Professor FUNG Ming-Chiu Department of Biology The Chinese University of Hong Kong

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


Introduced CHS

Endogenous CHS



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

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16 17 18 19 20

Logical deduction1 2

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3 4 5

8 9

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16 17 18 19 20

Scientific Research needs

CuriosityKeen observationCorrect interpretation ImaginationLuck


Introduced CHS

Endogenous CHS



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….”


• 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.


• 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


• 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)

http://en.wikipedia.org/wiki/Bourgeois_pseudoscience

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


Question

Hypothesis Set


[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


[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


Question

Hypothesis Set


[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)


Question

Hypothesis Set


[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.

Professor FUNG Ming-Chiu Department of Biology The Chinese University of Hong Kong

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