ASR – Introduction to Basic Research Methods
The student will learn concepts that will enable them to better understand andplan scientific experiments.
Types of research
Types of data
- will discuss the components of a scientific experiment, carefully consideringexperimental design and data analysis.
- will also discuss the components of a scientific paper and how to criticallyanalyze scientific work.
If we knew what it was we were doing, it would not be called research,would it?-Albert Einstein, 1879 - 1955
Research Methods
What do we do?
How do we do it?
Scientific Method
“Truth is sought for its own sake. And those who are engaged uponthe quest for anything for its own sake are not interested in otherthings. Finding the truth is difficult, and the road to it is rough.”
Ibn al-Haytham (Alhazen, 965–1039)
Scientific Method
1.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.
![MCj03971840000[1]](data/images/img5.png)
Hypotheses
• A hypothesis provides a conceptual framework to explainexisting 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 acceptedtheory.
• An accepted theory is not a fact.
![MCj04419020000[1]](data/images/img6.png)
![MCSY00861_0000[1]](data/images/img7.png)
Choosing a Hypothesis: Ockham’s Razor
• Ockham's Razor is the principle proposed by William of Ockham inthe 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 competingtheories that make exactly the same predictions, thesimpler one is the better."
•Example in medicine:
Diagnostic parsimony advocates that whendiagnosing a given injury, ailment, illness, or diseasea doctor should strive to look for the fewest possiblecauses that will account for all the symptoms.
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 thesun 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 thesun which decreases as the square of the distance.This force is generated by the will of some powerfulaliens.
Formulation of a Hypothesis
• When formulating our hypothesis, we typically formulate anull and alternative hypothesis.
• The alternative hypothesis is typically explains theobservation.
• The null hypothesis is the opposite.
• Experiments are done to reject the null hypothesis in favor of the alternative.
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 haveoccurred by chance.
Evaluation of a Hypothesis
In statistics, a result is called statistically significant if it is unlikely to haveoccurred by chance.
Evaluation of a Hypothesis
Karl Popper's hypothetico-deductive method demands falsifiablehypotheses, so that the scientific community can prove them false. In otherwords, can disprove the null hypothesis.
According to this view, a hypothesis cannot be "confirmed", because there isalways the possibility that a future experiment will show that it is false.
A hypothesis that has been rigorously tested and not falsified can form areasonable basis for action, i.e., we can act as if it is true, until such time asit is falsified.
Example: Just because we've never observed rain falling upward, doesn'tmean that we never will—however improbable, our theory of gravity may befalsified some day.
Hypothesis testing is generally used when you are comparing two or moregroups.
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 ofstars in sky, 5th century BC
-proposed that the Earth was round
[What is the null hypothesis for Pythagoras’s alternative hypothesis?]
2Indian mathematician and astronomer Aryabhata used descriptiverecords 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 experimentsattempting to make gold from other substances, 9th century,
Evidence that scientific approach to addressingquestions about natural world has been present inmany cultures for a LONG time!
modern scientific research methods began with Scientific Revolution thatoccurred in Europe in 16th, 17th centuries
Polish astronomer Nicolaus Copernicus published De RevolutionibusOrbium Coelestium (On the Revolutions of the Heavenly Spheres) in 1543
- careful observation and description of movement of planets in relation toEarth
-hypothesized that Sun, not Earth, was center ofsolar system
- planets revolved around the Sun inprogressively larger orbits in the following order:Mercury, Venus, Earth, Mars, Jupiter,and Saturn
[What is Copernicus’s null hypothesis?]
Galileo, Kepler, Newton challenged traditionalgeocentric view of universe by rejecting philosophicalapproaches to natural science by Aristotle.
Rejection of the philosophical method = publication of Novum Organum: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 researchmethodology
Four Rules of Scientific Reasoning byIsaac Newton English physicist & mathematician, 1686
Sir Isaac Newton was significant contributor to Scientific Revolution
-believed that scientific theory should be coupled with rigorousexperimentation
-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 andsufficient 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 withinexperiments, are to be esteemed universal, and
4- propositions collected from observation of phenomena should beviewed as accurate or very nearly true until contradicted by otherphenomena
Quiz on Epigenetics
1What are 2 different ways that the epigenomecan be modulated?
2Explain, in your words, the definition of theepigenome. Give an example/s.
3What is the application for the epigenome indisease?
4How are WE responsible for the epigeneticmodulation of our future generations?
Discovery Based Science
• Discovery based science is based on exploration of the data for patterns toyield 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 bediscovery based.
Parts of a Research Article
• Abstract or Summary
• Introduction
• Methods
• Results
• Discussion
• Conclusions
Critical Analysis
• Paper Goals
• Methods
• Results
• Discussion
Paper Goals
• Do the authors describe the goals of the
paper?
• What scientific question are they trying to
answer?
• This is usually described in theintroduction.
Methods
• Do the authors adequately describe the
methods used?
• Are the methods appropriate to achieve
their goals?
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?
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.
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
Why Biostatistics?
• When data is gathered, it must beevaluated
to see if the results are meaningful – testsof
statistical significance.
• When designing an experiment, howmuch
data should be gathered – experimental
design.
• Statistics used in bioinformatics, for
example, microarray analysis