SCIENTIFIC THINKING

Part II

Scientific Era (1600 AD – 2000 AD)

M N EL-Bolkainy

2013

OBJECTIVES

A The Search for a Method

(Scientific revolution)

B The Search for Etiology & Mechanisms 1. Gross pathology

2. Epidemiology

3. Microscopic pathology

4. Molecular pathology

(Biotechnology revolution)

THE SCIENTIFIC REVOLUTION

(1650 – 1800)

AIM To replace the historic approach of

gaining knowledge based on speculation by a more rational objective method

THE PIONEER FOUNDERS

Galileo Galilei

Italy

(1564-1642)

Francis Bacon

England

(1561-1626)

Rene Descartes

France

(1596-1650)

THE ADVANCEMENT OF LEARNING

(Bacon, 1605)

THE VISION

• Science and technology could transform the world to the better

• Science placed in unworthy (irresponsible) hands could be destructive

• Young scientists are more creative than old ones

THE TWO WORLD SYSTEMS

(GALILEO, 1623)

ACADEMIC FREEDOM

The first to revolt against dogmatism by

supporting the heliocentric theory

QUANTITATION OF OBSERVATIONS

Hence allowing mathematical analysis

DISCOURSE ON METHOD

(Descartes, 1637)

SKEPTICISM

• We start by doubt (hypothesis) in order to reach truth (conclusion)

• The only reliable knowledge is mathematics

• Except for God and Soul, the whole universe is mathematical

• The aim of science is to control nature

THE STEPS OF SCIENTIFIC METHOD

1. Definition of a problem

2. Collect data (observations)

3. Formulate a hypothesis

4. Test hypothesis (experiment)

5. Draw conclusions

6. Publication of results

7. Reproducibility by others

RESEARCH ERRORS

SAMPLE Selected sample

Few cases

METHODS Outdated reagents

Equipment error

Personal error

Statistical mischoice

CONCLUSION Invalidity

Causality error

THE TREE OF LIVE Association or Causal Relation ?

Medieval concept

of genesis of

Animals from plants

CRITERIA OF CAUSALITY

1. Strong association

2. Direct relation

3. Temporal relation

4. Explanatory mechanism

IMPORTANT QUESTION • Can we gain knowledge without

applying the scientific method ?

ANSWER: YES 1. If experiment is impossible (Darwin theory of evolution) 2. Scientific discovery by chance

EVOLUTION BY NATURAL SELECTION AND SURVIVAL OF THE MOST FIT

Charles Darwin

(1809 – 1882)

Birds of same species

have different peaks in

different habitats

THE DURATION OF DARWIN RESEARCH (1809 – 1882)

Step Years

Observations (Beagle tour) Formulation of theory (Inductive reasoning) Publications: 1. The origin of species ( 1859) 2. Descent of man (1971)

5

22

13

Total 40

THE BROAD APPLICABILITY OF DARWIN THEORY

Natural Science

Evolution of Species

Bacterial resistant strains

Cancer cell progression

Social Science

Religious, colonial,

class and ideological struggle

THE FUTURE OF SOCIAL STRUGGLE

1. END OF HISTORY

(Francis Fukuyama, 1992)

2. CLASH OF CIVILIZATIONS

(Samuel Huntington, 1996)

Judeo – Christian against Islam

The west against the reset

3. DIALOGUE AMONG CIVILZATIONS (Mohamed khatami, 2000)

THE GENETIC CONFIRMATION OF DARWIN THEORY

1. Discovery of chromosomes,

(Wilhelm Hofmeister, 1848)

2. Laws of heredity,

(Gregor Mendel, 1866)

3. Reproduction of Mendel laws,

(Hugo de Vries et al, 1900)

4. Mutation in Drosophila,

(Thomas Morgan, 1919)

5. Discovery of genes

(Walter Fiers, 1972)

MUTATIONS IN DROSOPHILA (Thomas Morgan, 1919)

Differences in eye color

and length of wings

SCIENTIFIC DISCOVERIES BY CHANCE

1. Ovary – breast hormonal relation,

(Sir George Beatson, 1896)

2. Radioactivity of uranium,

(Antoine Becquerel, 1896)

3. Penicillin, the first antibiotic,

(Alexander Fleming, 1928)

4. Cancer Chemotherapy (Mustard gas, 1943)

(Gilman et al, 1946)

THE SEARCH FOR THE CAUSE AND

MECHANISM OF DISEASE

18th cent Gross Pathology (Morgagni, 1761)

18th cent Epidemiology (Pott, 1775)

19th cent Cellular Pathology (Virchow, 1858)

20th cent Molecular Pathology (Multiple authors, 1950 – 2013)

“Clinicopathological

Correlation of 700 Autopsies”

GIOVANNI BATISTA

MORGAGNI

(1682 – 1771)

SEATS AND CAUSES

OF DISEASES, 1761

EPIDEMIOLOGY REVEALS ETIOLOGY AND ALLOWS PREVENTION

ETIOLOGY Scrotal Cancer is common among chimney sweepers (Sir Percival Pott, 1775)

PREVENTION Legislation to ban this occupation

ASBESTOS AND MESOTHELIOMA IN USA

Fabricated Research Delayed Banning 29 Years

1. Mesothelioma is related to asbestos

exposure (J. Eagner 1960)

2. Industry – Supported fabricated research to prove otherwise

3. Carcinogenic risk firmly established (Roggli, 1987)

4. Production of asbestos was finally banned in USA (1989), but, continued in developing countries

TOBACCO SMOKING & LUNG CANCER IN USA Money Talks / Thanks to Clever Lawyers

1. Smoking is related to

lung cancer

(Wynder,Doll,1950)

2. Lawsuit in USA against tobacco industry

3. Billions of dollars compensation but production continues

VAN GOGH, 1886

LIGHT MICROSCOPY The Most Important Technology

of the 19th Century

THE INVENTION OF MICROSCOPE

EARLY INVENTORS 1. Compound microscope

(Galileo, 1610)

2. Simple microscope

(Leeuwenhoek, 1721)

MASS PRODUCTION (Ernest Abbee,

Carl Ziess, 1900)

CONTRIBUTIONS

OF LIGHT MICROSCOPY

1. The cell theory (Schwan & Schleiden

1838)

2. Bacteriology (Ferdinand Cohn, 1853)

3. Cell Pathology (Muller & Virchow, 1858)

4. Cell division (W. Flemming, 1882)

5. Microsurgery (Carl Nylen, 1921)

6. Laser microsurgery (Strong & Jako, 1972)

CONTRIBUTIONS OF LIGHT MICROSCOPY

(Continued)

7. Phase Contrast (First Zernike, 1932)

8. Cytophotometry (T. Casperson, 1936)

9. Immunohistology (A. Coons, 1942)

10. Cytogentics (Tjio & Levan, 1956)

11. Molecular Genetics (Langer- Safer,1982)

12. Laser Capture Micro dissection, LCM

(Emmert – Buck, 1996)

• Cells are the units of disease

• Microscopic studies are more precise than gross examination

RUDOLF VIRCHOW

(1821 – 1902)

CELLULAR PATHOLOGY

1858

THE BIOTECHNOLOGY

REVOLUTION

(1950 – 2013)

AIM To study biological phenomena at

molecular level, thus, revealing mechanisms and allowing the application of targeted therapy

THE FOUNDATIONS AND

PREREQUISITES OF

BITOTECHNOLOGY REVOLUTION

1. Well-trained staff

2. Team work (multidisciplinary)

3. Efficient equipments

4. Research funds

NATIONALITY OF 32 NOBEL PRIZEWINNERS IN BIOTECNOLOGY (1950 – 2013)

American 15

British 4

French 4

German 3

Swiss 1

Australia 1

India 1

Japan 1

Egypt 1

Israel 1

RESEARCH SPENDING BY COUNTRIES (Billions of US Dollars per year)

USA 405 India 40

China 297 Russa 30

Japan 160 Israel 9

Germany 70 Egypt 1

(Wikipedia, 2011)

NB Figures included military spending

TECHNOLOGY INSTITUTES BY COUNTRIES

USA 28 India 16

China 11 Russa 9

Japan 6 Israel 2

Germany 17 Egypt 2

(Wikipedia, 2013)

BIOTECHNOLOGY NOBEL PRIZES ARRANGED BY SUBJECT

No

Genomics 8

Proteomics 11

Infections and Cancer 5

Laser 2

Total 26

MOLECULAR SRUCTURE OF DNA

James Watson

(American)

Francis Crick

Maurice Wilkins (British)

1962

DNA

MOLECULAR STRUCTURE & DOUBLE HELIX MODULE

ORGANIZATION PACKAGE OF DNA TO NUCLEOSOMES AND CHROMOSOMS

THE BILOGIC DOGMA

DNA

mRNA

Protein

GENE REGULATION 1962 Francis Jacob & Jaques Monod Activator and suppressors in E. Coli 2006 Roger Kornberg RNA polymerase and nucleosome 2006 Anderw Fire Epigenetic m-RNA silencing 2009 Elizabeth Blackburn Telomerase

REGULATOR GENES MODEL

Activator

Suppressor

Re

gu

lato

r G

en

es

EPIGENETIC GENE CONTROL

“A change of gene expression

apart from mutation or the conventional regulator gene model”

CHROMATIN REMODELING BY HISTONE ACETYLATION

Packed nucleosomes

(Silent genes)

Dissociated nucleosomes

(Active genes)

CYTOSINE METHYLATION

m-RNA SILENCING

POLYMERASE CHAIN REACTION

(PCR)

Kary Mullis

(American)

1993

PCR

A segment

of DNA is amplified to a million in

20 cycles

RESTRICTION ENDONUCLEASES GENETIC ENGINEERING

Weber Arber (Swiss)

1978

GENETIC ENGINEERING IN VITRO

Restriction Endonucleases Diagnostic Probes

TARGETING GENES TO CHANGE PHENOTYPE (Genetic Engineering in Vivo) 2007 Mario Capeechi Transfer of a gene to replace its

homologous gene in embryonic stem cells (Knockout mice)

2012 John Gurdon & Shinya Yamanaka Conversion of mature cell to a stem cell (Genetic reprogramming) applied in (Frog, Cheep, Mice and

Humane)

PROTEIN STRUCTURE

TRANSLATION, MODIFICATIONS, TRANSPORT AND DEGRADATION

2009 Venkatraman Ramakrishnan Ribosome and protein synthesis 2013 James Rothman Intracellular vesicle transport 2004 Aaron Ciechanover Ubiquitin – Proteasome pathway (UPP) of protein degradation.

PROINSULIN

Translation,

Modification,

And transport

THE BILOGIC PARADOX

DNA (25,000 Genes) mRNA

Protein (1000,000 Proteins)

EXPLANATION

1- One gene produces multiple proteins

2- One protein has different activities through

modifications

UBIQUITIN- PROTEASOME PROTEIN DEGRADATION

SIGNAL TRANSDUCTION

1999 Gunter Blobel Protein Signaling 2012 Brain Kobilka G- protein – coupled receptors

SIGNAL TRANSDUCTION

CELL CYCLE CONTROL Discovery of Cyclin Genes in Yeasts

Leland Hartwell

(American)

2001

CELL DIVISION CYCLE (cdc) CONTROL

IMMUNOLOGY 1972 Gerald Edelman Structure of antibodies 1980 Baruj Benacerrof Major histocompatibility complex (MHC) 1984 Georges Kohler The hybridoma technology 1984 Neils Jerne Lymphocyte clonal selection 2011 Bruce Beutler Innate immunity (Dendritic Cells)

THE STRUCTURE OF ANTIBODIES

THE HYBRIDOMA

TECHNOLOGY

“The evil is used

to produce the good”

CLONAL SELECTION OF B- LYMPHOCYTES

First encounter

(memory cells)

Second encounter

(Clonal expansion)

ANTIGEN PRESENTATION TO T-LYMPHOCYTES IN ASSOCIATION WITH (MHC)

INFECTIONS AND CANCER 1966 Francis Rous First virus-induced tumar 1974 David Baltimore Retrovirus oncogenesis (in vitro) 2005 Barry Marshall H. pylori and gastric cancer 2008 Harold Hausen HPV and Cervical Cancer 2008 Luc Montagnier & Francois Bane-Sinoussi HIV Discovery (AIDS)

ROUS RETROVIRUS-INDUCED SARCOMA IN CHICKENS

LASER BEAM DISCOVERY

Charles Towns

(American)

1964

The most important technology of

the 20th Century

GENERATION OF LASER BEAM

(Chromium)

PROPERTIES OF LASER BEAM

Single wave, coherent, parallel

Monochromatic, high energy, long distance

REGULAR LIGHT

APPLICATIONS OF LASER

Computers Industry Medicine Show Light

Barcodes Lunar Distance Military Biology

APPLICATION OF LASER IN BIOLOGY

1. Flow cytometry (W.H. Coulter, 1953)

2. Flow fluorescent microscopy (W. Gohde, 1968)

3. Laser capture micro dissection, LCM (E. Buck, 1995)

4. Photo thermal effect of laser on gold nano particles (M. El – Sayed, 2006)

5. Dynamics of molecular reactions femtochemistry

(A. Zewail, 2009)

FLOW CYTO PHOTO METRY

Rapid multi-parameter

Analysis of thousands

of cells

LASER CAPTURE MICRODISSECTION isolation of individual cells for study

FEMTOCHEMISTRY DYNAMICS USING ULTRAFAST LASER

1999 Ahmed Zewail

• The Academic Discovery (1990)

(Femtosecond = 0.000,000,000,000,001)

• The Technologic application (2009)

(The 4-Dimentional EM)

“Technology determines

the power of nations,

not natural resources,

population size or ideology”