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Scientific Research : Pr inciples and Method s. 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. - PowerPoint PPT Presentation
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Professor FUNG Ming-ChiuDepartment of Biology
The Chinese University of Hong [email protected]
Scientific Research:Principles and Methods
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
SmallpoxCowpox
Vaccine- Vacca mean “Cow”
Edward Jenner- 1798
“Mother of Vaccination” ?
Monoclonal antibodyOne 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(Nobel Price in Physiology or Medicine 1962, James D Watson and Francis Crick)
Southern BlotNorthern BlotDNA microarray
DNA replication(Nobel Price in Physiology or Medicine 1959, Arthur Kornberg)
PCR(Nobel Prize in Chemistry 1993, Kary B. Mullis)
Discovery Invention
DNA Sequencing(Nobel Prize in Chemistry 1980, Frederick Sanger)
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)
Chalcone synthase (CHS):
The key enzyme in pigment biosynthesis
In 1990, two research groups, Richard Jorgensen and Joseph N.M. Mol,
introduced CHS gene into petu-nia.
Discovery of post-transcriptional gene silencing
DiscoveryUnexpected results
Experimental expectation
Introduce CHS
(pigment en-hancing gene)
Experimental result
Introduction of a CHS transgene
inhibits anthocyanin pig-mentation
Comparison of steady-state CHS message levels in Vio-let and white flowers from transgenote
Introduced CHS
Endogenous CHS
RNase protection analysis
The expression of endogenous and introduced CHS genes was co-suppressed
Discovery
RNA interference(Nobel Prize in Physiology or Medicine 2006, Craig Mello and Andrew Fire)
Who made the first observation of RNA interference?
shRNAsiRNA
Invention
Comparison of steady-state CHS message levels in Vio-let and white flowers from transgenote
Introduced CHS
Endogenous CHS
RNase protection analysis
The expression of endogenous and introduced CHS genes was co-suppressed
Wrong analysis: allele interaction, gene methylation
The host fails to elicit any marked tissue response against the skin-
residing 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.
Life cycle of Schistosome
Discovery -- Logical deduction
The discovery of Sm16 in S. mansoni
Figure. intracellular levels of IL-1ra in human neonatal keratinocytes 72 hr after in vitro stimulation with:
ES, Sm16 (a), ES depleted with Sm16 (b), a + b, media (control)
Sm16
ES depleted with Sm16
Ramaswamy, B, et al. Journal of inflammation. 1996,46:13-22
Sm16 should be responsible for the anti-inflammatory effect of ES products of S. mansoni.
DiscoveryBy accident
Wall paint (乳膠漆 )
Spoiled milk was accidentally pour into calcium oxide
Logical deduction1 2
6 7
3 4 5
8 9
10 11 12 13 14 15
16 17 18 19 20
Logical deduction1 2
6 7
3 4 5
8 9
10 11 12 13 14 15
16 17 18 19 20
Scientific Research needs
CuriosityKeen observationCorrect interpretation ImaginationLuck
Comparison of steady-state CHS message levels in Vio-let and white flowers from transgenote
Introduced CHS
Endogenous CHS
RNase protection analysis
The expression of endogenous and introduced CHS genes was co-suppressed
Wrong analysis: allele interaction, gene methylation
Biased by the central dogma / past experiences
Against the central dogma
Mad cow disease found in Plurenden Manor farm, April 19851986, found in other far away farms
• Bovine Spongiform Encephalopathy
BSE (mad cow disease)
Scrapie-associate fibrils under electron microscopePatricia Merz, 1978
Stanley B. Prusiner
Nobel Prize in Physiology or Medicine
1997
1982, purified the prion protein
glutamate metabolism research
scrapie research
Proposed scrapie is caused by a protein but not a virus
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 InvestigationObservation
Question
Hypothesis Set
EvidencePresuppositions
[Archive]
Conclusions+
Major Steps in a Scientific InvestigationObservation
Question
Hypothesis Set
EvidencePresuppositions
[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 InvestigationObservation
Question
Hypothesis Set
EvidencePresuppositions
[Archive]
Conclusions+
• Answer from literatures (?)
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
Methodologye.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
EvidencePresuppositions
[Archive]
Conclusions+
Inductivelogic
Deductivelogic
• 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
• 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
Some Common Logical Fallacies
• 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
The Prediction Power of a Hypothesis Determines Its Validity
Major Steps in a Scientific InvestigationObservation
Question
Hypothesis Set
EvidencePresuppositions
[Archive]
Conclusions+
• 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?)
How to Collect True Evidences (Carefully Designed Experiments and Accurately
Recorded Observations)
Major Steps in a Scientific InvestigationObservation
Question
Hypothesis Set
EvidencePresuppositions
[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 controlsUse 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.