The Scientific Method in Theory and Practice

					The Scientific Method in
 Theory and Practice

Research & Technical Writing
     Donald Winslow
     22 January 2007
 The scientific method is a powerful tool for
     learning about the world, based on
           observation and reason.
Other ways of knowing:
 Maybe others…
The Scientific Method in Theory
• Logical positivists (e.g., Carnap, Hempel)
  – Knowledge derives from empiricism & reason.
  – Only verifiable statements have meaning.
• Karl Popper
  – Only falsifiable statements have meaning.
  – Observations have alternative explanations.
  – It is often easier to disprove than to prove.
    Steps of the scientific method
• Observe patterns.
• Devise alternative hypotheses to explain.
• Derive predictions of hypotheses.
• Design a study to test predictions.
• Perform study, record observations,
  evaluate whether predictions met.
• Revise hypothesis if necessary and
   Step one: observe patterns
• Example: Bean plants near chicken coop
  produce more pods than those on the
  other side of the garden.
   Step 2: Devise hypotheses.
• Devise one or more alternative
  hypotheses that may explain observed
• This requires inductive reasoning. There is
  no way to know at this point whether any
  hypothesis is correct.
• Example:
  – Nitrogen from manure increases growth.
  – Phosphorus from manure increases growth.
 Derive predictions of hypotheses.
• This involves deductive reasoning.
• Researcher should be certain that if the
  hypothesis is true, the prediction will hold.
• Example: Bean plants provided with
  supplementary nitrogen will produce more
• Alternatively: Bean plants provided with
  supplementary phosphorus will produce
  more pods.
Design study to test predictions.
• An experiment is a powerful study design in
  which a system is manipulated in order to
  observe results.
• Control group is treated exactly the same as
  experimental group, except for the factor of
• Example: grow beans with supplementary
  nitrogen, beans with supplementary phosphorus,
  beans with both, beans with neither.
     Step five: Perform study
Observe results.
Example: Beans with supplementary
 nitrogen produced more pods than
 controls, but beans with supplementary
 phosphorus did not. Bean plants that
 received both nitrogen and phosphorus did
 better than any other treatment.
                                Pod productivity of bean plants

Number of pods per plant






                                N           P               N+P   C
Evaluate predictions of hypotheses.
• Observation that bean plants treated with
  nitrogen produced more pods is consistent
  with nitrogen-limitation hypothesis.
• Observation that bean plants treated with
  phosphorus did not produce more pods
  falsifies phosphorus-limitation hypothesis.
• Observation that bean plants treated with
  both N & P produced more pods than
  those treated with only N…?
     Revise or refine hypothesis
            as needed.
• Nitrogen supplementation increases seed
• Phosphorus supplementation increases
  seed productivity only when there is
  abundant nitrogen.
• Design a new study to test different
  predictions of revised hypothesis.
  Falsifiability and frequentism
• If science can only proceed through
  falsifying hypotheses, how do we ever
  prove anything?
• Devise a null hypothesis of no effect.
• Test null hypothesis.
• If the null hypothesis is falsified, the
  alternative hypothesis (the explanation of
  interest) is accepted.
  Statistical hypothesis-testing
• Researchers would like to generalize
  results to entire population of interest.
• Not possible to measure every individual.
• Measure random sample of individuals
  from population.
• Draw conclusions about population from
• This is inductive (inferential) reasoning.
 The Scientific Method in Practice
• Science as a social & political
• Funding
• Peer Review
Scientists are social animals.
     Social structure of scientists
•   Work in research groups
•   Apply for funds from funding agencies
•   Hire technicians to conduct studies
•   Present results at conferences
•   Publish findings in peer-reviewed journals
    Research group at large university
•   Faculty member
•   Graduate students
•   One or more post-doctoral researchers
•   Lab and field technicians
•   Undergraduate students in research
       Research groups interact
          with each other…
• Within supporting institution.
  – (e.g. university, biotech company, research
• At conferences and meetings of
  professional societies.
• Through the process of peer review.
  Resources needed by scientists:
• Institutional support
• Scientific literature
• Money for research
  – Write grant proposals to funding agencies
• Human resources
• Access to study systems
    Seeking funds for research
• Submit grant proposal to funding agency
• Agency reviews proposal and determines
  if it is worthwhile—if the knowledge
  potentially generated is valuable and if it is
  likely the researchers will succeed.
• You will have the opportunity to write a
  research proposal in this course!
     Once funding is secured,
 research group carries out study.
• Submit abstract to professional society to
  present a talk or poster at a meeting.
• Write a manuscript to submit to refereed
• May also publish in books or conference
  proceedings or government documents,
  but main target venue is the professional
      Types of scientific journals
•   Broad scope: Science, Nature
•   Moderate scope: JAMA, BioScience
•   Specialized: Conservation Biology
•   Very specialized: Bulletin of the Oklahoma
    Ornithological Society.
        Peer review process
• Authors submit manuscript to journal.
• Editor determines if content is appropriate.
• If so, editor sends manuscript to other
  practicing scientists with similar interests.
• Reviewers read articles and send
  comments to editor.
• Editor rejects manuscript or accepts it with
  suggested revisions.
         Publication process
• Authors must usually revise a manuscript
  one or more times before final acceptance
  for publication.
• Revisions sent to editor; editor may return
  for further revisions as necessary.
• Publishing company sends page proofs to
  authors to check for errors.
• Authors send corrected proofs and journal
  issue is published.
 Obtaining grants and publishing
  papers are vital for survival of

“Publish or perish!” they say.
              Next week:
• Library resources
• Study design
• Research proposals
Read Chapter 2 & Appendix 1 in Knisely.

Supplemental readings from Gustavii:
 Chapters 1, 2, and 3

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