Other Classes that I teach:

Principles of • Herpetology

Biology 2009 • Human Anatomy

• Comparative Anatomy
Jeff Parmelee • Histology
gy
• Ecology Seminar
• May Terms: Costa Rica, Ecuador, Australia,
Borneo, Madagascar, Ecuador/Galapagos,
Belize 2010
• Senior Colloquium – Plagues & People

1
Scuba/rainforest Belize 2010

2
3
 Order
• Overview: Biology’s Most Exciting Era
Response
• Biology is the scientific study of life to the
environment
Evolutionary
adaptation

How to define life?

Regulation

Reproduction
Energy
processing Growth and
development

• Biologists explore life from the microscopic to

the global scale
• The study of life extends from molecules and cells
to the entire living planet
• Biological organization is based on a hierarchy of
structural levels

4
 The biosphere Organelles
1 µm

Ecosystems Cell
Cells

Atoms

10 µm
Molecules
Communities Tiss es
Tissues

50 µm
Populations

Organs and organ systems

Organisms

The biosphere

Ecosystems Communities

Fig. 1-4f Fig. 1-4g

Populations Organisms

5
Organs and Tissues
organ systems 50 µm

10 µm

Cell

1 µm

Organelles

Cells

Fig. 1-4a
The biosphere

Ecosystems

Atoms
Communities

Populations
Molecules Organisms

6
Fig. 1-4b
Emergent Properties

Cells
Organs and 10 µm • Emergent properties result from the
organ systems Cell arrangement and interaction of parts within a
system
Organelles • Emergent properties characterize nonbiological
entities as well
1 µm
– For example, a functioning bicycle emerges
Atoms
Tissues 50 µm
only when all of the necessary parts connect in
the correct way
Molecules

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The human body is composed of:

96.2% of body weight comes from "organic elements" present in
Biological systems are much more than the sum many different forms. DNA, RNA, proteins, lipids and sugars are
of their parts all composed of primarily O, C, H and N. Also, water (H2O) and
carbon dioxide (CO2) as well as other small molecules involve
• A system is a combination of components that these elements:
form a more complex organization
Oxygen (65%),Carbon (18.5%),Hydrogen (9.5%),Nitrogen(3.2%)
• Cells,, organisms,
g , and ecosystems
y are some 3 9% o
3.9% of body weight
e g cocomes
es from
o eelements
e e sp present
ese as sa
salts.
s
examples of biological systems 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 Ecosystem Dynamics

• Each organism interacts with its environment
• Both organism and environment affect each other
• The dynamics of an ecosystem include two major
processes:
– Cycling of nutrients, in which materials
acquired by plants eventually return to the soil
– The flow of energy from sunlight to producers
to consumers

7
Energy Conversion Sunlight

Ecosystem
• Activities of life require work
Producers
• Work depends on sources of energy (plants and other
photosynthetic
Cycling organisms)
• Energy exchange between an organism and of
Heat
chemical
environment often involves energy transformations nutrients
Chemical energy

• In transformations, some energy is lost as heat

• Energy flows through an ecosystem, usually Consumers
(such as animals)
entering as light and exiting as heat Heat

A Closer Look at Cells

• The cell is the lowest level of organization that can

perform all activities of life
• The ability of cells to divide is the basis of all
reproduction, growth, and repair of multicellular
organisms

25 µm

The Cell’s Heritable Information

• Cells contain DNA, the heritable information that

directs the cell’s activities Sperm cell

• DNA is the substance of genes

Nuclei
containing
• Genes are the units of inheritance that transmit DNA

information from parents to offspring Fertilized egg Embryo’s cells

with DNA from With copies of
Egg cell both parents inherited DNA
Offspring with traits
inherited from both parents

8
 Nucleus
DNA

• Each DNA molecule is made up of two long chains

Nucleotide
arranged in a double helix
Cell
• Each link of a chain is one of four kinds of
chemical building blocks called nucleotides

(a) DNA double helix (b) Single strand of DNA

Two Main Forms of Cells EUKARYOTIC CELL PROKARYOTIC CELL

DNA
(no nucleus)

• Characteristics shared by all cells: Membrane

Membrane

Cytoplasm
– Enclosed by a membrane
– Use DNA as genetic information
• Two main forms of cells:
– Eukaryotic: divided into organelles
DNA in nucleus
– Prokaryotic: lack organelles
DNA not separated in a nucleus
Organelles
Nucleus (contains DNA) 1 µm

The Power and Limitations of Reductionism Systems Biology

• Reductionism is reducing complex systems to • Systems biology seeks to create models of the
simpler components that are easier to study dynamic behavior of whole biological systems
• The studies of DNA structure and the Human • An example is a systems map of interactions
Genome Project are examples of reductionism between proteins in a fruit fly cell
• S
Suchh models
d l may predict
di t h
how a change
h iin one
part of a system will affect the rest of the system

9
 Outer membrane
and cell surface
Feedback Regulation in Biological Systems
Cytoplasm

Nucleus • Regulatory systems ensure a dynamic balance in

living systems
• Chemical processes are catalyzed (accelerated)
by enzymes
• Many biological processes are self
self-regulating:
regulating: the
product regulates the process itself

A A
Negative
• In negative feedback, the accumulation of a feedback
Enzyme 1 Enzyme 1
product slows down the process itself
B B
• In positive feedback (less common), the product
speeds up its own production Enzyme 2

C C

Enzyme 3
D

D D D D
D

D
D
D D
D

W W • Biologists explore life across its great diversity

Enzyme 4 Enzyme 4
of species
X Positive X • Biologists have named about 1.8 million species
feedback
Enzyme 5 Enzyme 5 • Estimates of total species range from 10 million to
Y Y over 200 million!
Enzyme 6 Enzyme 6

Z
Z Z Z Z
Z Z Z Z
Z Z
Z Z
Z Z Z Z Z
Z

10
 Grouping Species: The Basic Idea Species Genus Family Order Class Phylum Kingdom Domain

Ursus americanus
(American black bear)

• Taxonomy is the branch of biology that names and Ursus

classifies species into a hierarchical order
Ursidae
• Kingdoms and domains are the broadest units of
classification Carnivora

Mammalia

Chordata

Animalia

Eukarya

The 3 Domains of Life (a) DOMAIN BACTERIA

• The three-domain system is currently used, (b) DOMAIN ARCHAEA

and replaces the old five-kingdom system

• Domain Bacteria and Domain Archaea
comprise the prokaryotes (c) DOMAIN EUKARYA

• Domain Eukarya includes all eukaryotic

organisms
Protists

Kingdom
Plantae

Kingdom Fungi

Kingdom Animalia
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

11
Fig. 1-15a Fig. 1-15b

(a) DOMAIN BACTERIA

(b) DOMAIN ARCHAEA

• The domain Eukarya includes 3 multicellular

kingdoms:
– Plantae
Protists
– Fungi
– Animalia Kingdom
Plantae
• Other eukaryotic organisms were formerly
grouped into a kingdom called Protista, though Kingdom Fungi

these are now often grouped into many (c) DOMAIN EUKARYA Kingdom Animalia
separate kingdoms
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Protists Kingdom Fungi

12
Kingdom Plantae Kingdom Animalia

Unity in the Diversity of Life

15 µm 5 µm
• Underlying life’s diversity is a striking unity,
especially at lower levels of organization
• In eukaryotes, unity is evident in details of cell
structure

Cilia of Paramecium Cilia of windpipe cells

• Evolution accounts for life’s unity and diversity

0.1 µm • The history of life is a saga of a changing Earth
billions of years old

Cross section of cilium,

as viewed with an
Cilia of Paramecium electron microscope Cilia of windpipe cells

13
• The evolutionary view of life came into sharp focus
in 1859, when Charles Darwin published On the
Origin of Species by Natural Selection
• “Darwinism” became almost synonymous with the
concept of evolution

• The Origin of Species articulated two main points:

– Descent with modification (the view that
contemporary species arose from a
succession of ancestors)
– Natural selection (a proposed mechanism for
descent with modification)
• Some examples of descent with modification are
unity and diversity in the orchid family

LE 1-20
Natural Selection
Population
of organisms
• Darwin inferred natural selection by connecting
two observations:
– Observation: Individual variation in heritable
traits Hereditary
variations
Overproduction
and competition

– Observation: Overpopulation and competition

– Inference: Unequal reproductive success
Differences in
reproductive success
– Inference: Evolutionary adaptation

Evolution of adaptations
in the population

14
• Natural selection can “edit” a population’s
heritable variations
• An example is the effect of birds preying on a
beetle population

1 Population 2 Elimination 3 Reproduction 4 Increasing

with varied of individuals of survivors. frequency
inherited traits. with certain of traits that
traits. enhance
survival and
reproductive
success.

The Tree of Life

• Many related organisms have similar features
• Natural selection is often evident in adaptations of adapted for specific ways of life
organisms to their way of life and environment • Such kinships connect life’s unity and diversity to
descent with modification
• Bat wings are an example of adaptation
• Natural selection eventually produces new species
from ancestral species
• Biologists often show evolutionary relationships in
a treelike diagram
Warbler finches

Insect-eaters

Green warbler finch

Certhidea olivacea

COMMON
ANCESTOR
Gray warbler finch
Certhidea fusca • Biologists use various forms of inquiry to
Seed-eater

Sharp-beaked
ground finch explore life. Science = way of knowing
Bud-eater

Geospiza difficilis
Vegetarian finch
Platyspiza crassirostris

Mangrove finch
Cactospiza heliobates
• Inquiry is a search for information and explanation,
often focusing on specific questions
Insect-eaters
Tree finches

Woodpecker finch
Cactospiza pallida

Medium tree finch

Camarhynchus pauper
Large tree finch
Camarhynchus
• The p
process of science blends two main
psittacula
Small tree finch
processes of scientific inquiry:
Camarhynchus
parvulus
Cactus-flower-

Large cactus
– Discovery science: describing nature
eaters

ground finch
Geospiza conirostris
Cactus ground finch
Ground finches

Seed-eaters

Geospiza scandens

Small ground finch

Geospiza fuliginosa
– Hypothesis-based science: explaining nature
Medium ground finch
Geospiza fortis

Large ground finch

Geospiza
magnirostris

15
 Discovery Science Types of Data
• Discovery science describes nature through • Data are recorded observations
careful observation and data analysis
• Two types of data:
• Examples of discovery science:
– Quantitative data: numerical measurements
– understanding cell structure
– Q
Qualitative data: recorded descriptions
p
– expanding databases of genomes

Induction in Discovery Science

• Inductive reasoning draws conclusions

through the logical process of induction
• Repeat specific observations can lead to
important generalizations
– For example, “the sun always rises in the east”

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Deduction: The “If…Then” Logic of Hypothesis Hypothesis-Based Science

Based Science
• In science, inquiry usually involves proposing and
• Deductive reasoning uses general premises testing hypotheses
to make specific predictions
• Hypotheses are hypothetical explanations
• For example, if organisms are made of cells
(premise 1), and humans are organisms
(premise 2), then humans are composed of
cells (deductive prediction)

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

16
The Role of Hypotheses in Inquiry

• In science, a hypothesis is a tentative answer to a

well-framed question
Observations
• A hypothesis is an explanation on trial, making a
prediction that can be tested

Question

Hypothesis #1: Hypothesis #2:

Dead batteries Burnt-out bulb

A Closer Look at Hypotheses in Scientific Inquiry

Hypothesis #1: Hypothesis #2:
Dead batteries Burnt-out bulb
• A scientific hypothesis must have two important
qualities:
Prediction: Prediction:
Replacing batteries Replacing bulb
will fix problem will fix problem – It must be testable
– It must be falsifiable

Test prediction Test prediction

Test falsifies hypothesis Test does not falsify hypothesis

The Myth of the Scientific Method

• The scientific method is an idealized process of
inquiry
• Very few scientific inquiries adhere rigidly to the
“textbook” scientific method

17
 Home Ranges of S169/SBush Den Complex
N

Scent-Trailing Among Neonate

Timber Rattlesnakes
(Crotalus horridus)

Nick Blay & Jeff Parmelee

Simpson College
Indianola Iowa

500 0 500 1000 1500 Meters

The Question Chemoreception

How do newborns locate a suitable
hibernacula for the winter?
Older snakes?: Solar cues, Celestial
cues, Olfactory cues, Topographic
landmarks, or a combination of all
„ Pheromones deposited from glands
between scales when snake moves
„ Secretion made up of non-volatile lipids
„ Remains in the environment
„ Information on species, sex, condition?

18
 2 Trials with 1 clutch done in 2002,
9 of 11 made correct choice
Trial # Tagged Young M other Results Tim e

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 R ight Arm Aborted 30 m in
2 48-561-119 R ight Arm Right Arm 8 m in
3 48-549-637 Left Arm Left Arm 2 m in
4 48-571-565 R ight Arm Right Arm 2 m in
5 48-558-357 Left Arm Right Arm 13 m in
6 48-592-816 R ight Arm Aborted 30 m in
7 48-564-894 R ight Arm Right Arm 13 m in

9/24/2002 CON TRO L

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
Methods and Materials
• Neonates will trail their mother more „ 7 gravid females collected and allowed
successfully than a non-maternal to give birth in aquaria (46 young)
female.
female „ 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 Results

Trial Correct Path % # of Aborted %
„ Hypothesis not supported when looking
Chosen Trials Successfully
Completed
at neonate vs. mother
1* 3/4 75% 1 100%
„ 52% chose correct path
2 0/2 0% 1 50%
3 6/11 55% 0 73% „ Trend same with non-mother
4 3/9 34% 3 50% „ 63% chose correct path
5 3/7 43% 3 75%
6 2/5 40% 0 40%
7 1/8 13% 4 25%
Totals 18/46 39% 12 53%

19
 Imprinting Period…? Neonates vs. Mother
„ Neonates then placed with their Trial Correct Path % # of Aborted %
Chosen Trials Successfully
mothers for a period of time from a Completed
1* 2/4 50% 1 67%
week to over a month and rere-tested
tested
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 for
7-14 days after birth
„ Imprinting at this time?
„ Neonates from Trial 1 were left with the
mother while all others were separated
„ Neonate vs. Mother – 100%
„ Neonate vs. Non-Mother – 67%

Limitations of Science Theories in Science

• The limitations of science are set by its naturalism • A scientific theory is much broader than a
hypothesis
– Science seeks natural causes for natural
phenomena • A scientific theory is:

– Science cannot support or falsify supernatural – broad in scope

explanations
explanations, which are outside the bounds of – generall enough
h tto generate
t new hypotheses
h th
science
– supported by a large body of evidence

20
Model Building in Science From
body
From
lungs

• Models are representations of ideas, structures, or

processes
Right Left
atrium atrium
• Models may range from lifelike representations to
symbolic schematics

Right Left
ventricle ventricle

To lungs To body

The Culture of Science Science, Technology, and Society

• Science is an intensely social activity • The goal of science is to understand natural

• Both cooperation and competition characterize phenomena
scientific culture • Technology applies scientific knowledge for some
specific purpose

• A set of themes connects the concepts of

biology
• Biology is the science most connected to the
humanities and social sciences
• Underlying
y g themes p provide a framework for
understanding biology

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