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