Transcript Barbara McClintock a Model of Adamant Individually and

Scientific Research:
Principles and Methods
Professor FUNG Ming-Chiu
Department of Biology
The Chinese University of Hong Kong
[email protected]
What is scientific research?
Scientific research is an investigation of a
phenomenon (addressing a question) by
scientific method.
Discovery ?
or
Invention ?
Story of Vaccination
Smallpox
Cowpox
Smallpox
Edward Jenner
- 1798
Vaccine
- Vacca mean “Cow”
“Mother of Vaccination” ?
Invention
Discovery
One B cell one antibody
(Nobel Price in Physiology or Medicine
1984, Niels K. Jerne, Georges J.F.
Köhler and César Milstein)
DNA double helix structure
Monoclonal antibody
(Nobel Price in Physiology or Medicine
1962, James D Watson and Francis
Crick)
Southern Blot
Northern Blot
DNA microarray
DNA replication
DNA Sequencing
(Nobel Price in Physiology or Medicine
1959, Arthur Kornberg)
(Nobel Prize in Chemistry 1980,
Frederick Sanger)
PCR
(Nobel Prize in Chemistry 1993,
Kary B. Mullis)
What type of research are you going to do?
Discovery?
Invention?
Addressing a question?
•A question is raised by yourself
•A question has not been answered for long
time (every scientist want to get the answer)
Discovery
Unexpected results
Discovery of post-transcriptional gene silencing
In 1990, two research groups, Richard
Jorgensen and Joseph N.M. Mol,
introduced CHS gene into petunia.
Chalcone synthase (CHS):
The key enzyme in pigment
biosynthesis
Experimental expectation
Introduce CHS
(pigment enhanc
ing gene)
Experimental result
Introduction of a CHS transgene
inhibits anthocyanin pigmentation
RNase protection
analysis
The expression of endogenous
and introduced CHS genes was
co-suppressed
Comparison of steady-state CHS
message levels in Violet and white
flowers from transgenote
Introduced
CHS
Endogenous
CHS
Discovery
RNA interference
(Nobel Prize in Physiology or
Medicine 2006, Craig Mello and
Andrew Fire)
Who made the first
observation of RNA
interference?
Invention
shRNA
siRNA
RNase protection
analysis
Wrong analysis: allele interaction, gene
methylation
The expression of endogenous
and introduced CHS genes was
co-suppressed
Comparison of steady-state CHS
message levels in Violet and white
flowers from transgenote
Introduced
CHS
Endogenous
CHS
Discovery -- Logical deduction
Life cycle of Schistosome
The host fails to elicit any marked
tissue response against the skinresiding schistosomulae.
This reduced tissue response is evident only in live
parasites infecting native host.
Dead parasites can elicit a marked inflammatory
response.
A bird schistosome (T. ocellata ) often results in
severe dermatitis in humans.
The discovery of Sm16 in S. mansoni
Sm16
ES depleted
with Sm16
Figure. intracellular levels of IL1ra in human neonatal
keratinocytes 72 hr after in vitro
stimulation with:
ES, Sm16 (a), ES depleted with
Sm16 (b), a + b, media (control)
Sm16 should be responsible for the antiinflammatory effect of ES products of S. mansoni.
Ramaswamy, B, et al. Journal of inflammation. 1996,46:13-22
Discovery
By accident
Wall paint (乳膠漆)
Spoiled milk was accidentally pour
into calcium oxide
Logical
deduction
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Logical
deduction
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Scientific Research needs
6Curiosity
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Keen observation
Correct
interpretation
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Imagination
Luck
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RNase protection
analysis
Wrong analysis: allele interaction, gene
methylation
Biased by the central
dogma / past experiences
The expression of endogenous
and introduced CHS genes was
co-suppressed
Comparison of steady-state CHS
message levels in Violet and white
flowers from transgenote
Introduced
CHS
Endogenous
CHS
Against the central dogma
Mad cow disease found in Plurenden Manor farm, April 1985
1986, found in other far away farms
•Bovine Spongiform Encephalopathy
BSE (mad cow disease)
Scrapie-associate fibrils under electron microscope
Patricia Merz, 1978
Stanley B. Prusiner
glutamate metabolism research
scrapie research
1982, purified the prion protein
Proposed scrapie is caused
by a protein but not a virus
Nobel Prize in
Physiology or Medicine
1997
Key discoveries
•Prion protein -- cause scrapie
disease
•The infective agent (Prion) is a
protein alone
•The prion protein sequence 
leading to find the prion gene
Break for 5 minutes
Major Components of Science
• Inquiry: Why? How? What?
• Research: how to get the answer
– Experiments, observations, data analyses,
reasoning, etc.
Four Bold Claims of Scientific
Investigation
• Rationality
– I hold belief X for reason R with level of
confidence C, where inquiry into X is within
the domain of competence of method M that
accesses the relevant aspects of reality.
– e.g. “I believe what my physics teacher taught
is correct because I like him/her” versus “I
believe what my physics teacher taught is
correct most of the time because the contents
are coming from the most current edition of a
physics textbook. I have read the book and
compared it with my notes….”
Four Bold Claims of Scientific
Investigation
• Objectivity
– Knowledge on an object, not a subject or
knower; e.g. Dr. Fung is the speaker of this talk
(whether you like this talk or not will not
change the identity of the speaker)
– Verifiable; e.g. you have never heard the sound
of tree falling in a forest, did it really happen?
You can set a sound recorder etc.
Four Bold Claims of Scientific
Investigation
• Realism
– The correspondence of human thoughts with an
external and independent reality, including
physical objects
– The scientific method provides rational access
to physical reality, generating much objective
knowledge
– Does not come in degrees, either yes or no
Four Bold Claims of Scientific
Investigation
• Truth
– The property of a statement corresponds with reality
– Truth claims may be expressed with various levels of
confidence
– The price of holding onto the truth; e.g.
• The story of Heliocentric Model Giordano Bruno (burned at
the stake)
• The story of agricultural centers and Nikolai I. Vavilov
[jailed as a defender of the "bourgeois pseudoscience"
(genetics)]
• The story of jumping genes and Barbara McClintock
(received a Nobel Price more than 30 years after her
important discovery)
Major Steps in a Scientific Investigation
Observation
Question
Hypothesis Set
Presuppositions + Evidence
[Archive]
Conclusions
Major Steps in a Scientific Investigation
Observation
Question
Hypothesis Set
Presuppositions + Evidence
[Archive]
Conclusions
Making Important Observations is the
Essential First Step
• Sensitivity
– e.g. the story of penicillin and Alexander Fleming
• Comprehensiveness
Major Steps in a Scientific Investigation
Observation
Question
•Answer from literatures (?)
Hypothesis Set
Presuppositions + Evidence
[Archive]
Conclusions
What Kind of Questions to Ask?
Investigation of unknown (basic science)
•Delineating concepts related to life and nature; e.g. what
are the different life forms, how life functions, and how lives
interacting with each other and the environment
Applying known knowledge to modify/preserve
natural environment or enhance human life
(applied science)
Scientific concept
•e.g. Using penicillin as a medicine to kill bacteria
Methodology
e.g. Applying DNA fingerprinting techniques in forensic
sciences, etc.
e.g. Inventing new methodology to allow better
observation of the world; e.g. invention of PCR
Applying Logic in Making and Testing Hypothesis
Observation
Question
Hypothesis Set
Inductive
Deductive
logic
logic
Conclusions
Presuppositions + Evidence
[Archive]
• Inductive Logic
– From actual data to get an inferred model
– Strong if its premises support the truth of its conclusions
to a considerable degree, and is weak otherwise
– e.g. for 100 living bacteria observed, they all are capable
of doubling its DNA content during cell division;
conclusion: in all bacteria, they have a mechanism to
replicate DNA
• Deductive Logic
– From a given model to predict expected data
– The truth of its premises guarantees the truth of its
conclusions, and is invalid otherwise
– e.g. since our model that all bacteria can replicate their
DNA, we should expect to see DNA replication in
bacteria #101, #102, and etc.
• Presuppositions
– Science requires several common-sense
presuppositions, including that the physical world
exists and that our sense perceptions are generally
reliable; e.g. if you are not sure if you are real or
you are just a dreaming butterfly, no science
research can be done
• Archive
relevant knowledge
Irrelevant knowledge
Some Common Logical Fallacies
• Fallacies of Composition and Division
– Na and Cl2 are poisonous; Conclusion: NaCl is
poisonous
– Many horses are not white, a white horse is white;
Conclusion: a white horse is not a horse
• False Dilemmas
– My opponent’s theory is wrong; conclusion: my
theory is right
• Circular Reasoning
– I won’t be wrong because I am always right
• Fallacies of will
The Prediction Power of a Hypothesis
Determines Its Validity
• e.g. there were 2 hypotheses explaining why the neck of
giraffe is long
– Darwinism: mutations naturally occurred in giraffe
populations; when the environment changes (less leaves
close to the ground), the mutants survived better and
dominated today’s giraffe populations
– Prediction: mainly two kinds of giraffe fossils, long neck
and short neck
– Lamarck: when there were less leaves close to the
ground, giraffe needed to exercise their neck and gained
more muscles; this acquired ability passed onto
subsequent generations
– Prediction: giraffe fossils should exhibit a graduate
change of neck length
Major Steps in a Scientific Investigation
Observation
Question
Hypothesis Set
Presuppositions + Evidence
[Archive]
Conclusions
How to Collect True Evidences (Carefully
Designed Experiments and Accurately
Recorded Observations)
• Proper instrumentation; e.g. I. Newton
decomposes light by using a prism
• Careful experimental design: controls or
baseline (i.e. reference points)
• Accuracy of data; e.g. the story of phlogiston
(Johann Joachim Becher), oxygen and
Antoine Laurent Lavoisier
• How to handle quantitative data (errors occur
by chance): statistics; e.g. if your hypothesis
is that “man is taller than woman”, it may not
be always true (but can you generalize?)
Major Steps in a Scientific Investigation
Observation
Question
Hypothesis Set
Presuppositions + Evidence
[Archive]
Conclusions
Remark: data-driven
research in post-genomic era
You have to know the objective
/ hypothesis (purpose) of each
experiment
Set up all essential controls
Use more advance technology
References
• “Hypothesis, Prediction, and Implication in
Biology” by J.J.W. Baker and G.A. Allen
• “Great Scientific Experiments” by R. Harre
• “An Introduction to the Logic of the
Sciences” by R. Harre
• “Scientific Method in Practice” by H.G.
Gauch, Jr.