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 Francis Bacon Galileo Galilei Rene Descartes England Italy France (1561-1626) (1564-1642) (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 Reproducibility by others RESEARCH ERRORS SAMPLE Selected sample Few cases METHODS Outdated reagents Equipment error Personal error Statistical mischoice CONCLUSION Invalidity Causality error THE TREE OF LIVE Association or Causal Relation ?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 Birds of same species have different peaks in (1809 – 1882) different habitats THE DURATION OF DARWIN RESEARCH (1809 – 1882) Step Years Observations 5 (Beagle tour) Formulation of theory 22 (Inductive reasoning) Publications: 13 1. The origin of species ( 1859) 2. Descent of man (1971) 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 SEATS AND CAUSES MORGAGNI OF DISEASES, 1761 (1682 – 1771) 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 VAN GOGH, 1886 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 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 CELLULAR PATHOLOGY (1821 – 1902) 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 Regulator Regulator Genes 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