3001-4.pptx

MEASUREMENT: OTHER CONSIDERATIONS SCALES OF MEASUREMENT Discrete vs Continuous Variables Nominal, Ordinal, Interval, Ratio Low level vs high level (degree of precision) Once data is gathered, the PRECISION (accuracy) of the measure can be later DECREASED but it CANNOT be later INCREASED Four leve...

MEASUREMENT: OTHER CONSIDERATIONS SCALES OF MEASUREMENT Discrete vs Continuous Variables Nominal, Ordinal, Interval, Ratio Low level vs high level (degree of precision) Once data is gathered, the PRECISION (accuracy) of the measure can be later DECREASED but it CANNOT be later INCREASED Four levels of measurement Level Different Ranked Distances Between True Categories Categories Measured Zero Nominal Ordinal Interval Ratio Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes SOME CONSIDERATIONS The LIKERT scale, often used in surveys, uses an ORDINAL system Strictly speaking, STATISTICS (other than particular types of statistics) CANNOT be used on ORDINAL data Thus, specifically, inferential STATISTICS should only be used on interval and/or ratio data OTHER CONSIDERATIONS If possible, use MULTIPLE MEASURES of the same variable (increase stability/reliability) The measure should be SENSITIVE to changes in the variable (a different issue from precision) Regarding sensitivity of the measure, the RANGE of the measure: Floor and ceiling effects ONE MORE CONSIDERATION The ATTRIBUTES (values) of all measures should be MUTUALLY EXCLUSIVE and EXHAUSTIVE For example, in surveys using CLOSED questions, the responses available to a respondent should be both mutually exclusive and exhaustive NORMALIZATION/STANDARDIZATION Oftentimes it is necessary to NORMALIZE the DATA for purposes of COMPARISON or COMBINATION using some type of STATISTICAL ANALYSIS (e.g., averages) “There are three kinds of lies: lies, damned lies, and statistics.” Benjamin Disraeli "He uses statistics as a drunken man uses lamp-posts... for support rather than illumination." Andrew Lang MISSING DATA Participant 1 2 3 4 5 6 Before 46 44 47 41 49 43 After 51 46 48 55 46 DEALING WITH MISSING DATA (Some Options) Participant 1 2 Before 46 44 After 51 46 4 5 6 41 49 43 48 55 46 REMOVE all CASES (rows) that contain missing data. The BEST OPTION. DEALING WITH MISSING DATA (Some Options) Participant 1 2 3 4 5 6 Before 46 44 47 41 49 43 After 51 46 49 48 55 46 REPLACE the missing data with the MEAN score. Or some equivalent. DEALING WITH MISSING DATA (Some Options) Participant 1 2 3 4 5 6 Before 46 44 47 41 49 43 After 51 46 53 48 55 46 REPLACE the missing data with an EDUCATED GUESS. DEALING WITH MISSING DATA (Some Options) Participant 1 2 3 4 5 6 Before 46 44 47 41 49 43 After 51 46 49 48 55 46 REPLACE the missing data with a RANDOM VALUE. TYPES OF RESEARCH TYPES OF RESEARCH The purpose of research might be: EXPLORATORY: cf. what DESCRIPTIVE: cf. what, where, when, who EXPLANATORY: cf. how, why or some combination of the above. Research can be BASIC or APPLIED 4 BASIC: Knowledge driven. Seeks to advance knowledge in a fundamental way. Theoretical. APPLIED: Problem driven. Seeks to find answers (solutions) to real-world problems. Non-theoretical (meaning that theory is of secondary importance). Theory may be “borrowed” or “applied” but it is not “advanced”. COMMENT: Applied research tends to have broader appeal to the general public (including politicians). 4 BASIC RESEARCH Can be exploratory, descriptive or explanatory, the latter being most common “Used” in applied research (e.g., ideas, theories, hypotheses, methods, etc.) Significant contributions (to knowledge) 4 “New” Knowledge Major Branching Points “Old” Knowledge 4 STANDING ON THE SHOULDERS OF GIANTS “If I can see further than those before me, it is because I have stood on the shoulders of giants.” Isaac Newton Long-term outlook. “The means justify the ends” (i.e., knowledge for knowledge sake) The scientific community is the primary (immediate) consumer of basic research 4 Some (long) reading … 4 When Professor Richard Jorgensen, a plant scientist at the University of Arizona in Tucson, tried to make his petunia flowers a deeper shade of purple, he had little idea that he was about to find the key to one of the hidden mysteries of life. Jorgensen was interested in the esoteric mechanism that controls the regulation of genes in plants. In pursuit of this interest in basic biology, he decided he would try to make purple petunia flowers even more purple by injecting them with the gene for pigment coloration. To his surprise, the flowers bloomed white. Instead of the two sets of pigment-producing genes complementing each other, they seemed to interact by turning themselves off. Some flowers bloomed totally white, while others were variegated – including one that his wife and collaborator, Carolyn Napoli, named the "Cossack dancer" because it looked like a man in a voluminous costume with his arms and legs outstretched. In 1990, when the research was published, Jorgensen called the phenomenon "cosuppression" because it seemed that both sets of pigment genes were preventing each other from working properly. This was one of those unexpected and counter-intuitive findings that sometimes make scientific research so interesting, yet so frustrating. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 At first it was thought that this observation was unique to petunias, but other scientists repeated the work and found it was also true for other species of plants. Then some yeast scientists got in on the act as well and found that the process worked particularly well in their beloved laboratory creature, a micro-organism called Neurospora crassa. Just to show that they had done something different, they called it by another name – gene "quelling". But no one had any clear idea as to how this quelling or cosuppression worked, or even whether it had any particular importance outside the world of plants and yeasts. At the same time as these experiments were taking place, molecular biologists had been working on something called "antisense" technology. This was a way of turning genes off using a close cousin of DNA (deoxyribonucleic acid) called RNA (ribonucleic acid). But yet again something happened that was unexpected. Scientists working on the tiny nematode worm, the species Caenorhabditis elegans, found that the antisense technique worked best when the RNA was injected in the form of a double-stranded molecule, instead of its usual single-stranded form. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 The process remained something of a puzzle until a few years later, when Andrew Fire, a researcher at the Carnegie Institution at the Johns Hopkins University looked into the problem. He too had been interested in injecting antisense material into the nematode worm to study the switching on and off of genes. "What we found was that our control experiments never worked properly. Not only was the normal gene shut off but the gene we were putting in was shut off as well." Fire couldn't help but notice that the phenomenon was very similar to the original petunia experiment he had heard about. He called it gene "silencing" – the nematode version of cosupression in petunias and quelling in yeast. "My lab worked pretty hard to sort out what the actual structure of the RNA that was causing the silencing was. We were surprised because it turned out not to be the major component we were injecting, but a contaminant that is known to be present when you make RNA in a test tube," Fire said. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 That contaminant was double-stranded RNA – when a "sense" and an "antisense" strand wrap around each other to form a single molecule, rather like the double helix of DNA. The discovery revealed that, when RNA came in its double-stranded form, it was capable of silencing genes. Fire and his colleagues, including Craig Mello of the University of Massachusetts, published their results in the scientific journal Nature on 19 February, 1998. They called their discovery "RNA interference", or simply RNAi, and said how surprised they were about the power of double-stranded RNA to silence genes. Scientists in other disciplines began to take notice. It seemed that Fire [and Mello] had discovered a way of turning off genes using RNA, and this was not what every biology student had been told to expect. In fact, the "central dogma" of biology was that RNA was the necessary intermediary in the process of turning genes on and making the proteins that are essential for life. RNA was supposed to be the lubricant that allowed genes to make proteins, not the spanner in the works. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 Now, the giants of genetics – scientists working on the Drosophila fruit fly – went buzzing into action. Everybody wanted to know what, precisely, was going on. How could RNA be acting as a genetic switch? Meanwhile, on the other side of the Atlantic, plant scientists in Norwich were also working on a double-stranded problem. One scientist there, David Baulcombe, was interested in how plants defended themselves against attack by viruses, notorious for using double-stranded RNA as their primary genetic material. Baulcombe's findings interested Fire, who was still trying to solve his own problem. Fire said: "We were still thinking about it as something that was confouding our experiments and it was a cool, odd result. Baulcombe's group had been studying viral resistance in plants and they had come to the conclusion that something about foreign RNA mimicked the virus. "Putting those two things together led to a fundamental understanding of the issue." Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 Baulcombe had reanalysed Jorgensen's petunias and other plants and found very small stretches of double-stranded RNA floating around in the cells. The teams of fruit fly scientists raced to find the same stretches of double-stranded fragments in their lab animals. They, too, eventually found small RNAs that were interfering with the action of Drosophila genes. What seemed to be happening was that the large double-stranded RNA molecules were being chopped down into smaller units of a precise length. These units formed a deadly complex with enzymes, which would identify and chop up the critical "messenger" RNA that acted as the lubricant of protein synthesis by transferring genetic information from the genes inside the cell nucleus to the protein synthetic machinery of the cytoplasm – the region outside the nucleus. Suddenly everybody realised that it would be possible to make these short, double-stranded RNAs in a test tube and tailor them to target a specific messenger RNA from a particular gene. This would mean that scientists could turn off any gene at will. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 A critical question was whether this would also work in the cells of mammals, including those of man. If it did work, the medical potential could be enormous. It would mean that we could turn off genes involved in cancer, genes that allowed viruses to infect cells, genes that were involved in tissue rejection after transplant operations and, of course, genes of viruses that had already managed to infect a healthy cell. Last month came the first hard evidence that RNA interference affected mammalian cells. Scientists have managed, in the test tube, to make human cells resistant to attack by the polio virus as well as the Aids virus, HIV. Now the focus is on trying to find ways of introducing these short strands of RNA directly into cells. Biotechnology companies are ploughing millions of dollars into different ways to adopt the technology for medical use. Scientists are already working on ways of treating liver disease by silencing the genes of the hepatitis viruses in mice and of cancer by switching off tumour-inducing genes. Connor, S. (2002). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 4 "The whole thing's been exciting really from the word go. It's clear from Jorgensen's earlier work that something really interesting and strange was going on here," Fire said. "I think it's early days but it's really exciting early days. " Connor, S. (2007). How an experiment to change the colour of a petunia led to a breakthrough in the treatment of cancer and Aids. The Independent. 2002. Two American scientists, Andrew Fire and Craig Mello, won the 2006 Nobel Prize in medicine or physiology for their pioneering research into RNA-i, published in 1998. They worked on nematode worms and, some years later, other scientists found that the phenomenon also occurred in human cells - paving the way for clinical treatments for disorders ranging from heart disease to cancer. In its citation, the Nobel Assembly said RNA-i promised to be one of the most exciting developments in medical science. "RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future" it said. Connor, S. (2007). RNA-i: Discovered in a petunia, found in flies and now causing a medical revolution. The Independent. 4 Richard Jorgensen: Now an associate professor in the department of plants sciences at the University of Arizona in Tucson. Professor Jorgensen, left, carried out the seminal work on petunias that led to the idea of the "cosuppression" of genes. One variety he produced was named "Cossack dancer", above, by his wife and collaborator. His work was published in 1990 and it made the cover of the journal The Plant Cell but it took eight years for other scientists to realise the significance of his work. THE MEN BEHIND RNA Andrew Fire: The scientist at the Carnegie Institution, an affiliate of the Johns Hopkins University in Baltimore, who first coined the phrase RNA interference in a seminal paper published in the journal Nature in 1998. Dr Fire's findings set the scene for a race to develop the technique. Gordon Carmichael: A researcher in the department of microbiology at the University of Connecticut health centre in Farmington who has followed the work on RNA interference closely. He believes the work is leading to a revolution in the understanding of genes and possible treatments for cancer and viruses. Phillip Sharp: A Nobel prize-winner at the Massachusetts Institute of Technology in Cambridge who has put his intellectual resources behind RNA interference. He heads a $350m (£250m) brain research institute and has formed a company to develop the technique using venture capital. BASIC RESEARCH The Independent RNA-i: Discovered in a petunia, found in flies and now causing a medical revolution By Steve Connor, Science Correspondent 12 April 2007 There is barely an area of biomedical science that has not been touched by the revolutionary technique of RNA-interference (RNAi), an area of research which won last year's Nobel Prize in medicine because of its importance in modern molecular biology. RNA-i allows scientists to target a gene with exquisite accuracy by giving them a precise molecular tool for gradually turning down a gene's activity, much like a dimmer switch of an electric light bulb. RNA-i seems to be one of nature's ways of controlling gene activity and it appears to be ubiquitous among all living cells. Scientists discovered RNA-i in petunia plants in the 1990s, but have since found that it occurs in almost every organism studied, from fungi to fruit flies, from mouse to man. It is possible that the process of controlling gene activity using RNA-i evolved as a primitive form of defence against the lethal genes of invading viruses, before the evolution of sophisticated immune systems in higher animals. However, it became apparent that scientists could exploit the phenomenon to target specific genes that they wanted to control. For example, they could use it to shut off the vital genes for an invading virus such as HIV - and there are plans for at least one clinical trial to do just that. Another idea was to use RNA-i to switch off the genes in a human cell that are essential for the growth of a cancer. If these "oncogenes" are turned off or silenced, the cancer should die. Again, clinical trials are being planned. A further approach is to turn off the genes that are involved in stimulating the growth of new blood vessels. If this can be done in the eye, for instance, you might have a cure for macular degeneration - when new blood-vessel growth blocks vision in the retina. One other line of research is to use RNA-i to switch off damaged genes responsible for inherited genetic disorders, such as Huntington's disease. Suddenly it was possible to talk about potential cures for previously untreatable illnesses. There appears to be no limit to the range of disorders that can be addressed with RNA-i. Now, as the latest study in Nature has shown, the technique may even be used as a method of improving the efficacy and safety of existing - as well as future - anti-cancer drugs. One of the beauties of the RNA-i approach is that it is relatively easy for scientists to make the necessary drugs. In effect, they are just small strands of the RNA molecule, which can be synthesised automatically by machine. Each strand is about 22 units long - tiny compared with the 3 billion units that make up the entire DNA molecule of the human genome. Each of these "short-interfering" strands of RNA can be targeted specifically to work against a particular gene, which is one of the reasons why the technique is so attractive. It means there is less chance of cross-reactions or unintended side effects. However, one of the biggest problems with RNA-i is what is called "delivery" - how do you make sure that the synthetic RNA molecules actually get inside the cells that matter? That is the real problem with using RNA-i on patients. Solve that, and you have a potential treatment for many of the most intractable illnesses known to man. Two American scientists, Andrew Fire and Craig Mello, won the 2006 Nobel Prize in medicine or physiology for their pioneering research into RNA-i, published in 1998. They worked on nematode worms and, some years later, other scientists found that the phenomenon also occurred in human cells - paving the way for clinical treatments for disorders ranging from heart disease to cancer. In its citation, the Nobel Assembly said RNA-i promised to be one of the most exciting developments in medical science. "RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future," it said. APPLIED RESEARCH Various types E.g., Applied-Basic, Action, Impact Assessment, Evaluation, Etc. Addresses practical issues (hence the wider appeal to the general populace – and the politicians) 5 Since the consumers of applied research are practitioners, the applied researcher must relay the findings to the consumer in a suitable way Less likely to be published. (Less likely does not mean unlikely.) Susceptible to misinterpretation and/or misuse 5