the scientific method and historical perspectives in microbiology
TRANSCRIPT
The Scientific Method and
Historical Perspectives in Microbiology
Science
• 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 beyond reason 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)
“ All reasoning is thinking, but not all thinking is reasoning”-Irving Copi
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
The Scientific Method
• Make observation• Form a hypothesis• Design a controlled experiment• Evaluate data (test assumptions, assess
variability etc…)• Repeat or refine experiment
Observation Propose Hypothesis
Refine HypothesisRepeat Experiment
Determine if Data are Bias
Collect and Analyze Data
Design Experiment
Redesign Experiment
Repeatable
Not repeatable
Data are Bias
Propose Alternate Hypothesis
Accept as Theory
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
Direct (positive) Correlation
Observed disease symptoms
Presence of microbe in patients
Inverse (negative) Correlation
Immune system activity
Observed disease symptoms
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
AB 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
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
Robert Koch
• Koch identified causative agents of diseases such as anthrax and tuberculosis
• Introduced pure culture techniques
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
Koch’s Postulates
Culture the agent
Isolate each type of organism in a pure culture
X
Y
Z
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
Control
# of rats
Treatment
asymptomatic rats
diseased rats
N=4
What do the results suggest?
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 microorganisms are cofactors rather than etiological agents
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
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
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:
1. Animalia
2. Plantae
3. Fungi
4. Protista
5. Monera (Archaea, Bacteria)
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 groupsFamily tree of known
organisms
Percentage of Shared Characteristics
70%
80%
90%
90%
Revised family tree
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
Chemistry
MedicineMicroscopy
Food Production
Classic Microbiology
World Population Growth
0
1000
2000
3000
4000
5000
6000
7000
1 200 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000
Year (common era)
Po
pu
lati
on
in M
illio
ns
696,947
557,271
162,672
124,816
106,742
73,249
65,681
58,866
40,974
33,865
0 100,000 200,000 300,000 400,000 500,000 600,000 700,000 800,000
Heart Disease
Cancer
Stroke
Chronic Low er Resp. Disease
Accidents
Diabetes Mellitus
Influenza/Pneumonia
Alzheimer's disease
Nephritis, nephrotic syndrome, andnephrosis
Septicemia
Dis
ease
Number of Deaths
Leading Causes of Death in U.S, CDC 2002
As of 2006 Alzheimer’s Deaths surpassed influenza
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
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
Anton van Leeuvenhoek
• 1677-Observed microorganisms which he called ‘animacules’
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
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
The 1900s1908-Paul Ehrlich develops drug to treat syphilis1928-Griffith discovers genetic transformation in bacteria1929-Alexander Fleming discovers penicillin1943-Luria and Delbruck demonstrate randomness of
mutations that confer antibiotic resistance1948-Barbara McClintock demonstrates transposable
elements1953-Crick and Watson crack genetic code1973-Boyer and Cohen clone DNA using plasmid1981-Stanely Prusiner discovers prions1983-Kery Mullis invents PCR1995-First complete bacteria genome sequenced
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