Transcript 01 Introduction-01

Chapter 1 – Exploring Life
1
Why Study Biology?

Science


Biology


Systematic method of inquiry
Scientific study of life
Important to study and understand science
Awareness and appreciation of life
 Important in decisions of life

o
Issues dealing with biology arise daily
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Science, Technology, and Society
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The goal of science -- understanding natural phenomena
The goal of technology – applying scientific knowledge
for some specific purpose
Science and technology -- interdependent

Science -- marked by “discoveries”

Technology -- marked by “inventions”
Science + Technology?
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DNA
Ethical issues?
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Building on the Work of Others

Cooperation
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Communication
Repeatability

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
Professionals, graduate students, undergraduate students
Different groups often work on same research
Model Organisms (e.g., Drosophila melanogaster or
Arabidopsis thaliana)
Diverse viewpoints -> Serendipity

Printing press -- China (paper and ink) and Europe (mass
production in mills)
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Logical Thought

Induction (Inductive Reasoning) – deriving
general principles from particular facts or
occurrences (esp. when repeated)


The sun always rises in the east!
Deduction (Deductive Reasoning) – deriving a
conclusion from the stated premises by
reasoning from the general to the specific

If organisms are made of cells (premise 1), and if
humans are organisms (premise 2), then humans are
composed of cells (deductive prediction)
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Scientific Inquiry
Inquiry -- search for information and
explanation
 The process of science:

 Discovery
o
science: describing nature
_________ Reasoning ?
 Hypothesis-based
o
science: explaining nature
_________ Reasoning ?
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Discovery Science
Describes nature
 Examples of discovery science:

 understanding
cell structure
 expanding databases of genomes
 Induction in Discovery Science
 Generalizations
based on specific observations
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Types of Data


Data are recorded
observations
Two types of data:
Quantitative data:
numerical
measurements
 Qualitative data:
recorded
descriptions

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Hypothesis-Based Science
Proposing and testing hypotheses
 Hypotheses -- hypothetical explanations

 deductive
reasoning
 tentative answer to a well-framed question
 an explanation on trial -- making a prediction
that can be tested and falsified
 can NOT prove …..
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The Scientific Method

Observation
Many ways to make
observations
 Leads to (a) question

o
o
Why?
How?
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Observations
Question
Hypothesis #1:
Dead batteries
Hypothesis #2:
Burnt-out bulb
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Hypothesis #1:
Dead batteries
Hypothesis #2:
Burnt-out bulb
Prediction:
Replacing batteries
will fix problem
Prediction:
Replacing bulb
will fix problem
Test prediction
Test prediction
Test falsifies hypothesis
Test does not falsify hypothesis
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Deduction: The “If…then” Logic of HypothesisBased Science

Flow of logic from the general to the specific
 If
a hypothesis is correct, then we can expect a
particular outcome
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The
Process of
Science
EXPLORATION
AND
DISCOVERY
FORMING
AND
TESTING
HYPOTHESES
SOCIETAL
BENEFITS
AND
OUTCOMES
COMMUNITY
ANALYSIS
AND
FEEDBACK
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Mimicry and Camouflage

One species resembling something else for
“personal gain!”
Cryptic coloration – camouflage
 Aposematic coloration – warning coloration
 Batesian mimicry – harmless species resembling a
harmful one
 Müllerian mimicry – two or more species resembling
each other


Also seen in reproductive strategies
(wasps/orchids) and predation (angler fish)
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A Case Study: Investigating Coat
Coloration in Mouse Populations
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Color patterns vary widely -- sometimes
between members of the same species
Peromyscus polionotus with different color patterns
-- different environments
The beach mouse lives on white sand dunes
 The inland mouse lives on darker soil
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Camouflage Coloration in Mice
Florida
GULF OF
MEXICO
Beach population
Inland population
Beach
population
Inland population
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Camouflage Coloration in Mice
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Overarching Hypothesis – camouflage coloration
benefits by protecting from predation

Specific Hypothesis – mice with coloration that didn’t match
the habitat would be preyed on more heavily than the native
well-matched mice.
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Camouflage Coloration in Mice


“hundreds” of plastic mice
Repeatability!
Results
Percentage of
attacked models
Beach habitat
Inland habitat
100
50
0
Light models
Camouflaged
(control)
Dark models
Non-camouflaged
(experimental)
Light models
Non-camouflaged
(experimental)
Dark models
Camouflaged
(control) 20
The Myth of the Scientific Method
Idealized process of inquiry
 Rarely true textbook
 Repeatability

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Variables
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Only test one thing at a time!
Independent – the thing I manipulate

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E.g., fertilizer
Dependent variable – the thing that you’re
investigating

How much to the plants actually grow?
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The idea of CONTROL

What makes the difference?
Random chance
 Experimental design
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Experimental group vs control group
Variable of interest changes
 Control variability
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Control groups
Positive control
 Negative control

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Theories in Science
Theory -- broader than a hypothesis
 A scientific theory:

 Must
explain a body of facts
 Be able to predict future similar occurrences
 Be falsifiable and survive empirical experimentation
 supported by a large body of evidence
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Characteristics of Living Organisms
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Order
Evolutionary adaptation
Responses to the environment
Regulation
Energy processing
Growth and development
Reproduction
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Order
Regulation
Evolutionary
adaptation
Reproduction
Energy processing
Growth and
development
Response
to the
environment
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Viruses: A Nasty Puzzle

Like living organisms:
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Contain DNA
Reproduce
Evolve
Lack characteristics of life:

Not made of cells:
o

Lack homeostasis, reproduction, and energy collection
o

Just genetic material and protein
Depend on cells to do these functions
Giant viruses …..
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Order



Part 1
http://www.youtube.com/
watch?v=ahXIMUkSXX0
Part 2
http://www.youtube.com/
watch?v=lOIP_Z_-0Hs
Part 3
http://www.youtube.com/
watch?v=14-NdQwKz9w
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A Hierarchy of Biological
Organization -- Ecological
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A Hierarchy of Biological
Organization -- Organismal
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New Properties Emerge at Each
Level in the Biological Hierarchy


Life can be studied at different levels -- molecular to
planetary
Study can be divided into different kinds of organization



Biological
Taxonomic
Study can be divided into different levels of biological
organization
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Looking at Biology

Emergent properties – arrangement and interactions as
complexity increases
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Can characterize nonbiological entities as well
o
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Reductionism -- reduction of complex systems to more
manageable simpler components


For example, a functioning bicycle …..
For example, studying the molecular structure of DNA
helps us to understand the chemical basis of inheritance
Understanding -- balances reductionism with emergent
properties

Studying the interactions of DNA with other molecules
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Structure and Function

Often related
Leaves for photosynthesis
 Hummingbird wings
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
Basic unit? The cell
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Two Main Forms of Cells
 Characteristics shared by all cells:
Plasma membrane
 Cytosol
 Ribosomes
 DNA -- genetic information
Eukaryotic
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divided into membrane-bound organelles
DNA – linear strands in nucleus
Prokaryotic
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
lack organelles
DNA -- single, circular strand
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EUKARYOTIC CELL
Eukaryotic cell
Membrane
Membrane
Prokaryotic
cell
PROKARYOTIC
CELL
DNA
DNA
(no
(nonucleus)
nucleus)
Membrane
Membrane
Cytoplasm
Cytoplasm
Nucleus
(membraneenclosed)
Organelles
Membraneenclosed organelles
Nucleus (contains DNA)
DNA (throughout
1 1µm
µm
nucleus)
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Plant vs Animal
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Organelles
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Major Organelles
 Mitochondria
– sites of cellular respiration
 Chloroplasts – sites of photosynthesis
 Peroxisomes – sites of H2O2 production
 Central Vacuole
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Minor Organelles
 Smooth
Endoplasmic Reticulum
 Lysosomes
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Site of Aerobic Respiration
Free
ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix
Mitochondrial
DNA
100 nm
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Site of Photosynthesis
Chloroplast
Ribosomes
Stroma
Chloroplast
DNA
Inner and outer
membranes
Granum
Thylakoid
1 µm
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Reproduction drives Continuity
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Genes -- units of inheritance
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Genes -> chromosomes
DNA -> genes
Cell Division – basis for growth, repair and reproduction
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DNA, the Genetic Material
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Eukaryotic chromosomes -- one long DNA
molecule with hundreds or thousands of genes
Genes -- units of inheritance
DNA -- controls growth, development and
maintenance
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A
Nucleus
C
DNA
Nucleotide
T
A
Cell
T
A
C
C
G
T
A
G
T
A
(a) DNA double helix
(b) Single strand of DNA
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(b) How do lens cells make crystallin proteins?
Crystallin gene
(a) Lens cells are
tightly packed
with transparent
proteins called
crystallin.
Lens
cell
A
DNA
T
C
G G
C
T
A A
T
T
A C
C G A
G G C
T
G
C
A
U
C
T
TRANSCRIPTION
U
mRNA
G G
U
U
U G G C
TRANSLATION
Chain of amino
acids
PROTEIN FOLDING
Protein
Crystallin protein
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A
Genomics: Large-Scale Analysis of
DNA Sequences

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
Genome – entirety of genetic instructions
Genomics – study within and between species
Depends on
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“High-throughput” technology
Bioinformatics
Interdisciplinary research teams
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Ecology

Importance
Interactions of environment and organisms
 Necessary to study impact of interactions
 Examples
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o
Introduced species: zebra mussels
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o
Habitat restoration
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o
Economic cost
Long-leaf pine forest & red-cockaded woodpecker
Damage to biosphere: chlorofluorocarbons

Health and organism damage
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A Closer Look at Ecosystems

Organisms interact
 environment
 other
organisms
Organisms and environment affect each other
 Ecosystem dynamics:

 Cycling
of nutrients
 Food Webs
 Energy flow
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Energy Flow

Energy/Nutrients flows through biological systems

Sun  Producers  Consumers
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Producers and Consumers
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Plants are producers


Convert sunlight energy to chemical energy
Consumers
Harvest energy developed by producers
 Often several levels of consumers
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o
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1°, 2°, 3°
Detrivores
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Trophic
Structure
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Feeding relationships
between organisms
Food chains link
trophic levels
Food webs – link food
chains
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Grouping Species: The Basic
Idea
Taxonomy -- names and classifies species
 Kingdoms and domains -- broadest units of
classification


King Philip Cleverly Ordered Fried Green squid
…
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Species Genus Family
Order
Class Phylum Kingdom Domain
Ursus
americanus
(American
black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
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Families, Genera & Species
Family – Ursidae
 Genera

 Ailuropoda
 Helarctos
 Melursus
 Tremarctos
 Ursus
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Families, Genera & Species
Family Ursidae – species Ursus americanus
 Species in different genera

 Ailuropoda
melanoleuca – Giant Panda
 Helarctos malayanus – Sun Bear
 Melursus ursinus – Sloth Bear


Tremarctos ornatus – Spectacled Bear
Species in the same genus
 Ursus
arctos – Brown Bear
 Ursus arctos horribilis – Grizzly Bear
 Ursus
 Ursus
arctos ssp. horribilis
maritimus – Polar Bear
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Binomial Scientific Names



The scientific name of an organism is formed from the
genus name and specific epithet
Each two-part scientific name is unique and recognized
worldwide
Names are treated as Latin and always underlined or
italicized




Species name is always paired with its genus name


The first letter of the genus name is always capitalized
The first letter of the species name is always lower case
Authorities, “variety,” etc. unitalicized.
Homo sapiens
Specie == Money
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Biological Diversity
Biologists have named about 2 million species
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Biological Diversity
ATBI in Great Smoky Mountains National Park
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Biological Diversity
Estimates of total species range from 10 million to over 200 million
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History of Classification Schemes


Until 1969 – 2 Kingdoms (Plant & Animal)
1969 – Robert Whittaker: 5 Kingdoms


all bacteria in Kingdom Monera
1990 – Carl Woese: 3 Domains
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The Five Kingdoms of Life
 Prokaryotes
 Archaea
 Bacteria
 Cyanobacteria
 Animals
 Plants
 Fungi
 Protists
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Kingdoms and Domains
 Prokaryotes
 Archaea
– Domain Archaea
 Bacteria
– Domain Bacteria
 Cyanobacteria – Domain Bacteria
 Animals – Domain Eukarya
 Plants – Domain Eukarya
 Fungi – Domain Eukarya
 Protists – Domain Eukarya
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Biological Diversity
Bacteria
Archaea
4 µm
0.5 µm
Protists
Kingdom Fungi
100 µm
Kingdom Plantae
Kingdom Animalia
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70
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Classification & Biology


Taxonomy – study of how things are classified
Phylogenetics -- Reconstructing evolutionary
history
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Species
Panthera
Mephitis
Lutra lutra
Canis
Canis
pardus
mephitis
(European
familiaris
lupus
(leopard) (striped skunk)
otter)
(domestic dog) (wolf)
Genus
Systematists depict
evolutionary
relationships in
branching
phylogenetic trees
Panthera
Felidae
Order

Family
Systematics:
Links Taxonomy and Phylogeny
Mephitis
Lutra
Mustelidae
Canis
Canidae
Carnivora
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Species
Panthera
Mephitis
Lutra lutra
Canis
Canis
pardus
mephitis
(European
familiaris
lupus
(leopard) (striped skunk)
otter)
(domestic dog) (wolf)
Genus
Clades can be
nested in larger
clades, but not all
groupings or
organisms qualify
as clades
Panthera
Felidae
Order

Family
Cladistics / Phylogenetics
Mephitis
Lutra
Mustelidae
Canis
Canidae
Carnivora
75
The Tree of Life
 Related organisms -- similar adaptations
 Such kinships connect life’s unity and diversity
to descent with modification
 Natural selection eventually produces new
species from ancestral species
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Homologies and “Tree Thinking”


Homology – similarity from common ancestry
Evolutionary/ Phylogenetic trees -hypotheses about relationships between
organisms


Often nested patterns
Different types of data …
anatomical
 DNA sequence data
 Morphology
 Environment

LE 25-11b
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram
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Phylogenetic Groupings



Monophyletic -- ancestral species and all its
descendants
Paraphyletic -- ancestral species and some, but
not all, of the descendants
Polyphyletic -- various species that lack a
common ancestor
79
LE 25-10a
Grouping 1
Monophyletic
80
LE 25-10b
Grouping 2
Paraphyletic
81
LE 25-10c
Grouping 3
Polyphyletic
82
Taxonomy
A Constant State of Flux

Classifications Change ……
Systematists regularly propose changes in
classification
 Classifications Change When New Information Is
Discovered

83
Early Biological
Thought

Expressed by ancient Greek
philosophers
Plato (427-347 B.C.)
 Aristotle (384-322 B.C.)
arranged all organisms on a
linear scale of increasing
complexity (“ladder of Nature”)

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The Three Domains of Life
Source: Wikipedia
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89
See also:
http://come
nius.susqu.ed
u/biol/202/t
axa.htm
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Unity in the Diversity of Life
Underlying diversity – unity
 Evident in details of cell structure

91
Unity in the Diversity of Life

DNA -- made up of two long chains in a
double helix
 Four
“letters”
 Twenty “words”
 Unity of pathways
 Unity of structures
92
LE 1-16a
15 µm
5 µm
Cilia of Paramecium
Cilia of windpipe cells
93
LE 1-16b
0.1 µm
Cilia of Paramecium
Cross section of cilium,
as viewed with an
electron microscope
Cilia of windpipe cells
94
Living Organisms Evolve

Individual organisms change rapidly
Growth of individual
 A seed becomes a tree


Groups of organisms change slowly
Species
o Group of interbreeding organisms
o Produce fertile offspring
 Evolution
o Characteristics of a species changing over time


Individuals change – populations evolve
95
Adaptation: Adjusting to
Environmental Challenges



Change/ Mutation
Acted on by natural selection
Over time -- adaptive evolution
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Natural versus
Artificial Selection
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