Practice for Causal Reasoning Science and Experimental Methods Part I - Review of Concepts- circle either true or false.

Tristan

Consider the methods for establishing facts discussed in class and decide whether the following statements are consistent with that method (true) or inconsistent with it (false). True False True False True False True False True False True False causes. True False 1. An unfalsifiable explanation can be a scientific explanation. 2. Anecdotal evidence is a kind of conclusive evidence. 3. Scientific explanations are infallible. 4. Science is a belief system with no more justification than any other. 5. No one has shown scientifically that ghosts do not exist, therefore ghost exist. 6. Because some things cant be explained means that such things have supernatural 7. Conclusive scientific explanations are right solely because they are derived from a system in which the concepts are theoretically defined and are consistent with one another.

(A) Science and pseudo-science differ in several respects: True True True True True True False 8. Pseudo-science can occur within a scientific discipline. False 9. Scientific explanations change over time, but pseudo-science rarely does. False 10. Further scientific investigation tends to correct prior errors in scientific theories. False 11. Scientific theories are supported by anecdotal evidence. False 12. Pseudo-science develops ad hoc explanations to deal with anomalies. False 13. Scientists tend to ignore anomalies and explain them away with ad hoc hypotheses.

Part II - Establishing Causal LinksShort answer 1. Explain the role of standards in establishing facts. Give examples of two kinds of standard.

2. What is an anomaly? _____________________________ ________ 3. The main value of anomalies is _____________________________

4. What is an operational definition? Give an example. _________________________________

5. What is an ad hoc explanation and how is it used?

Establishing Causal Links Establishing causal links require operations that link a suspected cause to the observed effect. Linking operations must be standardized. Standards are often inventions created for other purposes, and are as various as the kinds of phenomena to be explained. Standards include not only conceptual international standards of weights and measures, but standards are embodied in instruments such as telescope and microscope lenses, chemical analysis tools that isolate elements, spectroscopes that detect wavelengths of light, recording devices for earthquakes, photographs, film, and music, and an assortment of weighing scales and measuring tools. In addition, mathematical sciences function as standards that serve in a variety of ways to assist in establishing causal links. Standards make repetition of procedures possible. And repetition of procedures is necessary for confirmation of results of experiments. One observation is never enough to establish a causal link. Kinds of causal experiments Investigators invent experiments and while there is no one-size-fits-all procedure, there are general kinds of experiment based on the general approach. The three discussed below are distinguished on the basis of their reliability. Retrospective experiments positive results may suggest a correlation that warrants a prospective or randomized experiment, but cannot rule out other potential causes. Prospective experiments positive results may suggest that further randomized research is warranted, but cannot rule out other potential causes. Randomized experiments positive results are most reliable because it has the best chance of ruling out other potential causes.

Retrospective experiments search the past by means of records that already exist, or by designing

questionnaires. To be significant the sample size must be large, often 10,000 or more subjects. Prospective experiments find a population that already has been exposed to the suspected cause and keeps records over a course of months or years to observe what happens. To be significant the sample size must be large, but smaller groups may yield other useful information. Randomized experiments control at least two groups. The experimenters administer the suspected cause to members of one group, and do nothing to the other control group. Even a small group of 20 can yield significant results. Many such results from many different research teams can establish a causal link, when all other potential causes are ruled out. Randomized studies are often expensive, time-consuming, and in some cases, are unethical to perform on human subjects. Prospective studies are conducted when a randomized experiment is impossible for one or more of the reasons listed above. Retrospective studies are conducted primarily to find correlations (possible causal links).

Experimental Methods Directions: Briefly explain the point of asking the following questions:
Follow this model in answering:

Is the sample representative?

If the sample does not represent the isolated group under investigation, then the experimental result is irrelevant. If the sample is representative, then a higher degree of trust may be placed in the experimental result and its conclusion.

1. What does randomized mean in the context of experiment? o Random means that the sample studied in the experiment is representative of the population under study. o Lets say a population of marbles has 12 colors. A random sample should be large enough to contain each color in the porportion in which they occur in the population. 2. What are the risks of treating a proximate cause as the only causal factor?

3.

Has the experimental design ruled out confirmation bias?

4. Are there other more plausible alternative explanations for the observed phenomenon?

5. Is the conclusion too specific? 6. Is the conclusion too general?

7. Even though a randomized experiment gives more reliable results, why might a researcher decided to use a prospective experiment instead?

8. Retrospective studies can only establish correlations. So, why might a researcher spend years conducting a retrospective study?

9. Experimental operations and equipment produce new observations. Why is this important for establishing facts?

Directions: Identify the type of experiment. Then evaluate its findings (conclusion). Study links Parkinson's disease to industrial solvent By NeilBowdler Health reporter, BBC News Parkinson's can result in limb tremors, slowed movement and speech impairment, but the exact cause of the disease is still unknown, and there is no cure. Research to date suggests a mix of genetic and environmental factors may be responsible. A link has previously been made with pesticide use. Researchers wanted to examine the impact of solvent exposure - specifically trichloroethylene

(TCE) on Parkinson's disease. Their study was based on analysis of 99 pairs of twins selected from US data records: one twin with Parkinson's, the other without. Because twins are genetically identical and often share certain lifestyle characteristics, twins were thought to provide a better control group, reducing the likelihood of spurious results. The twins were interviewed to build up a work history and calculate likely exposure to solvents. They were also asked about hobbies. This study found a six-fold increase in the risk of developing Parkinson's in individuals exposed in the workplace to (TCE). "Our study confirms that common environmental contaminants may increase the risk of developing Parkinson's," said Dr Samuel Goldman of The Parkinson's Institute in Sunnyvale, California, who co-led the study published in the journal Annals of Neurology. He added: "Our findings, as well as prior case reports, suggest a lag time of up to 40 years between TCE exposure and onset of Parkinson's, providing a critical window of opportunity to potentially slow the disease before clinical symptoms appear." Water contaminant TCE has been used in paints, glue, carpet cleaners, dry-cleaning solutions and as a degreaser. It has been banned in the food and pharmaceutical industries in most regions of the world since the 1970s, due to concerns over its toxicity. In 1997, the US authorities banned its use as an anaesthetic, skin disinfectant, grain fumigant and coffee decaffeinating agent, but it is still used as a degreasing agent for metal parts. Groundwater contamination by TCE is widespread, with studies estimating up to 30% of US drinking water supplies are contaminated with TCE. In Europe, it was reclassified in 2001 as a "category 2" carcinogen, although it is still used in industrial applications. Bacteria 'linked' to Parkinson's disease
Could this bacterium cause Parkinson's disease? The bacteria responsible for stomach ulcers have been linked to Parkinson's disease, according to researchers in the US. Researchers infected mice with Helicobacter pylori and the mice went on to develop Parkinson's like

symptoms. Middle-aged mice, the equivalent of being between 55 and 65 in humans, were infected. Six months later they showed symptoms related to Parkinson's, such as reduced movement and decreased levels of a chemical, dopamine, in the brain. These changes were not noticed in younger mice. Dr Traci Testerman, from the Louisiana State University Health Sciences Center, said: "Our findings suggest that H. pylori infection could play a significant role in the development of Parkinson's disease in humans. The results were far more dramatic in aged mice than in young mice, demonstrating that normal aging increases susceptibility to Parkinsonian changes in mice, as is seen in humans." The researchers believe the bacteria are producing chemicals which are toxic to the brain. They said H. pylori was able to "steal" cholesterol from the body and process it by adding a sugar group.

The bacteria responsible for stomach ulcers may have a role in Parkinson's say researchers.

Dr Testerman said this new chemical was almost identical to one found in seeds from the cycad plant, which had been shown to trigger a Parkinson's-like disease among people in Guam. He told the BBC: "H. pylori eradication in late stage Parkinson's disease is unlikely to result in significant improvement. Certain neurons are killed before symptoms begin, and more are killed as the disease progresses. Those neurons will not grow back." He said there was some evidence that bacteria can prevent the main drug to treat Parkinson's, levodopa, being absorbed, but there was no strong evidence that people who have H. pylori in their gut are actually more likely to develop Parkinson's. He added: "The current study is interesting and suggests that the bacteria may release a toxin that could kill nerve cells. However, the results should be treated with caution. The research was carried out in mice that were infected with relatively high doses of the bacterium or its extract. While they developed movement problems, we don't know whether this was actually due to the death of nerve cells. Further research needs to be carried out".

Immune genes 'key in Parkinson's disease'

Parkinson's is a degenerative condition that affects the brain The immune system may have a key role in the development of Parkinson's disease, say US researchers. In a 20-year study of 4,000 people, half with Parkinson's disease, the team found an association between genes controlling immunity and the condition. The results raise the possibility of new targets for drug development, Nature Genetics reports. Parkinson's UK said the study strengthened the idea that immunity is an important driver of the disease. The teams were not just looking for a genetic cause of the disease, but also considered clinical and environmental factors.

Over the years, there have been subtle hints that immune function might be linked to Parkinson's diseaseDr Cyrus Zabetian,study leader. During their search, they discovered that groups of genes collectively known as HLA genes are associated with the condition. These genes are key for the immune system to differentiate between foreign invaders and the body's own tissues. In theory, HLA genes enable the immune system to attack infectious organisms without turning on itself but it is not always an infallible system. The genes vary considerably between individuals. Some versions of the genes are associated with increased risk or protection against infectious disease, while others can induce autoimmune disorders in which the immune system attacks the body's own tissues.

Low vitamin D levels 'linked to Parkinson's disease' Sunlight on the skin helps generate vitamin D
Having low vitamin D levels may increase a person's risk of developing Parkinson's disease later in life, say Finnish researchers. Researchers conducted a 30 year study of 3,000 people, published in Archives of Neurology, and found people with the lowest levels of the sunshine vitamin had a three-fold higher risk.

The researchers from Finland's National Institute for Health and Welfare measured vitamin D levels from the study group between 1978 and 1980, using blood samples. They then followed these people over 30 years to see whether they developed Parkinson's disease. They found that people with the lowest levels of vitamin D were three times more likely to develop Parkinson's, compared with the group with the highest levels of vitamin D. Most vitamin D is made by the body when the skin is exposed to sunlight, although some comes from foods like oily fish, milk or cereals. Vitamin D could be helping to protect the nerve cells gradually lost by people with the disease, experts say. Parkinson's disease affects several parts of the brain, leading to symptoms like tremor and slow movements.As people age, however, their skin becomes less able to produce vitamin D. Doctors have known for many years that vitamin D helps calcium uptake and bone formation. But research is now showing that it also plays a role in regulating the immune system, as well as in the development of the nervous system.

Vitamin target Writing in an editorial in the US journal Archives of Neurology, Marian Evatt, assistant professor of

neurology at Emory University School of Medicine, says that health authorities should consider raising the target vitamin D level. "At this point, 30 nanograms per millilitre of blood or more appears optimal for bone health in humans. However, researchers don't yet know what level is optimal for brain health or at what point vitamin D becomes toxic for humans, and this is a topic that deserves close examination." Dr Kieran Breen, director of research at Parkinson's UK, said: "The study provides further clues about the potential environmental factors that may influence or protect against the progression of Parkinson's. "A balanced healthy diet should provide the recommended levels of vitamin D. Further research is required to find out whether taking a dietary supplement, or increased exposure to sunlight, may have an effect on Parkinson's, and at what stage these would be most beneficial."

Worm could offer Parkinson's clue Scientists believe that worms could hold the key to why some people develop Parkinson's Disease. Worms share 50% of their genes with humans, including those involved with inherited Parkinson's. Dundee University researchers will study a simple worm called C. elegans to try to work out why the condition causes patient's brain cells to die. Worms will be used in this analog model study as they are one of the simplest organisms with a nervous system. The way worms' nerve cells communicate with each other is also similar to how it works in humans. Several genes, including one known as LRRK2, have been linked to the hereditary form of Parkinson's Disease. Dr Gartner's team want to understand how changes or mutations in this gene lead to the development of Parkinson's - and how drugs could stop the damage that these mutations cause to nerve cells. Dr Kieran Breen, from the Parkinson's Disease Society, said: "It's fascinating that such a simple animal as a worm can be an excellent model for Parkinson's researchers to study what happens in specific nerve cells.

"We are delighted to be funding this research with Dr Gartner in Dundee. It will help us to understand better what causes nerve cells to die in Parkinson's, and will help us to develop new treatments for the condition."

Directions: In light of your understanding of the difference between observational studies and studies that discover causal mechanisms, evaluate the judge's decision in the Daubert case: In the 1980s, two women who had taken the drug Bendectin to combat morning sickness and gave birth to children with severe birth defects. The drug is a combination of the antihistamine doxylamine and vitamin B6. William Daubert, the husband of one of the two women, and other members of the two families sued. The trial judge examined proposed evidence from nine experts and ruled that only the defendant'sthe drug maker'sexpert could testify. The defendant's physician-epidemiologist had reviewed dozens of observational studieswhich had used statistics to probe for correlations between Bendectin use and health effects in large groups of womenand concluded that the data didn't support a link between the drug and birth defects. The plaintiffs' experts had intended to refer to animal studies, which had outlined a causal mechanism by comparisons of the chemical structure of the drug with that of agents known to cause fetal harm, and an unpublished reanalysis of prior

observational and randomized studies. All these studies supported the plaintiff's claim that the drug might cause birth defects. The judge decided that because there existed a wealth of published human data observational studies (prospective and retrospective studies) that had included some 130,000 womenadmitting any evidence other than the published studies was unjustified. Directions: (a) Write a paragraph to evaluate the judge's decision in this case. (b) Decide whether it was fair to both the plaintiff (drug takers) and the defendant (drug makers). (c) Provide at least two different reasons for your decision. (d) Include at least one assumption or fact implied by or (easily inferred from) the information provided that might play a role in deciding this question.