What is Life?
How is it Organized?
How do we Classify it?
What is Knowledge?
How do we obtain it?
• Get out a piece of paper and a pen.
• Watch this video
• Write down anything that you recognize, or
any thoughts that come to your mind as you
watch.
Scale: 10-16 meters = 100 am = 100 attometers
Scale: 10-15 meters = 1 fm = 1 femtometer
Scale: 10-14 meters = 10 fm = 10 femtometers
Scale: 10-13 meters = 100 fm = 100 femtometers
Scale: 10-12 meters = 1 pm = 1 picometer
Scale: 10-11 meters = 10 pm = 10 picometers
Scale: 10-10 meters = 100 pm = 100 picometers
Scale: 10-9 meters = 1 nm = 1 nanometer
Scale: 10-8 meters = 10 nm = 10 nanometers
Scale: 10-7 meters = 100 nm = 100 nanometers
Scale: 10-6 meters = 1 µm = 1 micrometer
Scale: 10-5 meters = 10 µm = 10 micrometers
Scale: 10-4 meters = 100 µm = 100 micrometers
Scale: 10-3 meters = 1 mm = 1 millimeter
Scale: 10-2 meters = 1 cm = 1 centimeter
Scale: 10-1 meters = 10 cm = 10 centimeters
Scale: 100 meters = 1 meter
Scale: 101 meter = 10 meters
Scale: 102 meters = 100 meters
Scale: 103 meters = 1 km = 1 kilometer
Scale: 104 meters = 10 km = 10 kilometers
Scale: 105 meters = 100 km = 100 kilometers
Scale: 106 meters = 1 Mm = 1 megameter
Scale: 107 meters = 10 Mm = 10 megameters
Scale: 108 meters = 100 Mm = 100 megameters
Scale: 109 meters = 1 Gm = 1 gigameter
Scale: 1010 meters = 10 Gm = 10 gigameters
Scale: 1011 meters = 100 Gm = 100 gigameters
Scale: 1012 meters = 1 Tm = 1 terameter
Scale: 1013 meters = 10 Tm = 10 terameters:
Scale: 1014 meters = 100 Tm = 100 terameters
Scale: 1015 meters = 1 Pm = 1 petameter
Scale: 1016 meters = 10 Pm = 10 petameters (1ly)
Scale: 1017 meters = 10 Pm = 100 petameters (~10 light years)
Scale: 1018 meters = 1 Em = 1 exameter (~100 light years)
Scale: 1019 meters = 10 Em = 10 exameters (~1 000 light years)
Scale: 1020 meters = 100 Em = 100 exameters (~10 000 light years)
Scale: 1021 meters = 1 Zm = 1 zettameter (~100 000 light years)
Scale: 1022 meters = 10 Zm = 10 zettameters (~1 million light years)
Scale: 1023 meters = 100 Zm = 100 zettameters (~10 million light years)
Scale: 1024 meters = 1 Ym = 1 yottameter (~100 million light years)
Scale: 1025 meters = 10 Ym = 10 yottameters (~1 thousand million light years)
Quarks
Within the proton
The carbon nucleus
The nucleus
Within the electron cloud
The inner electron cloud
Carbon's outer electron shell
The molecules of DNA
DNA within a virus
A virus
Virus on a bacterium
Bacteria
Pollen
A bee's eye
A bee's head
A lily and a bee
The one-meter square
A pond with lily pads
Japanese Tea Garden
Golden Gate Park
San Francisco
The San Francisco Bay Area
California
North and Central America
Earth
Earth and Moon
Four days in July
Venus, Earth, and Mars
The orbit of Jupiter
The Solar System
Sol
Sol
Sol
The nearest stars
Stars within 50 light years
The stars within the arm
Our spiral arm
The Milky Way
The local group
The Virgo Cluster
Galactic Clusters
The limit of our knowledge
Nature appears to have order. There is an underlying organization to it.
How do we know this?
It is a basic human instinct to seek order in things. There is an, underlying premise to the way in
which we examine things.
How we learn:
Authority (“Look both ways before crossing the street!”)
Experience (I should have looked both ways before crossing the street…)
Intuition (“If I’ve seen cars driving by fast, then when I get to the corner, I should probably look both
ways before crossing the street”)
Science (90% of people that cross the street but do not look both ways before moving cost upwards of
1.2 million dollars a year in public health costs. According to these statistics, we strongly recommend
those crossing streets to look both ways)*
*I made that up.
A
The Dumbbell Nebula
B
A Cancer Cell Nucleus
A
Cateye Nebual
B
Actin Filaments &
PML Bodies
• Our mind comprehends reality by categorizing and
dividing things up into chunks
• Science is the methodological way in which we go
about this. While it is of course prone to error (we’re
only human), when attempted faithfully, it removes
our emotions and subjectiveness, yielding the most
accurate information to the best of our ability.
The Scientific Method
It starts with a phenomenon. Something that piques our curiosity.
We take note of an observation.
Then, drawing on ….
current knowledge
past experiences
Intuition
discussions with others
Creativity
… we reason our way through our thoughts, and come up with an idea.
This kind of reasoning is Inductive.
The idea we call a hypothesis “the basis of an argument” hypo, under, thesis, proposition.
We sometimes refer to the hypothesis as a “model”.
We then make a prediction based on our idea, using Deductive Reasoning, which follows “if,
then” logic.
The Scientific Method
Our prediction leads us to an experimental design that gives us the opportunity to falsify our
prediction.
FALSIFIABILITY is the underlying concept here. It’s not science if it can’t be disproven. That
doesn’t mean it isn’t necessarily valid on various levels – it’s just not science.
We carry out an experiment (and include controls)
We obtain data, and analyze, and make conclusions.
Does it fit the hypothesis or model?
Inductive Reasoning
General Idea
Specific Knowledge
“My back is killing me”
Induces you to think
“Sitting for long periods of time
Can hurt my back”
Deductive Reasoning
Specific Knowledge
General Idea
“Old Milk Curdles”
You deduce that
“My milk might taste bad.”
Definitions
• Inductive Reasoning: Bottom-Up; moving from something
specific to something general. (“induce” brings something
from nothing – induce change, etc. It brings something new
into being.)
• Deductive Reasoning: Top-Down; moving from the general to
the more specific. (“Deduce” is subtracting – deduct a sum of
money from an account, etc. Take away the layers and
uncover what’s underneath.
– In the case of the science, you dig through the data and uncover a
conclusion.
Scientific Method - Summary
Phenomenon
Something Interesting
Observation
Senses / Instruments
Hypothesis
Inductive Reasoning
Prediction
Falsifiable
Experiment
Controls
Data
Analysis
Conclusion
Does it fit the hypothesis?
Cell Theory
Atomic Theory
Evolution Theory
Gravitational Theory
Etc.
Theory
A hypothesis that is
continually
supported by
experimental data
over time, with no
direct
contradictions
Principle / Law
A theory that has
been around long
enough without
being refuted.
• Gather into groups of 3-4. Designate a group leader.
• As a group, write a list of 5-10 biological objects. They can be anything
(reasonable). Keep It clean!
• As a group, discuss and pick two.
– Link them together in a creative way to describe some kind of phenomenon,
from which you will form a hypothesis using inductive reasoning.
– Raise your hand for help.
– Group leaders make final decisions if there are any disagreements.
• Each group will read their hypothesis out loud.
• Each group will then come up with a Prediction for that hypothesis by
deductive reasoning.
• From that prediction, each group will design a simple experiment to test
the prediction, and include appropriate controls.
– Each group will briefly describe their experiment and controls.
– We will try to go over each experiment’s strengths and weaknesses.
1.
2.
3.
4.
5.
Organized
Acquires material & energy
Respond to its environment
Reproduce & Develop
Adapt to its environment
Atoms make up molecules
…which make up macromolecules
…which make up cellular structures
…which make up cells
…which make up cell systems
…which make up organs
…which make up organ systems
…which make up organisms
…which make up populations
…which make up communities,
…which, together with the environment, make up ecosystems
…which make up the biosphere.
1
Emergence
Each new level of organization leads to new properties
of the system that the individual components do not
have (e.g. cells can’t see, but as a system, the eye
can)
Therefore, new properties emerge from the system as
it becomes more complicated.
These new traits are called emergent properties.
Can you think of other emergent properties?
1
Emergence
• Elementary particles (electrons, proteins, neutrons)
do not have color.
But together, they form particle systems (atoms), which can
absorb specific wavelengths of electromagnetic radiation.
Therefore, Color is an emergent property of elementary
particles
• Surface tension of water emerges as a result of the
hydrogen bonding of water molecules
• Emergent structures of groups of organisms: flocks
of birds, ant colonies, schools of fish.
1
Things that are alive can extract energy from
their environment, and use it to perform
work.
This work includes a vast amount of different
processes…
maintaining homeostasis (pH, salts, etc.)
Constantly repairing DNA against external insults
every cell in your body has about 20,000 DNA damage
events a DAY… and you have ~3 trillion cells
2
Homeostasis
Homos, same, stasis, standing still.
Maintaining a stable, constant set of parameters.
You sweat when you’re hot, shiver when you’re cold, hunger
when you’re low on energy, and thirsty when fluids get low.
You breath heavily when you run so you can maintain the
same level of oxygen in your system as it uses it faster.
There’s a ‘zone’ for each characteristic. Think of a standard blood
test – there is a range in which things can fall. The farther you
move out of the zone, the more uncomfortable you feel… pain
and discomfort are necessary survival traits.
2
Metabolism
Metabole, “change”
The total sum of all chemical reactions taking
place inside an organism responsible for
breaking down the raw materials (from food
usually) and building what they need to make
their parts (e.g. fix a damaged gene, patch a
hole in the membrane, etc.) and products (e.g.
hormones)
2
Ensures survival.
Running away from a bear, fire, or gun-wielding
crazy person; Getting closer to the fire on a
cold night
Moths to a flame… so it’s not always a good
thing.
Plants bend towards light. This is an example of
tropism, in this case, phototropism. What
other kinds of tropisms are there?
3
Modern Life only comes from other modern life.
Question: “What came first, the chicken or the egg?”
Answer: “There is no beginning or end to a circle”
Development: What decides that an embryo develops
into a human or a mouse?
Our Genes. We’re 85% genetically identical to mice and
99.98% (or so) identical to chimps.
4
It is important to understand that offspring are NOT identical to
parents. There are many processes at work that cause a
continual variation between generations.
“If you can’t beat it, join it.”
Brown Fat: instead of making ATP, the cells simply give off extra
heat.
Webbed feet of a duck
Natural Selection: The principle that organisms with beneficial
traits with respect to the environment, will, over time,
produce more offspring.
Descent with modification: All living being share the same basic
characteristics (particularly at the molecular level); this
suggests there was a single common ancestor (LUCA)
5
We will discuss this at more length when we cover the Principles
of Evolution.
We work to name all
living things.
Invented for our
Own understanding
Existing
relationships we
uncover through
research
We work to categorize all
living things based on their
similarity to each other.
We discover each living thing’s evolutionary
connections with each other
Binomial
Nomenclature
Taxonomy
Phylogenetics
Taxonomy: From greek taxis or tasso, meaning
“arrangement”
Nomia, “method”, “usage”, “law”
The swedish ‘natural philosopher’, Charles
Linnæus, is considered the father of modern
scientific classification.
• A human contrivance that attempts to pigeonhole every living
thing on earth, both extinct and extant, into a single category.
Problems:
• Things don’t always fit within the system (Platypus, anyone?)
• There is still MUCH to learn and discover.
– There are still huge realms of “undiscovered country” in the realm of life
science, and new surprises are happening on a regular basis.
» Recently: Largest virus discovered, found to be on par with bacteria –
and possess much – but not all – of what a cell is thought to have. How
do we classify it??
» Plasma in outer space is shown to actually develop organized structure.
This clearly does not fit within the paradigm of carbon-based life. Are
there other paradigms of life?
» Concept: Life as an emergent property of complex systems.
• Bottom Line: We’re still working on it.
•
Also a work in progress
•
There is a distinction between naming an organism or group of organisms, and
grouping them.
– Whether I group you according to where your ancestors came from, or whether I group
by your hair color, you are still homo sapiens and don’t change your name.
•
This is important, because while we can readily identify two different species (and
therefore give them unique names with confidence), because we are still trying to
understand the deepest complexities of biology at the molecular level, our
classifications schemes remain imperfect.
•
This is where Phylogenetics comes into play. This is the study of how related
species are based on their evolutionary relationships (particularly how their DNA
sequences fit together, forming branched lineages.
– This type of
• A “taxon” (plural taxa) is just a group of organisms – or
sometimes, just a species.
• The current system underwent its last major revision in 1990,
when the most inclusive taxon level (the kindgom) was
replaced by an even MORE inclusive taxon called a “Domain”.
• Have you ever played 20 questions and wondered why we
start by saying “is it an animal, vegetable, or mineral”? Those
were the original Three Kingdoms set up by Charles Linnaeus
in his Systema Naturae (1735-1758, 10 editions overall)
• We used to classify things by morphology (how
things looks), shared characteristics (bony fishes vs.
cartilaginous fishes; warm-blooded vs. coldblooded), etc. This is the field of taxonomy.
• With the advent of genetic research, things have
changed. We are now beginning to shuffle around
the way in which things are classified depending
upon their evolutionary relationship to one another.
– Ultimate goal: The Tree of Life, where every organism is
linked to every other through a continuous chain of
lineages.
Domain
Currently Accepted
Taxons
Kingdom
Phylum
Class
Order
Family
Taxons vary in
Botany
Zoology
Virology
Genus
Species
Domain
3
Bacteria
Archae
Eukarya
Domain
Kingdom
Bacteria
Archae
Eukarya
Kingdoms in progress….
4
Protista
Plantae
Fungi
Animalia
Protists are the “pot-luck” kingdom.
There are:
“Plant-Like” Protists
“Animal-Like” Protists
“Fungus-Like” Protists
Domain
Kingdom
Phylum
Over 70
Bacteria
Archae
Eukarya
Kingdoms in progress….
Protista
16 bacteria
Plantae
Fungi
Animalia
11 plant 6 fungi
38 animal
2-3 Archae
From the greek Phyle, “tribe” or “clan” and
phylon, “race” or “stock”.
Generally speaking, phylum (also known as
‘divisions’ sometimes, mostly by botanists) are
arranged based on shared evolutionary traits and
physical appearance (up until only a the last 2
decades have we been able to more accurately
classify life based on gene sequences)
Domain
Kingdom
Phylum
Chordates:
Have notocords.
Vertebrates and Invertebrates.
Includes both
(in higher vertrebrates the notocord is only
present during development, and is eventually
replaced by the spinal cord)
A ‘sub’ phylum includes the vertebrates. Here is
an example in which the current taxonomy isn’t
very orderly.
Domain
Kingdom
Phylum
Class
Mammals
Order
Family
Genus
Species
Domain
Kingdom
Phylum
Class
Carnivores.
Order
Family
Genus
Species
Domain
Kingdom
Phylum
Class
Generally named for a type of genus.
Order
Family
Genus
Species
Canidae (dogs, wolves, foxes, coyotes,
dingoes, jackals, etc.)
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Also named for a type of genus.
Canidae (dogs, wolves, foxes, coyotes,
dingoes, jackals, etc.)
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Domestic Dogs are Canis Lupus. However, some
classify them as a sub-species of Grey Wolf, Canis
Lupus Familiaris.
So genetically speaking, there is VERY little
difference between that little fluffy pocketbook dog
and the huge mastiff.
• Classical Taxonomy (organizing life by similar
characteristics) is still distinct from
Phylogenetics (connecting organisms by their
evolutionary relationships, mostly through
biochemical and genetic links)
• It is still unclear how these two will merge.