The Scientific Method and Historical Perspectives in Microbiology

1. The Scientific Method andHistorical Perspectives in Microbiology

2. Science “ All reasoning is thinking, but not all thinking is reasoning”-Irving Copi • Science is a systematic way of gaining knowledge and endeavors to eliminate bias • It is based on branch of philosophy that deals with logic and cannot answer questions beyondreason or beyond the natural world (i.e. metaphysical questions) • Unscientific thought is dogmatic (not based on proof). It is often based in belief in an absolute truth without possibility of modification or correction • Scientific propositions are regarded as hypotheses (theory and law are often misleading terms; they are refined hypotheses that are repeatedly supported by scientific observation)

3. Scientific Propositions Hypothesis- an unproven proposition based on observation Theory- a proposition that has been supported by scientific testing and observable facts (organic evolution, heredity, cell, gene) Law- a proposition that is invariably supported when tested (e.g. gravity, thermodynamics) All must be testable and are never dogmas or absolute truths

4. The Scientific Method • Make observation • Form a hypothesis • Design a controlled experiment • Evaluate data (test assumptions, assess variability etc…) • Repeat or refine experiment

5. Observation Propose Hypothesis Propose Alternate Hypothesis Design Experiment Collect and Analyze Data Redesign Experiment Not repeatable Determine if Data are Bias Data are Bias Refine Hypothesis Repeat Experiment Repeatable Accept as Theory

6. Causes and Correlations • Observing a correlation indicates a relationship exists between two variables • It does not imply that either of the variables causes the other • Correlational studies are valuable in the beginning stages of scientific investigations but require further investigation to demonstrate causality

7. Direct (positive) Correlation Observed disease symptoms Presence of microbe in patients

8. Inverse (negative) Correlation Observed disease symptoms Immune system activity

9. Cause • The science of cause is etiology • In science- it refers to a necessary and sufficient condition • Careful not to use imprecisely • Ex: cold virus is the cause of nasal congestion • Can be classified as either proximate or remote causes AB  C  D  E • A is a remote cause of E • D is a proximate cause of E • Etiological agents are the causative agents of disease • Koch’s postulates are used to prove that a specific agent is the cause of a particular

10. Using science to identify the etiological agents of disease • Signs and symptoms are indications that the body is sick, they are important observations in forming a hypothesis regarding the etiology of infectious disease • H: Agent X is the cause of the signs or symptoms • Diagnosing a disease doesn’t necessarily reveal the etiological agent • Some diseases are caused by more than one agent e.g. meningitis, pneumonia, wound infection • Indirect identification includes the use of signs or antibodies specific to the agent • Direct identification relies on observing the agent and its characteristics

11. Robert Koch • Koch identified causative agents of diseases such as anthrax and tuberculosis • Introduced pure culture techniques

12. Koch’s Postulates • The specific cause must be found in every case of the disease • The disease organism must be isolated in a pure culture • Inoculation of organism into healthy animal must produce the same disease • The disease organism must be recovered from the inoculated animal

13. Koch’s Postulates X Y Culture the agent Z Isolate each type of organism in a pure culture

14. Designing an Experiment Designing a scientific experiment to test the hypothesis that agent X is the cause of disease Inoculate Treatment Group with agent X (suspected pathogen) Inoculate Control Group with agent Z (not harmful) as a standard for comparison

15. What do the results suggest? N=4 # of rats Treatment Control asymptomatic rats diseased rats

16. How important are Koch’s postulates? • Koch’s postulates have not been satisfied for all organisms that we consider to be pathogenic • Remember that science does not deal with absolute truths and there are many factors that contribute to disease besides the agent • As we learn more about pathogens and hosts and the relationships between them from a scientific perspective, we are more likely to prevent and treat infectious disease • Many diseases actually result from homeostatic imbalance and therefore microorganismsare cofactors rather than etiological agents

17. Taxonomy/Systematics • The scientist Linnaeus (1707-1778) sought to classify organisms in an organized way to more easily study and keep track of them. • He also practiced medicine and specialized in syphilis • His method of binomial nomenclature utilizes Latinized names for groups of related organisms • The groups names most often used to identify organisms are genus and species • The genus and species names are italicized or underlined. • The genus name is capitalized and the species name is not. Example: Escherichia coli

18. Modern taxonomy (systematics) reflects evolutionary relationships Charles Darwin’s inquiries led to a chain reaction of scientific breakthroughs in biology The rapid evolution of microbes provides clear scientific evidence for evolution, but presents a great challenge to public health antibiotic resistance antigenic shift and drift host-parasite coevolution

19. Taxonomic Classification Domains- Archaea, Bacteria, Eukarya Kingdom- there are currently five or six kingdoms depending on how you slice them (viruses not included) Phylum Class Order Family Genus Species-there are millions of species Subspecies are also recognized • Five Kingdoms: • Animalia • Plantae • Fungi • Protista • Monera (Archaea, Bacteria)

20. Why is taxonomy/systematics important in microbiology and human disease? Suspect organism is cause of a new disease Organism is new species Can be placed into group that is most similar Can make testable hypotheses about new species based on similarity to known groups Family tree of known organisms

21. Percentage of Shared Characteristics 70% 80% 90% 90% Revised family tree

22. Historical Perspectives • History provides us with many good examples of the scientific method • The study of history itself can be studied scientifically • Knowledge of history gives us hindsight • History reminds us of what is possible in the future

23. Classic Microbiology Food Production Chemistry Microscopy Medicine

25. Leading Causes of Death in U.S, CDC 2002 As of 2006 Alzheimer’s Deaths surpassed influenza

26. The Black Death in Europe ca.1300s While outbreaks of plague occurred around the world throughout recorded history, there were three major pandemics: Justinian plague(500s A.D), black death( 1300s) and modern (1900s). The black death occurred during mediaeval times and killed millions

27. Timeline of Historical Events and People 1546 A.D.-Italian Physician Girolamo Fracastro Suggests that invisible organisms cause disease 1665-Robert Hooke publishes his observations of cells in cork Late 1600s-Francesco Redi tests the “theory” of spontaneous generation

28. Anton van Leeuvenhoek • 1677-Observed microorganisms which he called ‘animacules’

29. Edward Jenner 1796- discovered small pox vaccine (vacca=cow) This was before viruses were know as etiological agents of disease He noticed that milk maids who had cow pox (vaccinia virus) scars were resistant to small pox

30. The “Golden Age” of Microbiology 1840-J. Henle exposes germ theory of disease 1847-1850 Ignaz Semmelweis suggests hand washing to prevent childbed fever 1853-John Snow demonstrates the spread of cholera through contaminated water 1857-1860s-Pasteur’s work refutes spontaneous generation, he invents pasteurization, shows CO2 production in yeast 1862- Joseph Lister practiced antiseptic surgery

31. The 1900s 1908-Paul Ehrlich develops drug to treat syphilis 1928-Griffith discovers genetic transformation in bacteria 1929-Alexander Fleming discovers penicillin 1943-Luria and Delbruck demonstrate randomness of mutations that confer antibiotic resistance 1948-Barbara McClintock demonstrates transposable elements 1953-Crick and Watson crack genetic code 1973-Boyer and Cohen clone DNA using plasmid 1981-Stanely Prusiner discovers prions 1983-Kery Mullis invents PCR 1995-First complete bacteria genome sequenced

32. 21st century microbiology 2001-Anthrax attack in USA, huge increase in funding for biodefense research 2003-SARS epidemic 2005-chicken pox vaccine 2006-HPV vaccine 2007-Avian influenza vaccine