance genes (see figure 6), along with genes that allow bacteria to degrade toxins (such as polychlorinated biphenyls) or convert mercury to less noxious forms.24This ability is significant in the development of resistance to antibiotics produced by other organisms, allowing bacteria to survive and helping to maintain the balance so critical for ecology.Fig. 4. Bacteriophage ƛ DNA is inserted into the bacterial chromosome by cutting at the attachment sites and splicing. PP' and BB' are phage and bacterial attachment sites, respectively. BP' and PB' are hybrid sites (after Luria et al.)65An important category of small replicons are the prophages, phages and other virus types. Further, no bacterium ‘has yet been found in nature without such a temporary genetic supplement.’25Some of the replicons, especially those that are not useful to bacteria, eventually disappear. This process was once called curing because the replicons were then considered to be harmful infectious elements. We now know that the role of these viruses is important in conferring variation to bacteria. For this reason, viruses are critical for bacteria, and bacteria are critical for ecology.26To produce this variation‘each small replicon may visit thousands of different bacterial strains, and each bacterial cell, although usually harboring only a few different small replicons at a time, is able to be visited by tens or hundreds of different types.’27Bacteria are designed to actively engage in gene exchange by several complex and elaborate mechanisms. One of them is transduction, whereby temperate phages inject their DNA into bacteria.28Laboratory research has found transduction can spread bacterial genes far beyond the locale where the virus incorporated the genes. Miller noted that:‘… when a bacterium carrying a new gene enters a habitat, bacteriophages infect that cell and create more bacteriophage particles. If any particles end up containing the new gene, that gene can be passed on to the indigenous bacterial population. This model is equally applicable to the transduction of chromosomal and plasmid DNA. We have isolated bacteria and bacteriophages from various lakes and have demonstrated that bacteria do share genetic information by transduction in those settings. Many microbiologists originally thought transduction would not be an important means of gene exchange in the environment, because it requires viruses and bacteria—both of which were thought to be present in low concentrations—to interact. But … bacteriophages [exist] in very high concentrations (often 100 billion virus particles per milliliter) in fresh and marine waters. These observations have caused a re-evaluation of the frequency of interactions, including transduction, that occur between bacteriophages and their hosts.’29The incorporation of plasmids or prophages into the bacterial chromosomes is calledtransfection. The incorporation of only genes by a virus carrier or free DNA is calledtransformation. Transfection and transformation are not random, but tightly controlled processes. Specific surface receptors determine which genes or gene packets enter the cell.Although several ways exist in which genes can be transferred from one bacterium to another, transfer‘occurs very rarely by transfection. In nearly all prokaryotes, it occurs commonly through the intermediary of an infectious form of prophage, the temperate bacteriophage or phage.’30Plasmids rarely become integrated into a bacterial chromosome, but instead are like ‘book-mobile’ genes, passed around and used where needed, otherwise discarded (Figure 6). Not all viruses serve this function; many may serve some totally unknown function in the natural world. The realisation that some kinds of viruses have a wider role in life led to a revolution in biology. Using the past research as a guide, it is likely that the extant bacteria and viruses whose function we do not understand likewise will be found to have important roles in the natural world.A strong argument for the gene carrier role (and other functional roles for viruses) is that viruses are comparatively simple, while cells are extremely complex and have elaborate defence systems. It is logical that cells would have elaborate defences, since these are necessary to prevent genetic take-overs. This is a major problem with evolution theory. In the words of Syvanen,‘If viruses were nothing but bad news, you would expect cells to be taking great pains to evolve resistance to them and they do express resistance in some way but they also seem awfully accommodating in others.’31Pathogenic virusesThe traditional understanding that viruses are alien invaders competing against humans in a life or death struggle for the cell’s manufacturing facility is now understood to be oversimplified, if not incorrect. It is usually not expedient for a virus to kill its host, since this may cause the death of the virus. Viruses must have a reservoir of host species in which they can live permanently otherwise they would soon go extinct. AIDS, for example, infects some primates without causing illness or death, and has probably lived in them in a commensal relationship for generations. The host organism must tolerate them fairly well—in fact, some kinds of viruses form a symbiotic relationship with their hosts.Fig. 5. Replication cycle of a bacteriophage (after Stent and Calendar).16Evidently, inappropriate sexual acts by humans caused the transfer of a lentivirus from a monkey to humans. As long as the HIV lentivirus lived in monkeys, it was not a threat for humans. HIV in monkeys (called SIV), ‘appears not to cause disease in most of its natural hosts’, and ‘bacteria and viruses that cause disease today may not always have done so’.32The same situation also is true of syphilis (apparently from sheep) and many other infectious diseases. Baboons resist being adversely infected by HIV, and for years researchers have been exposing certain animals to the virus without infecting them.This supports the argument that viruses normally do not, and should not, cause disease. Only if something goes wrong, such as a mutation or accidental inappropriate movement of genes, do they cause problems. Dr Charles Stiles recognised this many years ago when he concluded that ‘germs were not created as they are today, but they later evolved into germs … those germs were originally created in some form other than as disease germs.’33Stiles claimed that germs developed as a result of the devolution that has occurred since creation.Evidence is accumulating to suggest that most or all harmful viruses and bacteria are mutated forms of non-pathogens. Pathogenic organisms result from gene shuffling, which inadvertently disrupts the normal species-host relationship. Diphtheria is likely not the only case of a harmless organism becoming ‘pathogenic because of virulence genes brought by a prophage or plasmid.’34The case of Vibrio cholerae (the causative agent responsible for the deadly disease known as cholera) illustrates this.‘Just one strain of the bacterial species Vibrio cholerae wreaked almost all the death and misery. This strain is known as O1, and it produces a toxin that binds to cells of the small intestine, setting off a cascade of reactions in which cells pump out vast amounts of chloride ions and water—some five gallons a day. If salts and water are not quickly replaced the patient dies. Surprisingly, most strains of V. cholerae are harmless organisms that live and multiply in rivers and the open sea. But at some time in its evolutionary history, the O1 strain turned lethal. What caused this deadly transformation? A virus, according to microbiologist Mathew Waldor … [Waldor] and his colleague John Mekalanos at Harvard discovered the virus while studying the stretch of bacterial DNA known to include the gene called CTX, that codes for the cholera toxin. They suspected that a virus might have infected the bacteria with the gene, since viruses often insert their own genetic material into bacteria.’35Later researchers confirmed that the cause was a virus. Although bacteriophages are similar to all other viruses, some differences exist. Viruses that function only as a parasite are defined by some researchers as true viruses, while bacteriophages are defined as non-viruses as some do not kill the cell but splice their DNA into the bacterial chromosome (see Figure 5). This terminology may have been coined to avoid some of the negative connotations of the word ‘virus.’ There is also some evidence that infectious agents still labelled viruses ‘carry favourable genes and help even in eukaryotic evolution.’ The research necessary to elucidate the origin of pathogenesis is complex, and the story‘of how the once-harmless cholera bacterium got its toxin and so became a killer is … the all-too-real finding of years of sophisticated molecular detective work and its implications, … The discovery of CTX is just one of a string of surprises to emerge in the past few months from studies of the ways microorganisms interact with each other and their hosts to cause disease. From BSE [Bovine Spongiform Encephalopathy] to AIDS and malaria, researchers are confronting tough questions about the evolution of disease.’36When bacteria were first discovered, few dreamed that they played such a critical positive role, as we now know they do in ecology—and that the same is also evidently true of viruses.37Furthermore, viruses are everywhere in abundance. A major science story of the last decade relates to the discovery by marine biologists that a major proportion of the sea’s biomass is microscopic and is comprised of viruses, bacteria, algae, and protozoa.‘A teaspoonful of seawater may contain more than a billion viruses—10,000 to 10 million times more than previously estimated. The world ocean is what laboratory scientists would call a culture medium, the largest petri dish known to mankind. There can be millions of individuals of a single species in an ounce of seawater, and presumably they play an enormous role in the planet’s carbon cycle. Whether Earth undergoes the global warming the world is watching for may be decided by organisms we didn’t know were there. As Bob Guillard of the Bigelow Laboratory of Ocean Sciences in Marine has observed: “A hundred years of oceanography, and the most abundant being in the world wasn’t recognized by anybody”.’38Humans normally live in an environment inhabited by trillions of microorganisms and as many as 300,000 microorganism species. Estimates run as high as 10,000 for different species of bacteria and viruses per gram of soil.39Many sea and land animals also live in a world of trillions of viruses, yet they rarely develop infections.40,41It is estimated that of the cells that make up or live on a human body, fully 90% of them are microorganisms.42Microorganisms are everywhere on, inside, and around us.Fig. 6. Assembly sequence for a bacteriophage (from Stent and Calendar).16A body of evidence indicates that the presence of viruses is not, in itself, the primary cause of disease. This evidence comes from research on animals that live in environments that contain a high number of viruses and bacteria. One example that has been studied extensively is the shark. Mestel states: ‘You’ll rarely see a sick shark in the wild, although the oceans are teaming with bacteria and viruses …’.43This is true in spite of the fact that sharks have simple immune systems that lack ‘T-cells’ (a type of immune system cell present in humans and animals), and thus only sluggishly reject tissue grafts.Sharks also lack a complex antibody response such as that exhibited in humans. If foreign protein is injected into a shark, it will produce antibodies that bind the foreign antigens but, in contrast to humans, the immune response is not improved by repeated injections. Thus, sharks do not develop memory immunity.It should not surprise us that in a post–Fall world, disease is a result of ‘something gone wrong’, as indicated from several lines of research, specifically research on‘a range of “emerging” diseases that appear … to have entered the human population only recently. And here, perhaps more than anywhere else in the field, myths abound. The standard theories hold that, when a microorganism moves from one species to another—as HIV is believed to have done—it will be nastier than it had been in its original host. Again, this is simply wrong. According to Ebert, parasites tend to be less infectious, less fit and less harmful in new hosts. Of course, there are exceptions, and these are the ones we notice, says Ebert. In reality, bacteria, viruses and other parasites probably jump species far more often than anyone knows, without doing much damage.’44Morse also states:‘Common wisdom held that an emerging virus sprang forth so suddenly because it had evolved de novo … As it happens, the great majority of “new” viruses are not really new at all but are by-products of … viral traffic: the transfer to humans of diseases that exist within some animal population.’45He also adds that ‘new’ viruses such as AIDS may have reflected only our imperfect knowledge of the natural world, not a radical new trend in viral evolution.46The problem, he argues, is a biological mismatch—an organism transferred from its host to where it does not belong. In Morse’s words, by humans ‘disrupting the established ecological order, people inadvertently encouraged the adaptation of a “weed” species that more often than not brought them fever and misery.’47This new understanding of pathogenesis origins is a major topic of scientific research, and is of special interest to creationists because this new evidence fits a creationist worldview. No doubt the Fall has contributed to problems developing in what once was a symbiotic, functional relationship between viruses and their hosts. Viruses may even be critical for the survival of certain life forms such as bacteria.Most pathogenic viruses are often more of a bother than a threat.Pathogenic viruses are only the ‘tip of the iceberg’ of virus types, and the more that is learned about the biological world the more scientists are coming to realise the critical role that viruses play in life.48The fact that so few kinds of microorganisms are pathogenic is evidence for the mutation theory of the origins of harmful viruses. Another piece of evidence is the fact that usually most strains are not pathogenic, with only one strain or a few strains causing problems. Furthermore, often viruses do not kill directly, but indirectly. For example, a hantavirus triggers a powerful immune attack by the host that may damage the host’s healthy cells.Most pathogenic viruses are often more of a bother than a threat. Of the tailed bacteriophages, only 1% are virulent, and the only known viruses that are fatal in virtually every case where infection is established (in unprotected persons) are rabies and AIDS.49The origin of this small fraction of pathogenic microorganisms is now a major focus of research.The use of viruses in medicineBacteriophages (literally eaters of bacteria) may help to control bacterial growth and spread. Almost all known bacteria have a specific predatory phage. Research indicates that in certain animals some virulent viruses may fight against bacterial infections. The advantages of using viruses to treat illness, and the reason for the importance of such a concept was reviewed by Radetsky, who noted that few persons in the past‘… wanted to fool around with live infectious viruses when you could pop a few penicillin pills … Western scientists bundled bacteriophage therapy into the dusty closets of history. Today it may be coming back. Some 50 years after antibiotics heralded the end of bacterial disease their golden age is waning … More and more microbes are developing resistance to our arsenal of antibiotic drugs, and scientists are again searching for miracle treatments. Some are looking to the past, to the almost forgotten bacteria eaters. In fact, bacteriophage therapy has never really disappeared. [Some] … doctors and health care workers routinely use bacteriophage therapy to cure a wide variety of maladies …’50The clear advantages of virus treatment include:‘… even if antibiotic–resistant bacteria were not such a burgeoning threat, phage therapy would still be appealing. Antibiotics involve certain risks. They kill a wide range of bugs, not just their particular targets, and so rid the body not just of harmful microbes but of useful ones as well—bacteria that aid in digestion, for example. For antibiotic therapy to be effective, patients must diligently take multiple doses over an extended period of time. Slack off and you may find yourself battling a renewed attack of disease, this time borne by resistant bacteria. Antibiotics can cause intestinal disorders and yeast infections. Finally, some people are violently allergic to antibiotics. In such cases, the cure can be worse than the disease. None of these problems apply to bacteriophages. Phages prompt no allergic reactions and are notoriously finicky—they target only the bugs they’re supposed to. And if you miss a dose of phage, no problem. Because they reproduce within the bacteria they attack, they stay around for a few days before the body can clear them from the system.’51Though not without problems, the technique holds much promise. Some examples of alleged success include treatment of dysentery, typhoid fever, food/blood poisoning, and skin/throat/urinary-tract infections:‘If someone has an intestinal disorder, the person can drink the phage … If it is a skin infection, phage can be applied to the spot. We have developed aerosol and tablet preparations.’52Bacteriophages usually attach onto the surface of only one specific bacterial species, a fact that can be used to distinguish between bacterial strains (a process known as bacterial typing).One potential example of the use of viruses to cure disease is to employ a virus to kill a virus. A virus can become a biological weapon to seek out HIV infected cells. A benign virus coated with special proteins can seek out cells infected with HIV, and then lock onto the cell’s surface. The HIV virus carries molecules that link with receptors on the surface of cells that it infects. When the HIV molecule connects with the receptor, it allows the virus to enter. A primary receptor used by HIV is CD4, the receptor present on immune system blood cells that are the primary targets of HIV. HIV also requires the use of at least one or two other receptors present on immune system cells. One is a receptor called CCR5, which is used by HIV early in the disease to infect a macrophage. Another receptor, the CXCR4, is used by HIV later to infect T-cells.Researchers used this information to coat the surface of a harmless virus with the molecules used by HIV to invade cells. The altered virus then was exposed in the laboratory to HIV-infected cells. The hunter virus coated with CD4 and CCR5 successfully locked onto HIV-infected macrophages. When coated with CD4 and CXCR4, the hunter virus sought out and locked onto HIV infected T-cells. In both cases, the hunter virus ignored normal cells that were not infected with HIV. ‘This approach could offer a way to deliver antiviral genes directly to HIV-infected cells in vivo …’53Viruses and the genetic revolutionAn infected animal cell can express thousands of copies of many kinds of proteins, but can produce only enough viral proteins for as many as six viruses. On the other hand, if the viral protein genes are spliced into a bacterium’s DNA by recombinant DNA means, the bacterium will mainly manufacture these viral proteins, making it far easier to separate and study them. This greatly simplifies the process of genetic research. Another advantage of using viruses in research is that virtually all viruses of a particular strain are identical.An infected animal cell can express thousands of copies of many kinds of proteins.Just how critical viruses are for medical and molecular research is now obvious to all molecular biology researchers. Zimmerman and Zimmerman (1993) noted that in molecular biology ‘today is the day of the virus’ and ‘nothing being studied in medicine, nothing in biology, is more important.’54Among the many tools that are critical in molecular biology, and that were either discovered in viruses or exist because of viruses, include: reverse transcriptase, restriction enzymes made by bacteria to control viruses, and many other enzymes. This research has aided virologists enormously in exploring the relationship between the virus and its host, and the mechanism of pathogenicity.The gene carrier function of viruses might soon be brought into service to perform a critical role in curing genetic diseases. Genetic defects cause over 5,000 known diseases, including Huntington’s chorea, sickle cell anaemia, and cystic fibrosis. The present goal of gene therapy, which was tried first with cystic fibrosis, is to load virus-carriers with healthy genes and then infect the relevant tissues so that the cell incorporates the new virus-carried genes into its own DNA. Viruses are ‘the ideal way to transport genes because they naturally infect cells to deposit genetic material.’55The most common vector virus, Moloney Murine Leukaemia Virus, has been used in about three-quarters of gene therapy treatments tried so far. Viruses modified by adding the genes for the enzyme cre–recombinase effectively cause the virus to ‘commit suicide after dispatching the therapeutic gene.’56Specifically, the cre–recombinase cuts out the viral DNA, leaving behind only the therapeutic genes. This reduces the likelihood that the virus will cause problems, or that its genes will be spliced in the wrong place.Viruses are still a source of major breakthroughs in genetic therapy. Researchers now have found a virus that‘… likes to hang around on its own … [which] has solved a vexing problem for scientists who have to shuttle foreign genes into mice … The technique … could vastly accelerate and simplify the analysis of new genes. Genetic research took a great leap forward when biologists discovered more than a decade ago that they could incorporate new DNA into a developing mouse embryo simply by injecting it straight in. But this technique suffers from one big drawback. Many millions of copies of a gene are injected into the embryo at once, and for unknown reasons they tend to mingle and form a long chain of genes before splicing themselves into the mouse chromosome.’57This virus may solve this aggregation problem because it usually infiltrates the chromosomes one at a time, evidently due to proteins that bind at the end of DNA and function as caps to prevent the viral copies from linking together.Virus therapy is especially promising for some neurological disorders (including Alzheimer’s and Parkinson’s), and many inherited disorders and types of brain tumours. A major difficulty in treating brain disorders is that many substances simply will not cross the blood/brain barrier. Certain viruses can pass through the blood/brain barrier to carry new genes to restore health. More than 100 different clinical trials are under way to research this very promising therapy.58Lentiviral vectors seem especially promising. Modified Herpes virus strains have already been used to treat brain tumours successfully in mice. This particular research used a virus that multiplied inside the tumour cells, producing an enzyme to function as a catalyst to convert a non-toxic drug into a compound that destroys only tumour cells.59The immune systemThe immune system of vertebrates usually is a highly effective defence against nearly all pathogenic viruses. When things go wrong, the problem often is caused by factors such as an immune system weakened by a genetic mutation, poor diet, poor sanitation, exposure to new pathogens (or such high numbers of pathogenes that the immune system is overloaded), emotional stress, lack of sleep or lack of exercise. Some viruses have the ability to change their antigenic structure so that the body’s defence system perceives it as a new, unknown foreign organism.Viruses generally do not evolve or mutate to overcome their hosts’ immune systems, but as Morse notes, the crucial event in generating new strains ‘has not been mutation but the successful reshuffling of preexisting genes.’60Many of these genes may have been transferred from animals. Thus their pathogenesis may be due not to design, but rather to an accident. Consequently, the host must develop a completely new immune response to the invaders—which takes time. For this reason, the acute phase of most illnesses lasts at least 2–3 days—until the body’s defence response can develop sufficiently to destroy the invaders. Flu, colds (rhinovirus infection), and the AIDS virus are more adept than most viruses at using this genetic process of reshuffling genes to produce new strains.Fig. 7. Diagrammatical representation of a bacterial cell carrying a multiple antibiotic resistance plasmid. Resistance genes for Ampicillin, Tetracyclin and Chloramphenicol designated Ampr, Tetr and Cmr, respectively.This reshuffling, often referred to incorrectly as a mutation, usually is a designed response to allow survival of the virus. Under ordinary circumstances, certain genes manufacture surface proteins that enable the host’s immune system to identify a virus as foreign. However, when shuffling of genes by a virus results in the production of new antigenic proteins, the virus is not immediately recognised by the immune system, thus slowing down the immune response. This gene reshuffling also occasionally may splice genes in the wrong place in the genome, producing pathogenic bacteria or viruses as discussed above.Beyond these programmed changes, we have no clear evidence of the evolution of viruses. All the extant evidence indicates that ancient viruses are identical to those found today.61The body’s defence system involves more than just the immune system. The skin excretes RNase, which cuts up the RNA in RNA-based viruses. The skin also secretes magainins, which can kill pathogens. This complex system almost always is effective; thus, the trillions of viruses all around us rarely cause problems.SummaryVirology is a relatively new field of study. Many researchers have concluded that we are now at the same point in our understanding of viruses that scientists were in researching bacteria at the turn of the 20th century. Viruses now are known to serve several beneficial roles, and research has indicated several others may be important. According to this model, disease is not a result of viruses as much as a breakdown of a virus/host relationship. Thousands of virus types exist in host cells without problems. Problems that do cause disease are a result of reshuffling of virus genes, genetic mutation of the host, or a breakdown in the general health of the host organism. Research is showing that viruses are a critical part of life. Holmes has noted:‘For sheer numbers, no other ocean beings can match viruses. Thousands, sometimes even millions of these molecular parasites inhabit every drop of surface seawater, outnumbering even bacteria by 10 to 1 … evidence that suggests that viruses are a powerful force in the sea, and one that determines how many plankton and ultimately how many fish, and even humans, an ocean ecosystem can support … viruses must have a profound influence on the entire oceanic ecosystem. When protozoans eat bacteria, energy passes along the food chain leading from protozoa to other zooplankton to larger predators, including fish. But when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. “Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.’62AcknowledgementsI wish to thank both Bert Thompson and John Woodmorappe for their suggestions and extremely helpful feedback.References and notesWoodmorappe, J., Noah’s Ark: A Feasibility Study, ICR, Santee, CA, 1996. Return to text.Young, W., Fallacies of Creationism, Detselig Enterprises, Calgary, Alberta, 1985.Return to text.Zimmerman, B. and Zimmerman, D., Why Nothing Can Travel Faster than Light,Contemporary Books, Inc., Chicago, IL, 1993. Return to text.Hsiung, G.D., Diagnostic Virology, Third Edition, Yale Univ. Press, New Haven, CT, 1982. Return to text.Curtis, H., The Viruses, The Natural History Press, Garden City, NY, 1966. Return to text.Stanley, B., Animal Viruses, Vol. 3 Academic Press, Inc., New York, 1959. Return to text.Valentine, R.C. and Pereira, H.G., Antigens and structure of the adenovirus, J. Mol. Biol.13(43):13–20, 1965. Return to text.Jensen, M., Wright, D. and Robinson, R., Microbiology for the Health Sciences,Prentice Hall, Upper Saddle River, NJ, 1996. Return to text.Gallo, R.C., The AIDS Virus, Scientific American 256(1):37–48, 1987. Return to text.Starr, C., Biology; Concepts and Applications, Wadsworth Pub. Co., Belmont, CA, p. 292, 1996. Return to text.Simon, L.D. and Anderson, T.F., The infection of Escherichia coli by T2 and T4 bacteriophages as seen in the electron microscope, I. II. Virology 32(158):279–305, 1967. Return to text.Coombs, D. and Ariska, F., T-4 Tail Structure and Function, p. 28, 1994. Return to text.Brooks, S., The World of Viruses, A.S. Barnes, London, 1973. Return to text.Talaro, K. and Talaro, T., Foundations in Microbiology, Wm C. Brown, Dubuque, IA, p. 132, 1993. Return to text.Evans, A.S., Viral Infections of Humans, Third Edition, Plenum Publishing Corp, New York, 1989. Return to text.Stent, G.S., and Claendar, R., Molecular Genetics: an Introductory Narrative, W.H. Freeman and Company, San Francisco, p. 319, 1978. Return to text.Starr, C., ref. 8, p. 294. Return to text.Hapgood, G., Viruses Emerge as a New Key for Unlocking Life’s Mysteries,Smithsonian 18(8):126, 1987. Return to text.Margulis, L., Foreword to Sonea and Panisset, p. vii, 1983. Return to text.Margulis, ref. 16. Return to text.Karam, J.D. (editor), Molecular Biology of Bacteriophage T-4 ASM Press, Washington, D.C., 1994. Return to text.Sonea, S. and Panisset, M., A New Bacteriology, Jones and Bartlett, Boston, MA, 1983. Return to text.Mathieu, L. and Sonea, S., A Powerful Bacteria World, Endeavor 13(3):115, 1995.Return to text.Miller, R., Molecular Biology of Bacteriophage T-4, ASM Press, Washington D.C., 1998.Return to text.Mathieu, ref. 20, p. 112. Return to text.Hecht, J., Rare Bug Dominates the Oceans, New Scientist 144(1952):21, 1994. Return to text.Sonea and Panisett, ref. 19, p. 36. Return to text.Mathieu and Sonea, ref. 20, p. 114. Return to text.Miller, ref. 21, p. 71. Return to text.Sonea and Panisett, ref. 19, p. 42. Return to text.Hapgood, ref. 15, p. 126. Return to text.Brown, P., How the parasite learnt to Kill, New Scientist 152(2056):32–36, 1996.Return to text.Quoted in The San Antonio Express 1 April 1923. Return to text.Mathieu and Sonea, ref. 20, p. 112. Return to text.Glausiusz, J., How Cholera Became a Killer, Discovery 17(10):28, 1996. Return to text.Brown, ref. 29, p. 32. Return to text.Mathieu and Sonea, ref. 20. Return to text.Wiley, J., Phenomena, Comment and Notes, Smithsonian 21(4):29, 1990. Return to text.Tiedje, J.M., Microbial Diversity: Of Value to Whom? American Society for Microbiology News 60(10):524, 1994. Return to text.Homes, B., Who Rules the Waves? New Scientist 152(2054):2 supp, 1996. Return to text.Mestel, R., Sharks’ Healing Powers, Natural History 105(9):40–48, 1996. Return to text.Creager, J., Black, J. and Davison, V., Microbiology Principles and Applications,Prentice Hall, Englewood Cliffs, NJ, p. 2, 1990. Return to text..Mestel, ref. 38, p. 41. Return to text.Brown, ref. 29, pp. 35–36. Return to text.Creager, ref. 39, p. 16. Return to text.Creager, ref. 39, pp. 16–18. Return to text.Creager, ref. 39, p. 18. Return to text.Zimmerman and Zimmerman, ref. 3. Return to text.Curtis, ref. 5, p. 14. Return to text.Radetsky, P. The Good Virus, Discover 17(11):52, 1996. Return to text.Radetsky, ref. 47, pp. 54–55. Return to text.Radetsky, ref. 47, p. 56. Return to text.Enders, M., et al., Targeting of HIV-and SIV-Infected Cells by CD4-Chemokine Receptor Pseudotypes, Science 278:1462–1463, 1997. Return to text.Zimmerman and Zimmerman, ref.3, p. 274. Return to text.Hotz, R., Researchers Alter Viruses to Combat Brain Disorders, The Journal Gazette, pp.2, 20 November 1996. Return to text.Coghlan, A., This Message Will Self-Destruct … , New Scientist 151(2042):20, 1996. Return to text.Cohen, P., Lone Virus Speeds the Gene Shuttle, New Scientist 151(2044):23, 1996. Return to text.Hotz, ref. 52, p. 1. Return to text.Hotz, ref. 52, p. 2. Return to text.Morse, S., Stirring up Trouble; Environmental Disruption Can Divert Animal Viruses into People, Science 30(5):20, 1990. Return to text.For a discussion of this, see Herrmann, B. and Hummel, S., Ancient DNA, Springer, New York, NY, 1994. Return to text.Holmes, B., Who Rules the Waves? New Scientist 152(2054):8–9, supp, 1996. Return to text.Luria, S.E., Darnell Jr., J. E., Baltimore, D. and Campbell, A., General Virology, John Wiley and Sons, New York, NY. p. 36, 1978. Return to text.Luria, ref. 63, p. 159. Return to text.Luria, ref. 63, p. 228. Return to text.

GGRE scores and other standardized test scores are used by many graduate programs to try to predict applicants’ academic performance. But low GRE scores can be overcome with strong letters of recommendation from professors and employers who know you well, and by strong academic records and a compelling personal statement.The importance of GRE scores depends on the specific field you want to enter, and on specific program requirements. If you are interested in how graduate school admissions committees make decisions, our CEO Gabe Ignatow, who moonlights as a Sociology Professor (just kidding), is answering questions in the forum on TheGradCafe.com under the alias SocProf. He’s also available on Quora, and of course you can reach us via email at [email protected] information on admissions counseling and application help from GradTrek partners is coming soon. In the meantime, check out some of our preferred graduate school counseling resources, including GradTrain and Accepted.com.How to make the best use of GradTrek’s degree search engine.GradTrek degree search uses program interests, location, GPA and test scores (GRE, TOEFL, GMAT) to find the masters degree programs that fit your criteria. The algorithm shows the programs that best matches the search criteria and will give you an idea of where it would be best to apply. Search recommendation results have extensive content aggregation and include useful information like, University pages, Catalogs, Videos, Inside information and Social media links like Facebook, LinkedIn, Professor Ratings. 15 minutes with this free tool can save you days of research on internet.1. Start on a laptop or desktopGradTrek works well on phones/tablets but a desktop or laptop computer is recommended. GradTrek is a powerful piece of software with many features, and everything goes more smoothly when you have more screen space.2. Focus on the Subjects pageThis is the most important page in the survey. We recommend coming back to this page several times to adjust your subject searches. Our database includes over 400 subjects, and many degrees fall into multiple subject categories. Don’t choose a Specific Degree unless absolutely necessary – there are almost a thousand different degree types in our data set. You’re better off choosing either doctoral-level, masters-level, or certificate-level degrees and then choosing subjects. This way you’re likely to find types of degrees that you may not have known about.3. Enter the preferred locationSpecify your choice of school location – options include distance from zipcode, or choose one or more of the States, Regions or entire US.4. Tuition costSpecify the importantance of tuition cost – Very little, Moderately and A great deal. In general, it is better to choose “Very little” on the slider scale and later narrow down the results based on tuition costs data from University pages.5. Test ScoresOptionally, enter your test scores. Gradtrek is probably the only site which uses your GPA and other standardised test scores to match you to University programs.5. The results of your degree searchA list of recommendations sorted by best fit are provided. The GradTrek database has every accredited university in US to make sure we provide a comprehensive list of results. Scroll down the list to find the next best options. The counter on the top updates in real time as you modify the search criteria. This helps in expanding (or narrowing) your criteria to get to manageable list of programs. You can run the survey multiple times, tweaking the search criteria.Program and Degree Details Page – Clicking a program will take you to program details page has extensive content aggregation and includes useful information like, University page, Catalog, Videos, Social media like Facebook, Professor Ratings, and also inside information. You can takes notes using the notes feature and save a program using the “+” sign. A snapshot of the program details page is below.When you reach GradTrek’s results page, whatever you do–don’t stop! You can click on the program to navigate to the degree program page, or on the “+” button to save the program to your profile. From there you can write notes for each program, and your notes will be automatically saved.GRE Graduate School Requirements was last modified: May 18th, 2016 by Sudhir Nayak« An MBA with a 2.8 GPA?An MBA with low GMAT scores? »Standardized Testing Preparation: The TOEFL Contents Introduction...................................................................................................................................................2 Which test should I take?..............................................................................................................................3 Philadelphia Testing Sites and Fees..............................................................................................................3 Creating a TOEFL Study Plan ......................................................................................................................4 General Testing Vocabulary .........................................................................................................................6 General Testing Speaking Practice ...............................................................................................................7 More Advanced Listening Practice...............................................................................................................9 Practice Speaking Prompts .........................................................................................................................10 General Writing Practice.............................................................................................................................11 TOEFL Overview .......................................................................................................................................12 Speaking Tips..............................................................................................................................................12 Reading Sample Question...........................................................................................................................13 TOEFL Writing: Integrated Tasks and Independent Tasks ........................................................................18 Sample TOEFL Writing Questions:............................................................................................................19 Web Resources............................................................................................................................................32 Writing 2 (last updated August 2014) Introduction This packet reviews basic testing strategies for the TOEFL. It is highly recommended to use this packet in a Conversation Partner session, but it can also be used for self-study. Start with general vocabulary, speaking and reading practice for comprehensive language review relevant to multiple tests. Further practice can be found under “Web Resources.” All answers to grammar exercises are included. You will also need headphones and internet access for some of the listening and speaking prompts. The TOEIC and IELTS packets also offer questions that are similar in nature and could be used for additional practice. Writing 3 (last updated August 2014) Which test should I take? I am a non-native speaker applying to… An undergraduate program in the U.S. TOEFL; ACT or SAT TOEFL is more commonly accepted in U.S. universities, although some schools now take the IELTS too. An undergraduate program in the UK, New Zealand, or Australia IELTS and Cambridge English Language Assessment tests As of 2014, the British council is no longer accepting TOEFL or TOEIC scores to obtain UK visas! A graduate program in the U.S. GRE; TOEFL The GRE is the test required for most native and non-native speakers applying to graduate level programs. In addition, non-native speakers may be required to take the TOEFL or IELTS exam. A graduate program in the UK, New Zealand, or Australia Cambridge English Language Assessment As of 2014, the British council is no longer accepting TOEFL or TOEIC scores to obtain UK visas! Business school GMAT; TOEIC The TOEIC is similar to the TOEFL and IELTS, but it specifically tests workplace English. Law school LSAT The LSAT is taken by native and non-native speakers applying to law school. Philadelphia Testing Sites and Fees TOEFL ibt: $180 Test dates usually offered twice a month Prometric Testing Center 601 Walnut Street Curtis Center Suite 150 West United States of America 19106 215-238-8410 https://www.ets.org/toefl/ibt/register/centers_dates/ Writing 4 (last updated August 2014) Creating a TOEFL Study Plan There are a few different ways to study for the test. First, we recommend the following: 1. First, take a full-length practice test to identify areas that are most difficult for you. You may need to study some portions of the test more than others. Plan to take at least one practice test every 1-2 weeks to familiarize yourself with the test format. 2. When taking practice tests, pretend it is a real test. Go to a room with no distractions and if taking a paper-based version of the test, set a timer to follow the exact time allotment of the actual test. 3. We also recommend purchasing your own, up-to-date test prep book (check the publication date!). ETS has many book recommendations, as does Amazon. Although there are a lot of online resources, it’s helpful to have a book that you can write in and highlight. 4. Take at least one “rest day” to read fun things in English that aren’t study materials. Read news articles, watch a movie in English, or try reading a short story or poem (Here’s a local literary magazine with fiction stories and poems: http://www.philadelphiastories.org/) Plan 1: Devote each week to a different portion of the test. Example: Week 1: Speaking Week 2: Listening Week 3: Writing Week 4: Vocabulary (it actually helps to study a little vocabulary each week, since you likely won’t remember words if you memorize them quickly and in large quantities). Plan 2: Combine questions from each section for a daily study plan. Here’s one way you could structure a daily study plan that addresses each section of the test. Daily Plan: Study 1-2 new vocabulary words a day from a TOEFL list (10 per week). Don’t just memorize the definitions; practice using them in actual sentences! Most dictionaries have examples of sentences. Study one listening and one speaking question, and outline or write one practice essay. Take time to review the essay for grammatical issues. If you’ve forgotten a grammar rule, pick up a grammar textbook or go online and do a few practice grammar exercises. Learn one or two new idiomatic or transitional phrases a week. A good list can be found here: http://www.elc.byu.edu/classes/buck/w_garden/classes/buck/transitions.html and here: https://owl.english.purdue.edu/owl/resource/574/02/ Writing 5 (last updated August 2014) Learn one or two Latin and Greek roots a week. These are very helpful because even if you don’t know a word’s definition, you can guess its meaning if you know the root! A good list can be found here: http://www.readingrockets.org/article/40406 and here: http://academic.cuesta.edu/acasupp/as/506.HTM Online Study Plans: http://toeflgoanywhere.org/toefl-practice#whats-your-study-personality Using this website, figure out how you learn best, then download a free study guide. The Magoosh TOEFL blog also has a one-month study plan: http://magoosh.com/toefl/2013/one-monthtoefl-study-schedule/ Do NOT try to study the day before the test. Instead, just try watching a TV show you like in English or reading a short news article to keep yourself immersed in the language. Writing 6 (last updated August 2014) General Testing Vocabulary This page includes vocabulary that is good to study for any standardized test, as well as example sentences that might be used on a test. Affect and effect: How does the globalization of English affect other languages? According to the passage, what are the long-term effects of radiation exposure? Analogy: In the passage above, “a pack of wolves” is an analogy for what? Classification: The Dewey Decimal system is a form of book classification used in libraries. Conclude: What did the researchers conclude at the end of their study? Condition: What conditions must be met for a number to be prime? Connotation: In the passage, fast food has a negative connotation with laziness. Determine: How did scientists determine the origin of the fossils? Discourse: In sentence 5, the phrase “academic discourse” refers to language used in the classroom. Draw conclusions: We can draw conclusions about the author’s emotions based on his word choice. e.g. (for example) Legumes (e.g., beans and lentils) contain healthy fats. Genre: What is the genre of the passage? i.e. (in other words): The recent boycott (i.e., the embargo on imported goods) has slowed business. Impact: According to the argument above, how does pollution impact the fishing industry? Metaphor: In the text, “the lion” is a metaphor for the government. Passage: What can we infer from this passage? Significant: What significant changes does the author propose? Symbol/symbolize: What does the color black symbolize in the passage? Text: What is Smith’s analysis of the text? Tone: Which sentence below proves that the author’s tone is humorous? Valid/Invalid: If a=c, which argument is invalid? Period: In what time period does the story take place? Writing 7 (last updated August 2014) General Testing Speaking Practice For this section, you will need headphones and/or a quiet space and an internet connection. Most of these practice questions use 3-minute TED talks and Upworthy videos. Note that there are a variety of accents: non-native, American, and British. Practice 1: Ariana Huffington: How to succeed? Get more sleep http://www.ted.com/talks/arianna_huffington_how_to_succeed_get_more_sleep Based on what the speaker says in the video, decide if the statements below A: support the speaker’s claims B: do not support the speaker’s claims or C: information is not given. 1. Many people think that sleep deprivation is a sign of being productive and busy. 2. People are making poor decisions because they get too much sleep. 3. Having a high I.Q. means that you’re a good leader. Practice 2: Lee Cronin: Print your own medicine http://www.ted.com/talks/lee_cronin_print_your_own_medicine True or False? The 3-D printer in the talk is being used to print: a. Fabrics b. Beakers and test tubes c. Food How will the 3-D printer make medicine? a. Using special ink that prints molecules b. Using hair samples c. Using a superbug Someday, the 3-D printer will be able to print medicine specific to a person by using: a. That person’s special ink b. That person’s DNA c. That person’s image Writing 8 (last updated August 2014) Practice 3: True or False Lalitesh Katragadda: Making Maps to Fight Disaster, Build Economies http://www.ted.com/talks/lalitesh_katragadda_making_maps_to_fight_disaster_build_economies 1. Only 20% of the world was mapped in 2005. 2. Google Map Maker allows people to map things locally. 3. Maps could help in times of disaster by revealing hospitals and unknown roads. Practice 4: Matching 1. GPS 2. Characteristics of storms 3. Names of storms in 2010 4. Early origins of humanizing storms 5. Sixth sense A. Greek gods B. Alex, Bonnie, Collin C. Service area in 0.5 miles D. Mind reading E. Dangerous and unexpected Writing 9 (last updated August 2014) More Advanced Listening Practice Short Answer Listening Practice 5 Sarah Parcak: Archeology from Space http://www.ted.com/talks/sarah_parcak_archeology_from_space a. In what country was this research conducted? b. What kind of data was used to find an ancient city? c. What did the archeologists find five meters down underneath the mud? d. Who is being trained to use the satellite technology so that they can make discovers? Multiple Choice Listening Practice 6 Robin Nagle: What I discovered in New York City Trash http://www.ted.com/talks/robin_nagle_what_i_discovered_in_new_york_city_trash 1. Who cleans up the trash in New York City? a. Private companies b. Volunteers c. The Department of Sanitation 2. What is one reason that being a sanitation worker a dangerous job? Choose the best answer. a. People throw away too much trash b. Motorists do not pay attention when driving around garbage trucks c. People ignore sanitation workers 3. What does the speaker suggest at the end of the talk? a. Clean up your own trash b. Pay sanitation workers more c. Thank sanitation workers for what they do Answer Key: Practice 1: 1. A 2. B (people are making poor decisions because they are getting too little sleep, not too much) 3. B (The speaker says that having a high I.Q. does not mean you are a good leader) Practice 2: 1. B. Beakers and test tubes 2. A. Using special ink that prints molecules 3. B. that person’s DNA Writing 10 (last updated August 2014) Practice 3: 1. False (15% of the world was not mapped in 2005) 2. True 3. True Practice 4: • A: 4 • B: 3 • C: 1 • D: 5 • E: 2 Practice 5: a. Egypt b. Satellite data (or topography data) c. Pottery d. Young Egyptians Practice 6: 1. C. Department of Sanitation 2. B. Motorists do not pay attention when driving around garbage trucks 3. C. Thank sanitation workers for what they do Practice Speaking Prompts Listen to the video “Hannah Brencher: Love letters to strangers.” http://www.ted.com/talks/hannah_brencher_love_letters_to_strangers Do you ever write letters? For whom do you write them and why? Do you think letters are better than writing emails or texts? Why or why not? Writing 11 (last updated August 2014) General Writing Practice Look at a chart or graph and summarize information from the chart by selecting important features and comparing/contrasting them. Read a statement about a specific topic and provide your opinion on the topic. Provide relevant examples from your own knowledge or experience. Should more money be put into space exploration? Why or why not? Writing 12 (last updated August 2014) TOEFL Overview The TOEFL ibt (internet-based test) is the most common test form used, although some countries still use the pbt (paper-based test). The test has a reading, speaking, listening, and writing section. Reading: 60-80 Minutes (36-56 questions) Listening: 60-90 minutes (34-51 questions) Break (10 minutes) Speaking: 20 minutes (6 tasks) Writing: 50 minutes (2 tasks) Speaking Tips For the speaking portion, you have 60 seconds to prepare and respond to a question. Do not use words that you do not know how to pronounce or properly use in a sentence. You lose points for incorrect pronunciation or wrong usage of idioms and vocabulary words. Note that some questions will require you to read a passage, and some will require you to read a passage and then listen to two people discussing the topic. To practice, set a timer and try answering some basic questions first. Basic structure: 1. State your main opinion or argument 2. Provide 2-3 examples (use details to support your answer) 3. Brief concluding statement As you get more practice, you can move on to the difficult questions. Sample questions 1. Who is an important figure in the history of your country? Explain why he/she is or was important. 2. Air pollution is a huge problem in many big cities. What are three ways that people can lessen pollution in their everyday life? 3. Online courses are becoming popular alternatives to studying in a classroom. Would you prefer to study online or in a class? Provide examples and details to support your answer. 4. Describe a hobby you love. Why is it so important to you? Why does it interest you? Writing 13 (last updated August 2014) Example of a question and answer: Reading books is one of my favorite hobbies because there is always something new and interesting to read. First, reading is important to me because I can learn about new topics that I might not study in school. I can learn about new worlds, cultures, and vocabulary just from reading. Second, I love to read because it reduces my stress. I love to enter a new world and follow the characters in their emotional journey. Third, reading allows me to practice my English and better understand English grammar. In conclusion, I never get bored while I’m reading. There are so many new worlds to explore. Reading Sample Question Despite Protests, Canada Approves Northern Gateway Oil Pipeline By Ian Austin Excerpted from: http://www.nytimes.com/2014/06/18/business/energy-environment/canada-approvesnorthern-gateway-pipeline.html?ref=science&_r=0 1 The Canadian government’s approval of a major pipeline running from the Alberta oil sands to a new port on the coast of British Columbia has intensified opposition from aboriginal groups, environmentalists and community advocates. 4 The Northern Gateway project, which the government approved on Tuesday as expected, would send heavy, oil-bearing bitumen to Asia, giving Canadian producers better access to the world markets. The pipeline, being built by Enbridge, has been championed by the federal government as a way to diversify Canada’s energy industry from its current dependence on exports to the United States. 10 But opponents in British Columbia, who span the political spectrum, threatened to block the pipeline altogether. The fear is that the pipeline would make the province vulnerable to an oil spill, damaging the rugged and scenic coastline. 13 Tom Mulcair, the leader of the opposition New Democratic Party, said that Prime Minister Stephen Harper and his Conservative government had ignored broad public opinion. 16 “Stephen Harper continues to act as if this is 1948,” Mr. Mulcair told reporters outside of the House of Commons. “You can no longer force pipelines from the top down.” Calling oil tankers off the coast of British Columbia “madness,” Mr. Mulcair said that the decision was a “severe threat to social order, social peace.” Writing 14 (last updated August 2014) 20 In the statement, Greg Rickford, the minister of natural resources, acknowledged that Enbridge’s efforts to win over British Columbia and native groups had fallen short. “The proponent clearly has more work to do in order to fulfill the public commitment it has made to engage with aboriginal groups and local communities.” 25 The president and chief of Enbridge, Al Monaco, seemed to agree during a conference call with reporters. “The economic benefits are not enough to secure public support,” he said. 28 The company must meet about 100 conditions imposed by the regulator before construction begins. Mr. Monaco declined to say how long that would delay construction, but he suggested at one point that it would take at least four years. 31 The most pressing problem is addressing the concerns of the native Canadian tribes. About a decade ago, the Supreme Court of Canada ruled that such native groups must be consulted and accommodated about projects that cross their land. The definition of both terms remains fuzzy, but most legal experts say that the native groups do not have a veto. 36 Still, such groups are preparing for a fight. Art Sterritt, the executive director of Coastal First Nations, an alliance of nine native groups opposed to the pipeline, said his organization would take legal action and form political alliances to block the project. On Monday, the Coastal First Nations formed a group with Unifor, formerly the Canadian Auto Workers union, and several environmental groups to quash the project. 42 The main issue for his members, Mr. Sterritt said, was the oil industry’s inability to demonstrate that it could effectively clean up coastal oil spills. If legal and political challenges are ultimately unsuccessful, Mr. Sterritt added, “our people will be out there stopping the bulldozers.” 1. The word “championed” in line 7 is closest in meaning to: a. Won b. Supported c. Competed d. Agreed 2. In paragraph 9, why does the author include that the native groups must be consulted and accommodated? a. To support the claim that environmentalists fear oil spills b. To support the economic benefits of the pipeline c. To explain why aboriginal groups have a stake in the discussion d. To explain why aboriginal groups are powerless Writing 15 (last updated August 2014) 3. Which of the following can be inferred from paragraph 2 about the federal government’s support of the pipeline? a. The pipeline has full support b. The pipeline will be built quickly with the help of the Northern Gateway project c. Lessening U.S. imports will strengthen the Canadian economy d. The Asian oil market is failing 4. According to paragraph 3, who opposes the construction of the pipeline? a. Aboriginal groups b. Politicians c. Various stakeholders d. The Northern Gateway project 5. The word “spectrum” on line 10 is closest in meaning to: a. Range b. Diversity c. Level d. Ratio 6. The word “pressing” on line 31 is closest in meaning to: a. Forceful b. Desperate c. Urgent d. Complex 7. According to paragraph 2, all of the following phrases are true EXCEPT: a. Canada will now have access to Asian oil markets. b. The Canadian government wants to diversify its energy industry. c. The energy industry will stop exporting to the U.S. d. Enridge will be building the pipeline. 8. The phrase “from the top down” on lines 17 and 18 is closest in meaning to: a. Power relationships that move from the weakest to the strongest group b. Lying face-down c. Analyzing in detail d. Power relationships that move from the strongest to the weakest group 9. The word “fuzzy” on line 34 is closest in meaning to: a. Furry b. Unclear c. Mysterious d. Diverging Writing 16 (last updated August 2014) 10. Paragraph 5 supports which of the following statements? a. Building the pipeline could lead to an oil spill. b. The decision-making process used to approve the pipeline is antiquated. c. The pipeline must be approved from the top down. d. Oil tankers off the coast of British Columbia are angry. 11. Which of the sentences below best expresses the essential information in the following sentence? The definition of both terms remains fuzzy, but most legal experts say that the native groups do not have a veto. Incorrect choices change the meaning in important ways or leave out essential information. a. Although legal experts agree that native groups cannot overturn the decision, their other rights are clear. b. The native groups’ rights are weak, but the native groups have legal rights. c. The native groups’ rights are in disagreement, but the majority of legal experts agree that no one can oppose the vote. d. The native groups’ rights remain unclear, but most legal experts agree that the native group cannot vote against the decision. 12. According to the passage, who is opposed to the pipeline for environmental reasons? a. Al Monaco b. Greg Rickford c. Steven Harper d. Art Sterritt 13. Look at the four letters (A, B, C, and D) that indicate where the following sentence could be added to the passage in paragraph 6. If the environment were harmed, this could reduce tourism to the region and also affect wildlife habitats. Where would the sentence best fit? (A)But opponents in British Columbia, who span the political spectrum, threatened to block the pipeline altogether. (B) The fear is that the pipeline would make the province vulnerable to an oil spill, damaging the rugged and scenic coastline. (C) Tom Mulcair, the leader of the opposition New Democratic Party, said that Prime Minister Stephen Harper and his Conservative government had ignored broad public opinion. (D) Choose the place where the sentence fits best. a. Option A b. Option B c. Option C d. Option D Writing 17 (last updated August 2014) 14. An introductory sentence for a brief summary of the passage is provided below. Complete the summary by selecting the THREE answer choices that express the most important ideas in the passage. Some sentences do not belong in the summary because they express ideas that are not presented in the passage or are minor ideas in the passage. This question is worth 2 points. Write your answer choices in the spaces where they belong. You can write in the number of the answer choice or the whole sentence. A pipeline through Canada has been approved by the federal government, but faces opposition from environmentalists, aboriginal groups, and local communities. • • • Answer choices (1) The government has elected to open up its world market by expanding exports to Asia, which will lessen its reliance on the U.S. for business. (2) Aboriginal communities have a stake in the decision, although the exact outcome is still unclear. (3) Local groups will be out there stopping bulldozers if the pipeline is built. (4) Aboriginal groups have a right to accommodations if certain projects cross their land. (5) Environmental groups fear that oil spills and damage to the landscape could result from the pipeline construction. (6) Enbridge and Northern Gateway Project were both approved by the government. Writing 18 (last updated August 2014) TOEFL Writing: Integrated Tasks and Independent Tasks Integrated tasks ask you to summarize and compare/contrast information. Learn paraphrasing skills to master these questions. You will have three minutes to read an academic text. Then you will listen to a lecture on the same topic. Take notes while you listen. Independent tasks ask you to form your own opinions and evidence in response to a single question. General Tips: 1. For note-taking, it’s okay to abbreviate words so that you can write faster. Focus on keywords, not whole sentences. Some note-taking shortcuts: = equal to ex. Example > greater than b/n between