The Scientific Method
and
Historical Perspectives in
Microbiology
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 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)
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
Propose Alternate
Hypothesis
Design Experiment
Redesign
Experiment
Not
repeatable
Data are Bias
Determine if Data are
Bias
Refine Hypothesis
Repeat Experiment
Repeatable
Collect and Analyze
Data
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
Observed
disease
symptoms
Immune system activity
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
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
X
Y
Z
Culture the agent
Isolate each type of organism in
a pure culture
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
What do the results suggest?
N=4
# of rats
Treatment
asymptomatic rats
diseased rats
Control
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
Family tree of known
organisms
Can make testable hypotheses about new
species based on similarity to known
groups
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
Classic Microbiology
Food
Production
Chemistry
Medicine
Microscopy
World Population Growth
7000
6000
Population in Millions
5000
4000
3000
2000
1000
0
1
200
400
500
600
700
800
900
1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000
Year (com m on era)
Leading Causes of Death in U.S, CDC 2002
Septicemia
33,865
Nephritis, nephrotic syndrome, and
nephrosis
40,974
Alzheimer's disease
58,866
Disease
Influenza/Pneumonia
As of 2006 Alzheimer’s
Deaths surpassed
influenza
65,681
Diabetes Mellitus
73,249
Accidents
106,742
Chronic Low er Resp. Disease
124,816
Stroke
162,672
Cancer
557,271
Heart Disease
696,947
0
100,000
200,000
300,000
400,000
500,000
Num ber of Deaths
600,000
700,000
800,000
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 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
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