Lecture No.

1
Research Methodology and Biostatistics Course

LOGIC THINKING &

SCIENTIFIC METHOD
Aryandhito Widhi Nugroho, M.D., Ph.D.
Neurosurgeon, Dr. H. Chasan Boesoirie General Hospital, North Maluku, Indonesia
Lecturer, Dept. of Surgery, Faculty of Medicine, Khairun University
LOGIC THINKING
• Greek “logos” The study of correct reasoning or good arguments
• Reasoning: the activity of drawing inferences
• Arguments: the outward expression of reasoning, a set of
premises together with a conclusion
• Three fundamental laws of logic
1. Law of Identity: if any statement is true, then it is true.
2. Law of Non-Contradiction: no statement can be both true
and false at the same time and in the same sense.
3. Law of Excluded Middle: any statement is either true or false
• Formal logic and informal logic
FORMAL LOGIC (SYNTATIC/SEMANTIC)
• Deductive reasoning:
• Traditional Aristotelian logic
• Modern symbolic logic
• Inductive reasoning: evaluates evidences  an argument is
probably true or false; forms:
• Analogy
• Generalization
• Mill’s methods for experimental inquiry
• Hypothetical scientific reasoning
• Statistical reasoning
• Probability
INFORMAL LOGIC (PRAGMATIC)
• The uses of argumentation in a context of dialogue, an
essentially pragmatic undertaking  a.k.a. critical thinking
• The study of:
• Language
• Classification
• Definition
• Arguments
• Problem solving
• Logical fallacies
• Formal: violation of the rules of syllogism
• Informal: pure and simple bad form of reasoning
LOGICAL FALLACIES
• An error in reasoning that renders an argument invalid
• Distorting an issue, drawing false conclusions, misusing
evidence/language
• Two main categories:
• Formal  error in deductive reasoning
• Informal  error in inductive reasoning
• Common types:
• Ad hominem
• Straw man
• Slippery slope
• Post hoc propter ergo hoc fallacy
GALILEO GALILEI
• Born in Pisa, February 15, 1564
• Began studying medicine, but then drawn more toward
Euclidean geometry, mathematics, and scientific
• “The father of modern science” ~ A. Einstein
• Astronomy, physics, and scientific method
• The features of the Moon, Venus, Jupiter’s moons
• Telescope optimization for military and scientific use
• Rigorous experiments on materials, data collection,
mathematical analysis  objective & replicable results
THE GALILEO AFFAIR
• During his lifetime, the heliocentric
model was considered heretical in the
eyes of the Catholic Church  banned
from continuing to write on the subject
• However, in 1632, Galileo published a
book: the heliocentric VS geocentric
models.
• Tried for going against the Church, was
placed under house arrest, and was
forced to recant his beliefs
SCIENTIFIC METHOD

• Involves a question and suggested explanation (hypothesis)

• Based on observation
• Followed by careful design & execution of controlled experiments,
and…
• Finally validation, refinement or rejection of this hypothesis
Traditional S. Method: Hypothesis-driven
reduction
• Aristotle and Herophilus (+ 300 BC), Avicenna and Alhazen (+ 1,000
AD), Grosseteste & Robert Bacon (+ 1,250 AD), etc.
• The “gold standard of quality research” ~ the 17th and 18th
centuries, by Bacon & Descartes ~ the founders of scientific method
• Insisted on careful, systematic observations of high quality, rather than
metaphysical speculations prevalent among the scholars of the time
• In contrast to their peers, they strove for objectivity and insisted that
observations, rather than an investigator’s preconceived ideas or
superstitions, should be the basis for formulating a research idea
• Based on formulating and testing hypotheses, a deduction is made
The 2nd Dimension of S. Method: Data-
Mining Inspired Induction
• ~ Early 21st century  feasible to
perform high-throughput experiments
that generated thousands of data
• Typically characterizing the
expression/abundances of genes,
proteins, metabolites, or other
biological quantities in a sample
• The strategy of measuring large
numbers of items in a nontargeted
fashion is fundamentally different
from the traditional scientific method
The 3rd Dimension of S. Method:
Allochthonous Reasoning
• The use of mathematical and
computational models for understanding
biological phenomena
• Greek: in or from a “piece of land
different from where one is at home”; 
“outside one’s comfort zone”)
• Moving the hypothesis to the realms of
mathematics:
• Simplification & abstraction of origin
system
• Translation and correspondence rules
Traditional process of scientific method
1. Observing a particular biologic or physical phenomenon
2. Developing a hypothesis about the cause of the phenomenon (H0
VS Ha) research question
3. Designing an experiment to prove the hypothesis
4. Conducting the experiment to collect data
5. Data analysis to determine the rejection/acceptance of hypothesis
6. Reporting the results