🦠 MICROBIOLOGY — WEEK 1 STUDY NOTES
Microbiology Foundations
Assigned reading:
1.1 What Our Ancestors Knew
1.2 A Systematic Approach
1.3 Types of Microorganisms
3.1 Spontaneous Generation
3.2 Foundations of Modern Cell Theor/y
1.1 What Our Ancestors Knew
First: What is microbiology?
Microbiology = the study of very small organisms and infectious agents.
Microorganism / microbe = an organism that is generally too small to see without a microscope.
Examples include:
* Bacteria
* Archaea
* Fungi such as yeast and molds
* Protozoa
* Microscopic algae
* Some parasites
Viruses are also studied in microbiology, although viruses are acellular, meaning they are not made of cells.
Important idea
Microbes are NOT automatically bad.
Many microbes are harmless or helpful. They:
* help produce food
* live naturally in and on our bodies
* help ecosystems function
* can be used to make medicines and other products
Only some microbes cause disease.
🍞 Humans Used Microbes Before They Knew Microbes Existed
Humans were using microorganisms for thousands of years before microscopes existed.
One of the biggest examples is:
Fermentation
Fermentation = microorganisms change sugars/carbohydrates into substances such as:
* alcohol
* gases
* organic acids
Microbes involved can include:
bacteria + yeast + molds
Humans used fermentation to make:
* bread
* cheese
* yogurt
* beer
* wine
* pickled vegetables
Easy example
Yeast eats/metabolizes carbohydrates in bread dough.
↓
Yeast produces carbon dioxide (CO₂).
↓
Gas becomes trapped in the dough.
↓
Bread rises.
Remember
Fermentation = microbes changing sugars.
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🧊 Ötzi the Iceman
Ötzi was a preserved human mummy approximately 5,300 years old.
Scientists found evidence that he had:
* Trichuris trichiura → a parasitic worm
* Borrelia burgdorferi → bacterium that causes Lyme disease
He also carried a fungus called Fomitopsis betulinus, which has laxative and antibiotic properties.
Why does this matter?
It shows that ancient people were trying to treat disease long before they understood microorganisms.
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🦠 Early Ideas About Disease
Before microscopes, people didn’t know exactly what caused disease.
Some cultures believed disease came from:
* supernatural forces
* angry gods
* fate
* bad air
But some people began to realize that disease might spread between people.
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Quarantine
Ancient societies sometimes separated sick people from healthy people.
This is called:
Quarantine = separating potentially infected people to prevent disease spread.
Even though they didn’t know what bacteria or viruses were, they understood that some diseases could spread.
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🚿 Sanitation
Ancient civilizations also developed ways to improve sanitation.
Examples included:
* clean-water systems
* drainage systems
* sewers
* aqueducts
This was important because removing human waste and providing cleaner water can reduce disease transmission.
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Important People From Early Medicine
Hippocrates
Who?
Greek physician.
Important idea:
Disease had natural causes, rather than always being caused by supernatural forces.
He is commonly called:
“Father of Western Medicine.”
Remember
Hippocrates → disease has natural causes.
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Thucydides
Thucydides survived the Athenian plague.
He noticed that people who survived the disease usually did not become sick from the same disease again while caring for infected people.
This was an early observation of:
Immunity
Immunity = the body’s ability to resist a particular infection/disease.
Remember
Thucydides → early idea of immunity.
⸻
Marcus Terentius Varro
Varro proposed that extremely tiny creatures that could not be seen might cause disease.
He described tiny creatures entering the body through the:
* mouth
* nose
This was an important idea because microscopes did not yet exist.
Remember
Varro → invisible tiny creatures may cause disease.
⸻
Ibn Sina / Avicenna
Ibn Sina wrote the important medical work:
Canon of Medicine
He described ideas involving:
* contagion
* spread of disease
* transmission through breath
* isolation of sick people
His work contributed to ideas that later became important for quarantine and infectious-disease control.
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🔬 Birth of Microbiology
The development of the microscope completely changed science.
For the first time, scientists could actually see microorganisms.
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Antonie van Leeuwenhoek
Extremely important name.
In 1675, Antonie van Leeuwenhoek used powerful simple microscopes to observe tiny organisms.
He called them:
“animalcules”
Today we know that some of the organisms he observed were:
* bacteria
* protists
Remember
Leeuwenhoek → first to describe bacteria/microorganisms seen through a microscope.
Think:
Leeuwenhoek = LOOKED at microbes.
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⭐ Golden Age of Microbiology
Approximately:
1857–1914
During this period, scientists made major discoveries connecting microorganisms with:
* fermentation
* disease
* medicine
* infection
Two huge names:
Louis Pasteur
and
Robert Koch
You are going to see both names repeatedly in microbiology.
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Louis Pasteur
Pasteur showed that microorganisms are responsible for fermentation.
He also developed:
Pasteurization
Pasteurization = using controlled heat to kill/reduce microorganisms that cause spoilage or disease.
He also worked on vaccines, including a vaccine against:
rabies
Pasteur will become especially important again in Section 3.1.
Remember
Pasteur
→ fermentation
→ pasteurization
→ vaccines
→ helped prove germ theory
→ disproved spontaneous generation
⸻
Robert Koch
Koch showed that particular microbes could cause particular diseases.
He identified microorganisms associated with diseases including:
* anthrax
* tuberculosis
* cholera
Remember
Koch → specific microbe → specific disease.
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🧪 Basic Microbiology Laboratory Tools
You don’t need to master these yet, but recognize the terms.
Microscope → magnifies microbes.
Stains/dyes → add color/contrast so microorganisms are easier to see.
Growth media → nutrients/material used to grow microorganisms in the laboratory.
Petri dish → shallow dish commonly used to hold growth media.
Test tube → can contain liquid or solid/semi-solid growth media.
Bunsen burner → flame that can be used during laboratory sterilization procedures.
These will make much more sense once you start doing microbiology lab work.
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1.2 A Systematic Approach
Now we move from discovering microbes to:
“How do scientists organize and name all these different organisms?”
⸻
Taxonomy
Definition
Taxonomy = classification, description, identification, and naming of living organisms.
Think:
Taxonomy = biological organization system.
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Carolus Linnaeus
Linnaeus developed an important system for classifying organisms.
The main levels used in classification include:
Kingdom → Phylum → Class → Order → Family → Genus → Species
A common memory trick:
K P C O F G S
King Philip Came Over For Good Soup
You should know the order.
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Species
Species is the most specific/basic taxonomic level in this hierarchy.
Example:
Homo sapiens
Homo = genus
sapiens = species
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Binomial Nomenclature
Very important term.
Binomial = two names.
Every organism receives a scientific name consisting of:
Genus + species
Example:
Homo sapiens
Rules:
Genus
* first letter CAPITALIZED
species
* lowercase
Both should normally be italicized when typed.
Correct:
Homo sapiens
Not:
Homo Sapiens ❌
homo sapiens ❌
Homo Sapiens ❌
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🌳 Phylogeny
Phylogeny = evolutionary relationship/history between organisms.
Scientists can represent these relationships with a:
Phylogenetic tree
A phylogenetic tree shows how organisms are believed to be evolutionarily related.
Organisms with a more recent common ancestor are considered more closely related.
⸻
Classification Changed Over Time
Scientific classification did not stay the same.
Linnaeus
Originally divided nature into kingdoms including:
* animals
* plants
* minerals
The mineral kingdom was later abandoned.
⸻
Ernst Haeckel
Added:
Protista
for many unicellular organisms.
He later proposed Monera for organisms lacking nuclei.
Remember:
Haeckel → Protista
⸻
Robert Whittaker
Developed a five-kingdom system:
Animalia
Plantae
Fungi
Protista
Monera
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🧬 Carl Woese — VERY IMPORTANT
Carl Woese used differences in:
ribosomal RNA (rRNA)
to study evolutionary relationships.
His work helped establish the modern:
THREE-DOMAIN SYSTEM
🟠 Bacteria
🟣 Archaea
🔵 Eukarya
This is very important for your Week 1 material.
Memorize:
BAE
Bacteria
Archaea
Eukarya
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Bergey’s Manuals
These are important references used in bacteriology.
They help scientists:
* classify bacteria
* identify bacteria
You probably don’t need every detail yet, but recognize the name:
Bergey’s Manual
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How Can Bacteria Be Identified?
Scientists can identify microorganisms using things such as:
Biochemical tests
Look at chemical/metabolic characteristics.
DNA/RNA analysis
Examines genetic material.
Serological tests
Use reactions involving antibodies/antigens.
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1.3 Types of Microorganisms
This section is VERY IMPORTANT.
You need to understand the major groups.
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🌎 Three Domains of Life
Again:
1. Bacteria
2. Archaea
3. Eukarya
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Before We Continue: Two Big Cell Types
You will hear these words constantly:
PROKARYOTE vs EUKARYOTE
Prokaryotic cells
DO NOT have a membrane-bound nucleus.
Bacteria = prokaryotic
Archaea = prokaryotic
Eukaryotic cells
DO have a membrane-bound nucleus.
Examples include:
* animals
* plants
* fungi
* protozoa
* algae
Super important:
Prokaryote = NO nucleus
Eukaryote = HAS nucleus
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🦠 BACTERIA
Bacteria are:
* unicellular
* prokaryotic
* found almost everywhere
Some bacteria are helpful.
Some bacteria can cause disease.
Many bacteria have cell walls.
You’ll learn much more about bacterial structures later.
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🌋 ARCHAEA
Archaea are also:
* unicellular
* prokaryotic
Like bacteria, they do not have a nucleus.
BUT:
Archaea ≠ Bacteria
They differ in:
* genetics
* evolutionary history
* metabolic pathways
* cell membrane composition
* cell wall composition
Archaea occur in many environments.
Important textbook point
No archaea have been identified as human pathogens.
Remember
Bacteria + Archaea = Prokaryotes
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🔵 EUKARYA
Eukaryotic microorganisms include:
Algae
Protozoa
Fungi
Helminths
These have eukaryotic cells.
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🌿 ALGAE
Algae can be:
* unicellular
* multicellular
They are similar to plants in an important way:
They perform photosynthesis.
Photosynthesis = using light energy to make chemical energy/food.
Remember:
Algae → photosynthesis.
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🧫 PROTOZOA
Protozoa are:
* unicellular
* eukaryotic
* structurally more complex than bacteria
Many are capable of movement.
Remember
Protozoa → single-celled eukaryotes, often motile.
Motile = able to move.
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🍄 FUNGI
Fungi studied in microbiology include:
Yeasts
Usually unicellular.
Molds
Usually grow as multicellular filament-like structures.
Examples of fungi can be microscopic even though other fungi, such as mushrooms, are large.
Remember
Fungi → yeast + molds
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🪱 HELMINTHS
Helminths = parasitic worms.
You may think:
“A worm isn’t microscopic. Why is it in microbiology?”
Good question.
Adult worms may be large enough to see.
BUT their:
* eggs
* larvae
can be microscopic.
Therefore they are studied in microbiology.
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🦠 VIRUSES
Viruses are different from cellular organisms.
Viruses are ACELLULAR.
Acellular = not made of cells.
Viruses cannot reproduce independently.
They require a:
Host cell
to reproduce.
Remember
Virus = acellular + requires host to reproduce
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⭐ Major Microorganism Comparison
Group Cell type Nucleus? Important idea
Bacteria Prokaryotic ❌ Some cause disease
Archaea Prokaryotic ❌ Different from bacteria; no known human pathogens
Fungi Eukaryotic ✅ Yeasts + molds
Protozoa Eukaryotic ✅ Unicellular, often motile
Algae Eukaryotic ✅ Photosynthesis
Helminths Eukaryotic ✅ Parasitic worms
Viruses Acellular No cell Need host to reproduce
🔥 This table is worth knowing very well.
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3.1 Spontaneous Generation
This is mainly about one historical question:
Where does life come from?
People once believed:
Spontaneous Generation
Spontaneous generation = the belief that living organisms can arise from nonliving material.
Examples people once believed:
rotting meat → maggots
mud → frogs
old food → microorganisms
Today we know this idea is incorrect.
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Francesco Redi
Redi tested whether maggots appeared spontaneously from meat.
He compared meat that flies could reach with meat protected from flies.
Result
Maggots appeared when flies could access the meat.
This suggested:
Maggots came from flies — not directly from the meat.
Remember
Redi → meat + flies + maggots
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John Needham
Needham performed experiments with broth.
He boiled broth and then observed microbial growth afterward.
He interpreted this as evidence supporting:
Spontaneous generation.
Remember
Needham → supported spontaneous generation.
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Lazzaro Spallanzani
Spallanzani disagreed.
He boiled broth for longer and sealed the containers more carefully.
The sealed broth did not show microbial growth.
He argued that microbes came from contamination from the environment rather than being generated spontaneously.
Remember
Spallanzani → argued against spontaneous generation.
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🦢 Louis Pasteur’s Swan-Neck Flask Experiment
This is VERY IMPORTANT.
Pasteur used flasks with long curved necks.
Why the curved neck?
Air could enter the flask.
BUT:
Dust and microorganisms became trapped in the curved neck.
So the broth remained uncontaminated.
When microorganisms could reach the broth, microbial growth occurred.
Conclusion
Microorganisms did NOT spontaneously appear.
They came from microorganisms already present in the environment.
Pasteur helped establish the principle:
“Life comes from life.”
Exam memory
Pasteur → swan-neck flask → disproved spontaneous generation.
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3.2 Foundations of Modern Cell Theory
Now we move from:
“Where do microbes come from?”
to:
“What is life made of?”
Answer:
CELLS
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🧬 Cell Theory
The textbook describes the development of the idea that cells are the fundamental units of life.
The central ideas are:
1. All living organisms are made of one or more cells.
2. The cell is the fundamental/basic unit of life.
3. Cells arise from pre-existing cells.
Think:
Life → cells → cells come from cells.
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Robert Hooke
In the 1660s, Robert Hooke examined cork with a microscope.
He saw tiny compartments and called them:
“cells”
Remember
Hooke → named/described cells.
Don’t mix him up with Leeuwenhoek:
Hooke → cells
Leeuwenhoek → microorganisms
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Matthias Schleiden
Schleiden studied plants.
He concluded that:
Plants are made of cells.
Remember:
Schleiden → plants
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Theodor Schwann
Schwann studied animals.
He concluded:
Animals are made of cells.
Remember:
Schwann → animals
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Robert Remak
Remak provided evidence that cells form through the division of existing cells.
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Rudolf Virchow
Virchow strongly promoted the idea:
Cells come from other cells.
So:
New cells do not spontaneously appear.
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Easy Scientist Memory
Hooke → saw/named cells
Schleiden → plants
Schwann → animals
Remak/Virchow → cells come from existing cells
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🧬 Endosymbiotic Theory
This sounds difficult, but the basic idea is simple.
Endosymbiotic theory says:
Mitochondria and chloroplasts were originally bacteria-like prokaryotic cells.
A larger ancestral cell engulfed them.
Instead of being destroyed, the cells developed a mutually beneficial relationship.
Eventually, the engulfed bacteria evolved into:
Mitochondria
and
Chloroplasts
inside eukaryotic cells.
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Evidence for Endosymbiotic Theory
Mitochondria and chloroplasts have similarities to bacteria.
They have:
Their own DNA
Their DNA resembles bacterial DNA.
Their own ribosomes
Their ribosomes resemble bacterial ribosomes.
They reproduce through a process similar to binary fission
Binary fission is a major way bacteria reproduce.
Easy version
Mitochondria and chloroplasts act strangely like bacteria because their ancestors were bacteria.
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Lynn Margulis
Lynn Margulis helped develop and promote the modern endosymbiotic theory.
Remember
Margulis → endosymbiotic theory
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🦠 Miasma Theory vs Germ Theory
This distinction is very important.
Miasma Theory
Old idea:
Disease comes from “bad air” associated with rotting material.
Think:
Bad smell → disease.
This theory was eventually replaced.
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Germ Theory
Germ theory = many diseases are caused by microorganisms.
Think:
Microbe enters/infects body → disease
Scientists whose work helped establish germ theory included:
* Ignaz Semmelweis
* John Snow
* Louis Pasteur
* Joseph Lister
* Robert Koch
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🧼 Ignaz Semmelweis
Semmelweis worked around childbirth.
He noticed that patients treated by doctors and medical students had much higher rates of puerperal fever than patients cared for by midwives.
Medical students often went from:
autopsies → examining living patients
without washing their hands.
Semmelweis introduced handwashing with chlorinated lime solution.
Result
Maternal deaths fell dramatically.
Remember
Semmelweis → HANDWASHING
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💧 John Snow
John Snow investigated cholera outbreaks in London.
He connected cholera cases with:
contaminated water.
His work helped show that disease wasn’t simply coming from “bad air.”
He is important in the history of:
Epidemiology
Epidemiology = study of disease patterns and spread in populations.
Remember
Snow → cholera + contaminated water + epidemiology
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Joseph Lister
Lister applied ideas about microorganisms to surgery.
He promoted:
* handwashing
* cleanliness
* sterilization
* antiseptic techniques
He used carbolic acid (phenol) to reduce infections during surgery.
Result
Surgical infections decreased.
Remember
Lister → antiseptic surgery
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Robert Koch — Again
Koch developed:
Koch’s postulates
These helped scientists determine whether a particular microorganism causes a particular disease.
Basic idea:
specific microorganism → specific disease
You will learn Koch’s postulates in more detail later.
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🔥 WEEK 1 — PEOPLE YOU NEED TO KNOW
Scientist/person Remember THIS
Hippocrates Disease has natural causes
Thucydides Early observation of immunity
Varro Invisible creatures may cause disease
Leeuwenhoek Observed microbes/bacteria
Linnaeus Taxonomy + naming organisms
Haeckel Added Protista
Whittaker Five kingdoms
Woese Three domains; used rRNA
Redi Meat + flies + maggots
Needham Supported spontaneous generation
Spallanzani Evidence against spontaneous generation
Pasteur Swan-neck flask; fermentation; germ theory
Hooke Described/named cells
Schleiden Plants are made of cells
Schwann Animals are made of cells
Remak/Virchow Cells come from cells
Margulis Endosymbiotic theory
Semmelweis Handwashing
John Snow Cholera + contaminated water
Lister Antiseptic surgery
Koch Specific microbes cause specific diseases
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🚨 THE 15 THINGS I WOULD MEMORIZE FIRST
Don’t try to memorize every paragraph tonight. Start here:
1. Microbiology = study of microorganisms.
2. Fermentation uses microbes to convert sugars into products such as alcohol, gases, or acids.
3. Leeuwenhoek observed microorganisms.
4. Pasteur and Koch were major scientists during the Golden Age of Microbiology.
5. Taxonomy = classification and naming of organisms.
6. Binomial nomenclature = Genus + species.
7. Three domains = Bacteria, Archaea, Eukarya.
8. Bacteria + Archaea = prokaryotes.
9. Prokaryote = no membrane-bound nucleus.
10. Eukaryote = has membrane-bound nucleus.
11. Virus = acellular and needs a host to reproduce.
12. Spontaneous generation = life arises from nonliving matter.
13. Pasteur’s swan-neck flask helped disprove spontaneous generation.
14. Cell theory = organisms are made of cells, cells are the basic unit of life, and cells come from existing cells.
15. Germ theory = microorganisms can cause disease.
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🧠 Super-Simple Week 1 Mental Map
Think about the entire week’s reading as one story:
PART 1 — Humans discover microbes
People used microbes before knowing they existed.
↓
Leeuwenhoek sees them.
↓
Scientists begin studying them.
⸻
PART 2 — Scientists organize microbes
Linnaeus → Taxonomy
↓
Woese → 3 domains
↓
Bacteria | Archaea | Eukarya
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PART 3 — Scientists ask where life comes from
People believed in spontaneous generation.
↓
Redi + Spallanzani question it.
↓
Pasteur disproves it.
↓
Life comes from existing life.
⸻
PART 4 — Scientists understand cells
Hooke → cells
↓
Schleiden → plants
Schwann → animals
↓
Remak/Virchow → cells come from cells
↓
Cell Theory
⸻
PART 5 — Scientists understand disease
Old:
Miasma = bad air causes disease ❌
↓
New:
Germ theory = microorganisms can cause disease ✅
↓
Semmelweis → handwashing
Snow → contaminated water
Lister → antiseptic surgery
Pasteur → microbes
Koch → specific microbe causes specific disease
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