ASR – Introduction to Basic Research Methods

1. ASR – Introduction to Basic Research Methods The student will learn concepts that will enable them to better understand and plan scientific experiments. Types of research Types of data - will discuss the components of a scientific experiment, carefully considering experimental design and data analysis. - will also discuss the components of a scientific paper and how to critically analyze scientific work.

2. Research Methods What do we do? How do we do it? If we knew what it was we were doing, it would not be called research, would it? -Albert Einstein, 1879 - 1955

3. Scientific Method “Truth is sought for its own sake. And those who are engaged upon the quest for anything for its own sake are not interested in other things. Finding the truth is difficult, and the road to it is rough.” Ibn al-Haytham (Alhazen, 965–1039)

4. Scientific Method • Make an observation • 2. Form a hypothesis to explain the observation • 3. Make predictions from the hypothesis • 4. Test the hypothesis with experiments and additional observations • 5. Revise the hypothesis, make new predictions, and test again.

5. Hypotheses • A hypothesis provides a conceptual framework to explain existing observations and predict new ones • We do not prove hypothesis. • We either reject them or fail to reject them. • If we do not reject a hypothesis is becomes an accepted theory. • An accepted theory is not a fact.

6. Choosing a Hypothesis: Ockham’s Razor • Ockham's Razor is the principle proposed by William of Ockham in the 14th century: “Pluralitas non est ponenda sine neccesitate”, which translates as “entities should not be multiplied unnecessarily”. • • The hypothesis which makes the least number of • assumptions that explains the observation is best. • • Translation: Keep things simple. • Better translation: "when you have two competing theories that make exactly the same predictions, the simpler one is the better." • Example in medicine: • Diagnostic parsimony advocates that when diagnosing a given injury, ailment, illness, or disease a doctor should strive to look for the fewest possible causes that will account for all the symptoms.

7. Occam’s (Ockham’s) Razor Another example • The planets move around the sun in ellipses because there is a force between any of them and the sun which decreases as the square of the distance. • The planets move around the sun in ellipses because there is a force between any of them and the sun which decreases as the square of the distance. This force is generated by the will of some powerful aliens.

8. Formulation of a Hypothesis • When formulating our hypothesis, we typically formulate a null and alternative hypothesis. • The alternative hypothesis is typically explains the observation. • The null hypothesis is the opposite. • Experiments are done to reject the null hypothesis in favor of the alternative.

9. Evaluation of a Hypothesis When doing experiments to test a hypothesis, the results must be: • Reproducible • Statistically significant In statistics, a result is called statistically significant if it is unlikely to have occurred by chance.

10. Evaluation of a Hypothesis In statistics, a result is called statistically significant if it is unlikely to have occurred by chance.

11. Evaluation of a Hypothesis Karl Popper's hypothetico-deductive method demands falsifiable hypotheses, so that the scientific community can prove them false. In other words, can disprove the null hypothesis. According to this view, a hypothesis cannot be "confirmed", because there is always the possibility that a future experiment will show that it is false. A hypothesis that has been rigorously tested and not falsified can form a reasonable basis for action, i.e., we can act as if it is true, until such time as it is falsified. Example: Just because we've never observed rain falling upward, doesn't mean that we never will—however improbable, our theory of gravity may be falsified some day. Hypothesis testing is generally used when you are comparing two or more groups.

12. History of a Hypothesis, 3 examples • other than Alhazen • 1 Greek mathematician Pythagoras • -first person to promote a scientific hypothesis • -based on his descriptive study of the movement of stars in sky, 5th century BC • -proposed that the Earth was round • [What is the null hypothesis for Pythagoras’s alternative hypothesis?] • Indian mathematician and astronomer Aryabhata used descriptive records regarding movement of objects in the night sky • -proposed Sun was the center of the solar system, 6th century • 3 Chinese alchemists invented gunpowder while performing experiments attempting to make gold from other substances, 9th century,

13. Evidence that scientific approach to addressing questions about natural world has been present in many cultures for a LONG time! • modern scientific research methods began with Scientific Revolution that occurred in Europe in 16th, 17th centuries • Polish astronomer Nicolaus Copernicus published De Revolutionibus Orbium Coelestium (On the Revolutions of the Heavenly Spheres) in 1543 • - careful observation and description of movement of planets in relation to Earth • hypothesized that Sun, not Earth, was center of solar system • planets revolved around the Sun in progressively larger orbits in the following order: Mercury, Venus, Earth, Mars, Jupiter, and Saturn • [What is Copernicus’s null hypothesis?]

14. Galileo, Kepler, Newton challenged traditional geocentric view of universe by rejecting philosophical approaches to natural science by Aristotle. • Rejection of the philosophical method = publication of NovumOrganum: New Directions Concerning the Interpretation of Nature by Francis Bacon (English phiosopher,1620) • inductive method of reasoning • superior to the philosophical approach of Aristotle • Baconian method involved repeating cycles of observation, hypothesis experimentation, and independent verification • objective, logical and empirical method • formed basis for development of scientific research methodology

15. Four Rules of Scientific Reasoning by Isaac Newton English physicist & mathematician, 1686 • Sir Isaac Newton was significant contributor to Scientific Revolution • believed that scientific theory should be coupled with rigorous experimentation • published 4 rules of scientific reasoning in Principia Mathematica (1686) that form part of modern approaches to science: • 1- admit no more causes of natural things than are both true and sufficient to explain their appearances, • 2- to the same natural effect, assign the same causes, • 3- qualities of bodies, which are found to belong to all bodies within experiments, are to be esteemed universal, and • 4- propositions collected from observation of phenomena should be viewed as accurate or very nearly true until contradicted by other phenomena

16. Quiz on Epigenetics • What are 2 different ways that the epigenome can be modulated? • Explain, in your words, the definition of the epigenome. Give an example/s. • 3 What is the application for the epigenome in disease? • 4 How are WE responsible for the epigenetic modulation of our future generations?

17. Discovery Based Science • Discovery based science is based on exploration of the data for patterns to yield new hypothesis. • It does not replace the scientific method. • It yields a way of finding new hypotheses from complex and abundant data. • Engineering approaches that build tools or inventions can be considered to be discovery based.

18. Parts of a Research Article • Abstract or Summary • Introduction • Methods • Results • Discussion • Conclusions

19. Critical Analysis • Paper Goals • Methods • Results • Discussion

20. Paper Goals • Do the authors describe the goals of the paper? • What scientific question are they trying to answer? • This is usually described in the introduction.

21. Methods • Do the authors adequately describe the methods used? • Are the methods appropriate to achieve their goals?

22. Results • Are the results meaningful? • Are the results statistically significant? • Do the results make sense given the methods used? • Are their other experiments that would clarify the results?

23. Reproducibility of Results • Result shown in an experiment should be able to be duplicated. • The results should have multiple trials, ie. need meaningful statistics. • The results should be reproducible by others.

24. Discussion • Do the authors put the results in context? • Do the results support the conclusions drawn? • Do the authors address alternative interpretations of the results? • What should be done next? Web Links for Scientific Method http://teacher.nsrl.rochester.edu/phy_labs/AppendixE/AppendixE.h tml http://www.selu.edu/Academics/Education/EDF600/Mod3/ http://phyun5.ucr.edu/~wudka/Physics7/Notes_www/node5.html

25. Why Biostatistics? • When data is gathered, it must be evaluated to see if the results are meaningful – tests of statistical significance. • When designing an experiment, how much data should be gathered – experimental design. • Statistics used in bioinformatics, for example, microarray analysis