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Principles ofBiology 2009
Jeff Parmelee
Other Classes that I teach:
Herpetology
Human Anatomy
Comparative Anatomy
Histology
Ecology Seminar
May Terms: Costa Rica, Ecuador, Australia,Borneo, Madagascar, Ecuador/Galapagos,Belize 2010
Senior Colloquium Plagues & People
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Scuba/rainforest Belize 2010
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Overview: Biologys Most Exciting Era
Biology is the scientific study of life
How to define life?
Order
Evolutionaryadaptation
Responseto theenvironment
Reproduction
Growth anddevelopment
Energy
processing
Regulation
Biologists explore life from the microscopic tothe global scale
The study of life extends from molecules and cellsto the entire living planet
Biological organization is based on a hierarchyofstructural levels
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Ecosystems
The biosphere
Communities
Cells
Organelles
Molecules
Cell1 m
Atoms
10 m
Organisms
Populations
ssues
Organs and organ systems
50 m
The biosphere
Ecosystems Communities
Fig. 1-4f
Populations
Fig. 1-4g
Organisms
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Organs andorgan systems
Tissues50 m
Cell
10 m
Cells
1 m
Organelles
Atoms
Molecules
The biosphere
Ecosystems
Fig. 1-4a
Communities
Populations
Organisms
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Fig. 1-4b
Organs andorgan systems
Cells
Cell
Organelles
10 m
Atoms
Molecules
Tissues
1 m
50 m
Emergent Properties
Emergent properties result from thearrangement and interaction of parts within a
system
Emergent properties characterize nonbiologicalentities as well
For example, a functioning bicycle emergesonly when all of the necessary parts connect inthe correct way
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Biological systems are much more than the sumof their parts
A system is a combination of components thatform a more complex organization
Cells, or anisms, and ecos stems are someexamples of biological systems
The human body is composed of:
96.2% of body weight comes from "organic elements" present inmany different forms. DNA, RNA, proteins, lipids and sugars areall composed of primarily O, C, H and N. Also, water (H2O) andcarbon dioxide (CO2) as well as other small molecules involvethese elements:
Oxygen (65%),Carbon (18.5%),Hydrogen (9.5%),Nitrogen(3.2%)
3.9% of bod wei ht comes from elements resent as salts.Calcium (1.5%),Phosphorus (1.0%),Potassium (0.4%),Sulfur (0.3%),Sodium (0.2%),Chlorine (0.2%),Magnesium (0.1%)Iodine (0.1%),Iron (0.1%)
The trace elements compose < 0.5% of total body weight:Chromium,Cobalt,Copper,Fluorine,Manganese,Molybdenum,Selenium,Tin,Vanadium,Zinc
A Closer Look at Ecosystems
Each organism interacts with its environment
Both organism and environment affect each other
Ecosystem Dynamics
The dynamics of an ecosystem include two majorprocesses:
Cycling of nutrients, in which materialsacquired by plants eventually return to the soil
to consumers
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Energy Conversion
Activities of life require work
Work depends on sources of energy
Energy exchange between an organism andenvironment often involves energy transformations
In transformations, some energy is lost as heat
Energy flows throughan ecosystem, usuallyentering as light and exiting as heat
Sunlight
Ecosystem
HeatCyclingof
chemicalnutrients
Producers(plants and otherphotosynthetic
organisms)
Chemical energy
Heat
Consumers(such as animals)
A Closer Look at Cells
The cell is the lowest level of organization that canperform allactivities of life
The ability of cells to divide is the basis of allreproduction, growth, and repair of multicellularorganisms
25 m
The Cells Heritable Information
Cells contain DNA, the heritable information thatdirects the cells activities
DNA is the substance of genes
Genes are the units of inheritance that transmitinformation from parents to offspring
Sperm cell
Nuclei
containing
Egg cell
Fertilized eggwith DNA from
both parents
Embryos cellsWith copies of
inherited DNAOffspring with traitsinherited from both parents
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Each DNA molecule is made up of two long chainsarranged in a double helix
Each link of a chain is one of four kinds ofchemical building blocks called nucleotides
NucleusDNA
Cell
Nucleotide
(a) DNA double helix (b) Single strand of DNA
Two Main Forms of Cells
Characteristics shared by all cells:
Enclosed by a membrane
Use DNA as genetic information
Eukaryotic: divided into organellesDNA in nucleus
Prokaryotic: lack organellesDNA not separated in a nucleus
Membrane
Cytoplasm
EUKARYOTIC CELL PROKARYOTIC CELL
DNA(no nucleus)
Membrane
1 mOrganellesNucleus (contains DNA)
The Power and Limitations of Reductionism
Reductionism is reducing complex systems tosimpler components that are easier to study
The studies of DNA structure and the HumanGenome Project are examples of reductionism
Systems Biology
Systems biology seeks to create models of thedynamic behavior of whole biological systems
An example is a systems map of interactionsbetween proteins in a fruit fly cell
uc mo e s may pre ct ow a c ange n onepart of a system will affect the rest of the system
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Outer membraneand cell surface
Cytoplasm
Nucleus
Feedback Regulation in Biological Systems
Regulatory systems ensure a dynamic balance inliving systems
Chemical processes are catalyzed (accelerated)by enzymes
-product regulates the process itself
In negative feedback, the accumulation of aproduct slows down the process itself
In positive feedback (less common), the productspeeds up its own production
Enzyme 1
A A
BB
C C
Enzyme 2
Negativefeedback
Enzyme 1
DD
D
DD
D
D
D
DDD
Enzyme 3
W
Enzyme 4
W
XX
Enzyme 5
Positivefeedback
Enzyme 4
Enzyme 5
Y Y
ZZ
ZZ
Z ZZ
ZZ Z
Enzyme 6 Enzyme 6
Z
Z Z Z
Z
Z
Z
Z
Z
Biologists explore life across its great diversityof species
Biologists have named about 1.8 million species
Estimates of total species range from 10 million to
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Grouping Species: The Basic Idea
Taxonomy is the branch of biology that names andclassifies species into a hierarchical order
Kingdoms and domains are the broadest units ofclassification
SpeciesGenus Family Order Class Phylum KingdomDomain
Ursus americanus
(American black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
The 3 Domains of Life
The three-domain system is currently used,and replaces the old five-kingdom system
Domain Bacteria and Domain Archaea
comprise the prokaryotes
Domain Eukarya includes all eukaryoticorganisms
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
(a) DOMAIN BACTERIA
(b) DOMAIN ARCHAEA
(c) DOMAIN EUKARYA
Protists
Kingdom Fungi
Kingdom
Plantae
Kingdom Animalia
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Fig. 1-15a
(a) DOMAIN BACTERIA
Fig. 1-15b
(b) DOMAIN ARCHAEA
The domain Eukarya includes 3 multicellularkingdoms:
Plantae
Fungi
Animalia
Other eukaryotic organisms were formerlygrouped into a kingdom called Protista, thoughthese are now often grouped into many
separate kingdoms
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Protists
(c) DOMAIN EUKARYA
Kingdom Fungi
KingdomPlantae
Kingdom Animalia
Protists Kingdom Fungi
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Kingdom Plantae Kingdom Animalia
Unity in the Diversity of Life
Underlying lifes diversity is a striking unity,especially at lower levels of organization
In eukaryotes, unity is evident in details of cellstructure
15 m 5 m
Cilia of windpipe cellsCilia of Paramecium
0.1 m
Cilia of windpipe cellsCilia of Paramecium
Cross section of cilium,as viewed with anelectron microscope
Evolution accounts for lifes unity and diversity
The history of life is a saga of a changing Earthbillions of years old
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The evolutionary view of life came into sharp focusin 1859, when Charles Darwin published On theOrigin of Species by Natural Selection
Darwinism became almost synonymous with theconcept of evolution
The Origin of Speciesarticulated two main points:
Descent with modification (the view thatcontemporary species arose from asuccession of ancestors)
descent with modification)
Some examples of descent with modification areunity and diversity in the orchid family
Natural Selection
Darwin inferred natural selection by connectingtwo observations:
Observation: Individual variation in heritabletraits
Observation: Overpopulation and competition
Inference: Unequal reproductive success
Inference: Evolutionary adaptation
LE 1-20
Overproductionand competition
Populationof organisms
Hereditaryvariations
Evolution of adaptationsin the population
Differences inreproductive success
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Natural selection can edit a populationsheritable variations
An example is the effect of birds preying on abeetle population
Populationwith variedinherited traits.
Eliminationof individualswith certaintraits.
Reproductionof survivors.
Increasingfrequencyof traits thatenhancesurvival andreproductivesuccess.
4321
Natural selection is often evident in adaptations oforganisms to their way of li fe and environment
Bat wings are an example of adaptation
The Tree of Life
Many related organisms have similar featuresadapted for specific ways of life
Such kinships connect lifes unity and diversity todescent with modification
Natural selection eventually produces new speciesfrom ancestral species
Biologists often show evolutionary relationships ina treelike diagram
COMMONANCESTOR
Warblerfinches
Insect-eaters
Seed-eater
Bud-eater
Insect-eaters
Treefinches
Green warbler finch
Certhidea olivacea
Gray warbler finchCerthidea fusca
Sharp-beakedground finch
Geospiza difficilis
Vegetarian finchPlatyspiza crassirostris
Mangrove finchCactospiza heliobates
Woodpecker finchCactospiza pallida
Medium tree finchCamarhynchus pauper
Largetree finch
Camarhynchuspsittacula
Small tree finchCamarhynchus
parvulus
Large cactusground finch
Geospiza conirostris
Cactus ground finchGeospiza scandens
Small ground finchGeospiza fuliginosa
Medium ground finch
Geospiza fortis
Large ground finch
Geospiza
magnirostris
Groundfinches
Seed-eaters
Cactus-flower-
eaters
Biologists use various forms of inquiry toexplore life. Science = way of knowing
Inquiry is a search for information and explanation,often focusing on specific questions
The process of science blends two mainprocesses of scientific inquiry:
Discovery science: describing nature
Hypothesis-based science: explaining nature
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Discovery Science
Discovery science describes nature throughcareful observation and data analysis
Examples of discovery science:
understanding cell structure
expanding databases of genomes
Types of Data
Data are recorded observations
Two types of data:
Quantitative data: numerical measurements
Qualitative data: recorded descri tions
Induction in Discovery Science
Inductive reasoning draws conclusionsthrough the logical process of induction
Repeat specific observations can lead toimportant generalizations
For example, the sun always rises in the east
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Deduction: The IfThen Logic of HypothesisBased Science
Deductive reasoning uses general premisesto make specific predictions
For example, iforganisms are made of cells
(premise 1), and humans are organisms(premise 2), thenhumans are composed ofcells (deductive prediction)
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Hypothesis-Based Science
In science, inquiry usually involves proposing andtesting hypotheses
Hypotheses are hypothetical explanations
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The Role of Hypotheses in Inquiry
In science, a hypothesis is a tentative answer to awell-framed question
A hypothesis is an explanation on trial, making aprediction that can be tested
Observations
Hypothesis #1:Dead batteries
Hypothesis #2:Burnt-out bulb
Question
Hypothesis #1:Dead batteries
Hypothesis #2:Burnt-out bulb
Prediction:Replacing batterieswill fix problem
Prediction:
Replacing bulbwill fix problem
Test prediction
Test falsifies hypothesis
Test prediction
Test does not falsify hypothesis
A Closer Look at Hypotheses in Scientific Inquiry
A scientific hypothesis must have two importantqualities:
It must be testable
It must be falsifiable
The Myth ofthe Scientific Method
The scientific method is an idealized process ofinquiry
Very few scientific inquiries adhere rigidly to thetextbook scientific method
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Scent-Trailing Among NeonateTimber Rattlesnakes
(Crotalus horridus)
Nick Blay & Jeff Parmelee
Simpson College
Indianola Iowa
N
Home Ranges of S169/SBush Den Complex
500 0 500 1000 1500 Meters
The Question
How do newborns locate a suitable
Older snakes?: Solar cues, Celestialcues, Olfactory cues, Topographiclandmarks, or a combination of all
Chemoreception
Pheromones deposited from glandsbetween scales when snake moves
-
Remains in the environment
Information on species, sex, condition?
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2 Trials with 1 clutch done in 2002,9 of 11 made correct choice
Trial # Tagged Young Mother Results Time
9/17/2002
1 48-592-816 Left Arm Aborted 31 m in
2 48-558-357 Left Arm Left Arm 6 m in
3 48-549-637 Left Arm Right Arm 5 m in
4 48-571-565 Left Arm Left Arm 5 m in
5 48-561-119 Left Arm Left Arm 25 m in
6 48-564-894 Left Arm Left Arm 7 m in
7 48-513-085 Left Arm Left Arm 27 m in
9/23/2002
1 48-513-085 Right Arm Aborted 30 m in
2 48-561-119 Right Arm Right Arm 8 m in
3 48-549-637 Left Arm Left Arm 2 m in
4 48-571-565 Right Arm Right Arm 2 m in
5 48-558-357 Left Arm Right Arm 13 m in
6 48-592-816 Right Arm Aborted 30 m in
7 48-564-894 Right Arm Right Arm 13 m in
9 /2 4/ 20 02 C ON TR OL
1 48-558-357 Aborted 30 m in
2 48-561-119 Aborted 30 m in
3 48-592-816 Aborted 29 m in
4 48-549-637 Aborted 26 m in
5 48-564-894 Right Arm 28 m in
6 48-513-085 Aborted 25 m in
7 48-571-565 Aborted 21 m in
Hypothesis
Neonates will trail their mother moresuccessfully than a non-maternal
.
Methods and Materials
7 gravid females collected and allowedto give birth in aquaria (46 young) Neonates were removed as soon as they
were discovered*
Y-maze Lined with paper
Female guided down arm of maze
Young were tested one at a time
Results: Neonate vs. Mother
Trial Correct PathChosen
% # of AbortedTrials
%SuccessfullyCompleted
1* 3/4 75% 1 100%2 0/2 0% 1 50%
3 6/11 55% 0 73%
4 3/9 34% 3 50%
5 3/7 43% 3 75%
6 2/5 40% 0 40%
7 1/8 13% 4 25%
Totals 18/46 39% 12 53%
Results
Hypothesis not supported when lookingat neonate vs. mother
Trend same with non-mother
63% chose correct path
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Imprinting Period?
Neonates then placed with theirmothers for a period of time from aweek to over a month and re-tested
Neonates vs. Mother
Trial Correct PathChosen
% # of AbortedTrials
%
SuccessfullyCompleted
1* 2/4 50% 1 67%
2 NA NA NA NA
3 6/11 55% 1 60%
4 2/9 22% 3 33%
5 3/7 43% 1 50%
6 3/5 60% 2 100%
7** 2/5 40% 3 100%
Totals 18/41 44% 11 60%
Explanations?
Neonates typically remain with mother for7-14 days after birth
Neonates from Trial 1 were left with themother while all others were separated
Neonate vs. Mother 100%
Neonate vs. Non-Mother 67%
Limitations of Science
The limitations of science are set by its naturalism
Science seeks natural causes for naturalphenomena
Science cannot support or falsify supernatural
,science
Theories in Science
A scientific theory is much broader than ahypothesis
A scientific theory is:
broad in scope
genera enoug o genera e new ypo eses
supported by a large body of evidence
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