01_Biology Lecture 1

8/8/2019 01_Biology Lecture 1

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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


(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


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

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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.

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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


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)


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





9/23/2002

1 48-513-085 Right Arm Aborted 30 m in

2 48-561-119 Right Arm Right Arm 8 m in



5 48-558-357 Left Arm Right Arm 13 m in

6 48-592-816 Right Arm Aborted 30 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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01_Biology Lecture 1

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