Bio 121: General Biology
Sections MC & SD
SC Room 309
Dr. Ippolito
Agenda
0:00
Opening Remarks
Attendance
Round Circle Introduction
Contact Information
0:30
Syllabus Handout & overview
Question to the Class: What are your technology expectations?
Break (10 minutes)
1:10
Lecture & Discussion: From Introduction & Parts of Topic 1 of the Syllabus
Knowledge, learning, and order; Hallmarks of Life; Organizing & Naming Life; The
Scientific Method
2:15
Break into Groups of 3-4
Activity: Scientific Method
3:05
Meeting Adjourned
Thoughts on Taking Good Notes
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What worked for me:
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Materials:
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Workflow:
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a spiral notebook, folder,
3-Ring Binder with Sections for every class
lots of 3-ring punched, college-ruled paper
A set of pens & pencils, etc.
Lecture notes taken in the spiral notebook. Handouts in the folder.
Same day of lecture (or day after): rewrite lecture notes (includes organizing it neatly) on fresh paper;
keep a separate page for questions I have; add this to my 3-ring binder section for the class.
Chapter reading: Add notes to my rewritten lecture notes; attempt to answer all confusing points and
questions from lecture.
End Product: EASY studying for tests. And I would actually remember the material for a
long time.
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Research shows clearly that spreading out your work over time – not doing work ‘last
minute’, or pulling all-nighters – is the BEST way to learn and retain information.
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This is Less important for peripheral classes. ESSENTIAL for “core” classes are the
backbone of the rest of your education!
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Recall HS Spanish; freshmen year chemistry (and then organic and physical)
Other Tips & Tactics
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Read the chapter summary FIRST.
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Our brains work best when we see the big picture and dig in, as opposed to the opposite
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(study on maps and remembering)
Keep a vocabulary list.
Make Flash Cards
Don’t just memorize. Understand the concept.
Form a study group today!
Everyone learns differently, having strengths and weaknesses in the following ways:
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Auditory (hear) (lectures)
Visual (see) (reading the book; handouts, etc.)
Tactile (do) (activities, lab reports, rewriting notes & diagrams yourself)
Doing all of these is best.
Survey the room to get a feel for the types of learners we have.
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STAY ORGANIZED. Have a folder for handouts and returned graded material. Keep up regularly
with your course work. Make it a priority.
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TIME MANAGEMENT: Rule of thumb for doing college work: For every hour in the classroom,
devote 2 hours outside of it. Some courses require even more; some less. CREATE A WEEKLY
SCHEDULE AND SET GOALS.
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Ideal: .5 to 1 hour of work a day (every day) if you can. Some days break this into two or more
sessions. Some days it might be 2 hours with short breaks. Do what works for you.
Lecture 1
What is life?
How do we classify it?
What is knowledge?
How do we obtain it?
Knowledge, Learning, and Order
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Nature appears to have order. There is an underlying organization to it.
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It is a basic human instinct to seek order in things. There is an, underlying premise to
the way in which we examine things.
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How do we know this?
Our book mentions 4 distinct paradigms of ordering the world
Religion
Esthetics
Ethics
Science
How we learn:
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Authority
Experience
“Intuition”
Science
A
B
The Dumbbell Nebula
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.
Five Hallmarks of Life on Earth
1. Organized
2. Acquires material & energy
3. Respond to its environment
4. Reproduce & Develop
5. Adapt to its environment
Five Hallmarks of Life on Earth
Organized
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.
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Can you think of other emergent properties?
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Emergence
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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.
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Five Hallmarks of Life on Earth
Acquires material & energy
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Things that are alive can extract energy from
their environment, and use it to perform work.
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This work includes a vast amount of different
processes…
maintaining homeostasis (pH, salts, etc.)
 Constantly repairing DNA against external insults
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every cell in your body has about 20,000 DNA damage
events a DAY… and you have ~3 trillion cells
Homeostasis
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2
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.
Metabolism
“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)
 Metabole,
2
Five Hallmarks of Life on Earth
Respond to its environment
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3
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?
Five Hallmarks of Life on Earth
Reproduce & Develop
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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”
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Development: What decides that an embryo develops
into a human or a mouse?
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Our Genes. We’re 85% genetically identical to mice and 99.98%
(or so) identical to chimps.
Five Hallmarks of Life on Earth
Adapt to its environment
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Brown Fat: instead of making ATP, the cells simply give
off extra heat.
Webbed feet of a duck
We will discuss this at more length when we cover the
Principles of Evolution.
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)
How we Organize Life
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
How Life is Currently Classified
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.
Taxonomy
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A human contrivance that attempts to pigeonhole every
living thing on earth, both extinct and extant, into a single
category.
Problems:
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Things don’t always fit within the system (Platypus, anyone?)
There is still MUCH to learn and discover.
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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 carbonbased life. Are there other paradigms of life?
 Concept: Life as an emergent property of complex systems.
Bottom Line: We’re still working on it.
Nomenclature
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Also a work in progress
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There is a distinction between naming an organism or group of organisms,
and grouping them.
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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.
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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.
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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.
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This type of
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A “taxon” (plural taxa) is just a group of organisms – or
sometimes, just a species.
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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”.
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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 (17351758, 10 editions overall)
Phylogenetics
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.
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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
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
Generally 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.
The Scientific Method
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It starts with a phenomenon. Something that piques our curiosity.
We take note of an observation.
Then, drawing on ….
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current knowledge
past experiences
Intuition
discussions with others
Creativity
… we reason our way through our thoughts, and come up with an idea.
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This kind of reasoning is Inductive.
The idea we call a hypothesis “the basis of an argument” hypo, under,
thesis, proposition.
We then make a prediction based on our idea. We make this prediction
using “deductive reasoning”.
The Scientific Method
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It starts with a phenomenon. Something that piques our
curiosity.
We take note of an observation.
Drawing on
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current knowledge
past experiences
Intuition
discussions with others
Creativity
we reason our way through our thoughts, and come up with an
idea.
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This process of reasoning is called Inductive reasoning
Inductive Reasoning
General Idea
Specific Knowledge
“My back is killing me”
Induces you to think
“Sitting for long periods of time
Can hurt one’s back”
Deductive Reasoning
Specific Knowledge
General Idea
“Old Milk Curdles”
You deduce that
“My milk might taste bad.”
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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.)
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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.
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In the case of the science, you dig through the data and uncover
a conclusion.