Chapter 1: Exploring Life

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• Chapter 1 Exploring Life

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Biologists explore life from the microscopic to
the global scale

• Each level of biological organization has
  emergent properties.
• Biological organization is based on a hierachy of
  structural levels, each level building on the
  levels below it.

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HIERARCHY OF BIOLOGICAL ORGANIZATION

• Molecules (built of many atoms to perform a
  function)
• Organelle (conglomerate of molecules which work
  together to perform a process)
• Cell (many organelle working together to form a
  living unit)
• Tissue(groups of cells forming a functional unit)

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Hierarchy continued

• Organ (many tissues forming a specialized center
  for a body function)
• Organism (many organs forming functional
  multicellar life)
• Populations all individuals of a species living
  within a specific area
• Communities The entire array of organisms
  inhabiting a particular ecosystem
• Ecosystems Includes both biotic and abiotic
  factors
• Biosphere All the environments on Earth that
  are inhabited by life.

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The biosphere
Organelles
1 µm
Cell
Ecosystems
Cells
Atoms
Molecules
10 µm
Communities
Tissues
50 µm
Populations
Organs and organ systems
Organisms
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A Closer look at Ecosystems

• Ecosystem Dynmaics
• Producers and consumers

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
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Energy Conversions

• Activities of life require work
• Work depends on sources of energy
• Energy exchange between an organism and
  environment often involves energy transformations
• In transformations, some energy is lost as heat
• Energy flows through an ecosystem, usually
  entering as light and exiting as heat

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LE 1-4
Sunlight
Ecosystem
Producers (plants and other photosynthetic organis
ms)
Heat
Chemical energy
Consumers (including animals)
Heat
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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

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LE 1-5
25 µm
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The Cells Heritable Information

• Cells contain DNA, the heritable information that
  directs the cells activities
• DNA is the substance of genes
• Genes are the units of inheritance that transmit
  information from parents to offspring

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• Each DNA molecule is made up of two long chains
  arranged in a double helix
• Each link of a chain is one of four kinds of
  chemical building blocks called nucleotides

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Two Main Forms of Cells

• Characteristics shared by all cells
• 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

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LE 1-8
PROKARYOTIC CELL
EUKARYOTIC CELL
DNA
(no nucleus)
Membrane
Membrane
Cytoplasm
Organelles
1 µm
Nucleus (contains DNA)
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Concept 1.2 Biological systems are much more
than the sum of their parts

• A system is a combination of components that form
  a more complex organization
• Cells, organisms, and ecosystems are some
  examples of biological systems

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The Emergent Properties of Systems

• With each step upward in the hierarchy new
  properties emerge.
• Each level must work for the whole to work.
• Disrupt one part of a molecule and the organ will
  cease to function properly.
• Diabetes

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The Power and Limitations of Reductionism

• In order to study an organism we break down the
  whole into its individual parts.
• But when broken down the organism no longer
  functions.
• Biology balances the reductionist strategy with
  understanding emergent properties.

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Systems Biology

• Systems biology seeks to create models of the
  dynamic behavior of whole biological systems
• An example is a systems map of interactions
  between proteins in a fruit fly cell
• Such models may predict how a change in one part
  of a system will affect the rest of the system

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LE 1-10
Outer membrane and cell surface
CELL
Cytoplasm
Nucleus
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Systems Biology

• The ultimate goal of systems biology is to model
  the dynamic behavior of whole biological systems.

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• Systems biology uses three key research
  developments
• High-throughput technology methods to generate
  large data sets rapidly
• Bioinformatics using computers and software to
  process and integrate large data sets
• Interdisciplinary research teams

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Feedback Regulation in Biological Systems

• Regulatory systems ensure a dynamic balance in
  living systems
• Chemical processes are catalyzed (accelerated) by
  enzymes
• Many biological processes are self-regulating
  the product regulates the process itself

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• In negative feedback, the accumulation of a
  product slows down the process itself e.g lac
  operon
• In positive feedback (less common), the product
  speeds up its own production e.g. partrition

Animation Negative Feedback
Animation Positive Feedback
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LE 1-11
A
A
Negative feedback
Enzyme 1
Enzyme 1
B
B
Enzyme 2
C
C
Enzyme 3
D
D
D
D
D
D
D
D
D
D
D
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LE 1-12
W
W
Enzyme 4
Enzyme 4
X
X
Positive feedback
Enzyme 5
Enzyme 5
Y
Y
Enzyme 6
Enzyme 6
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
Z
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Grouping Species The Basic Idea
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Grouping Species The Basic Idea

• Taxonomy is the branch of biology that names and
  classifies species into a hierarchical order
• Kingdoms and domains are the broadest units of
  classification

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TAXONMONY GROUPING SPECIES

• 3 Domains of life
• Bacteria
• Archaea
• Eukarya

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BACTERIA

• Contains part of the old Moneran Kingdom but now
  is called the Eubacteria kingdom
• Most diverse and widespread prokaryotes

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ARCHAEA

• Prokaryotic but live in extreme environments
• Molecular evidence indicates that they have many
  things in common with the Eukarya.

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EUKARYA

• Contains all eukaryotes
• Kingdoms
• Fungi
• Protista
• Plantae
• Animalia

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LEVELS OF CLASSIFICATION

• DOMAIN
• KINGDOM
• PHYLUM
• CLASS
• ORDER
• FAMILY
• GENUS
• SPECIES

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LE 1-14
Family
Phylum
Species
Genus
Order
Class
Kingdom
Domain
Ursus americanus (American black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
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UNITY IN THE DIVERSITY OF LIFE

• THE HUGE NUMBER OF SPECIES OF LIFE ON THIS PLANET
  GIVES US DIVERSITY
• YET THERE IS MUCH THESE ORGANISMS HAVE IN COMMON.
• ESPECIALLY IN THE LOWER LEVELS OF ORGANIZATION
  EG. DNA

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LE 1-16a
5 µm
15 µm
Cilia of Paramecium
Cilia of windpipe cells
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LE 1-16b
0.1 µm
Cross section of cilium, as viewed with
an electron microscope
Cilia of windpipe cells
Cilia of Paramecium
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• Concept 1.4 Evolution accounts for lifes unity
  and diversity
• The history of life is a saga of a changing Earth
  billions of years old

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• 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

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• 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

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Natural Selection

• Darwin inferred natural selection by connecting
  two observations
• Observation Individual variation in heritable
  traits
• Observation Overpopulation and competition
• Inference Unequal reproductive success
• Inference Evolutionary adaptation

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LE 1-20
Population of organisms
Overproduction and competition
Hereditary variations
Differences in reproductive success
Evolution of adaptations in the population
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• Natural selection can edit a populations
  heritable variations
• An example is the effect of birds preying on a
  beetle population

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• Natural selection is often evident in adaptations
  of organisms to their way of life and environment
• Bat wings are an example of adaptation

Video Soaring Hawk
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The Tree of Life

• Many related organisms have similar features
  adapted for specific ways of life
• Such kinships connect lifes unity and diversity
  to descent with modification
• Natural selection eventually produces new species
  from ancestral species
• Biologists often show evolutionary relationships
  in a treelike diagram

Videos on slide following the figure
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LE 1-23
Large ground finch
Large tree finch
Small ground finch
Large cactus ground finch
Camarhynchus psittacula
Geospiza magnirostris
Green warbler finch
Gray warbler finch
Geospiza fuliginosa
Woodpecker finch
Medium tree finch
Sharp-beaked ground finch
Geospiza conirostris
Medium ground finch
Certhidea fusca
Certhidea olivacea
Geospiza difficilis
Camarhynchus pauper
Cactus ground finch
Cactospiza pallida
Small tree finch
Mangrove finch
Geospiza fortis
Geospiza scandens
Camarhynchus parvulus
Cactospiza heliobates
Vegetarian finch
Cactus flower eaters
Seed eater
Seed eaters
Platyspiza crassirostris
Bud eater
Insect eaters
Ground finches
Tree finches
Warbler finches
Common ancestor from South American mainland
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Video Albatross Courtship Ritual
Video Blue-footed Boobies Courtship Ritual
Video Galapágos Islands Overview
Video Galapágos Marine Iguana
Video Galapágos Sea Lion
Video Galapágos Tortoise
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• Concept 1.5 Biologists use various forms of
  inquiry to explore life
• Inquiry is a search for information and
  explanation, often focusing on specific questions
• The process of science blends two main processes
  of scientific inquiry
• Discovery science describing nature
• Hypothesis-based science explaining nature

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Discovery Science

• Discovery science describes nature through
  careful observation and data analysis
• Examples of discovery science
• understanding cell structure
• expanding databases of genomes

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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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Induction in Discovery Science

• Inductive reasoning involves generalizing based
  on many specific observations

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Hypothesis-Based Science

• In science, inquiry usually involves proposing
  and testing hypotheses
• Hypotheses are hypothetical explanations

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The Role of Hypotheses in Inquiry

• In science, a hypothesis is a tentative answer to
  a well-framed question
• A hypothesis is an explanation on trial, making a
  prediction that can be tested

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LE 1-25a
Observations
Question
Hypothesis 1 Dead batteries
Hypothesis 2 Burnt-out bulb
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LE 1-25b
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 Ifthen Logic of
Hypothesis-Based Science

• In deductive reasoning, the logic flows from the
  general to the specific
• If a hypothesis is correct, then we can expect a
  particular outcome

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A Closer Look at Hypotheses in Scientific Inquiry

• A scientific hypothesis must have two important
  qualities
• It must be testable
• It must be falsifiable

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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

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A Case Study in Scientific Inquiry Investigating
Mimicry in Snake Populations

• In mimicry, a harmless species resembles a
  harmful species
• An example of mimicry is a stinging honeybee and
  a nonstinging mimic, a flower fly

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LE 1-26
Flower fly (nonstinging)
Honeybee (stinging)
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• This case study examines king snakes mimicry of
  poisonous coral snakes
• The hypothesis states that mimics benefit when
  predators mistake them for harmful species
• The mimicry hypothesis predicts that predators in
  noncoral snake areas will attack king snakes
  more frequently than will predators that live
  where coral snakes are present

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LE 1-27
Scarlet king snake
Key
Range of scarlet king snake
Range of eastern coral snake
Eastern coral snake
North Carolina
South Carolina
Scarlet king snake
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Field Experiments with Artificial Snakes

• To test this mimicry hypothesis, researchers made
  hundreds of artificial snakes
• An experimental group resembling king snakes
• A control group resembling plain brown snakes
• Equal numbers of both types were placed at field
  sites, including areas without coral snakes
• After four weeks, the scientists retrieved the
  artificial snakes and counted bite or claw marks
• The data fit the predictions of the mimicry
  hypothesis

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LE 1-28
(a) Artificial king snake
(b) Artificial brown snake that has been attacked
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LE 1-29
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In areas where coral snakes were absent, most
attacks were on artificial king snakes.
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Key
North Carolina
of attacks on artificial king snakes
of attacks on brown artificial snakes
South Carolina
Field site with artificial snakes
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In areas where coral snakes were present, most
attacks were on brown artificial snakes.
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Designing Controlled Experiments

• Scientists do not control the experimental
  environment by keeping all variables constant
• Researchers usually control unwanted variables
  by using control groups to cancel their effects

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Theories in Science

• A scientific theory is much broader than a
  hypothesis
• A scientific theory is
• broad in scope
• general enough to generate new hypotheses
• supported by a large body of evidence

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Model Building in Science

• Models are representations of ideas, structures,
  or processes
• Models may range from lifelike representations to
  symbolic schematics

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LE 1-30
From body
From lungs
Left atrium
Right atrium
Left ventricle
Right ventricle
To lungs
To body
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The Culture of Science

• Science is an intensely social activity
• Both cooperation and competition characterize
  scientific culture

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Science, Technology, and Society

• The goal of science is to understand natural
  phenomena
• Technology applies scientific knowledge for some
  specific purpose

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• Concept 1.6 A set of themes connects the
  concepts of biology
• Biology is the science most connected to the
  humanities and social sciences
• Underlying themes provide a framework for
  understanding biology

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SCIENCE IS A PROCESS OF INQUIRY THAT ICLUDES
REPEATABLE OBSERVATIONS AND TESTABLE HYPOTHESIES

• DISCOVERY SCIENCE
• INDUCTIVE REASONING
• HYPOTHETICO-DEDUCTIVE REASONING
• DEDUCTIVE REASONING
• HYPOTHESIS

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DISCOVERY SCIENCE AND INDUCTIVE REASONING

• GENERALIZATION THAT SUMMARIZES MANY CONCURRENT
  OBSERVATIONS.
• E.G. ALL ORGANISMS ARE COMPOSED OF CELL BASED
  ON CENTURIES OF OBSERVATIONS.

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THE SCIENTIFIC METHOD AND DEDUCTIVE REASONING

• HYPOTHESIS A TESTABLE EXPLAINATION
• DEDUCTIVE REASONING
• THE IFTHEN LOGIC

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IDEALIZED VERSION OF THE SCIENTIFIC METHOD

• OBSERVE
• FORMULATE QUESTION
• HYPOTHESIZE
• PREDICT
• TEST
• REPEAT

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CONTROLLED EXPERIMENT

• COMPOSED OF 2 GROUPS
• CONTROL GROUP (STAYS THE SAME)
• EXPERIMENTAL GROUP
• CREATED BY CHANGINE 1 VARIABLE

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A THEORY

• A THEORY IS A BROAD HYPOTHESIS.
• IT IS BACKED UP BY EXTENSIVE AND VARIED
  OBSERVATIONS AND DATA.
• USUALLY IT TIES TOGETHER A NUMBER OF SEEMINGLY
  UNRELATED OBSERVATIONS AND EXPERIMENTAL RESULTS.
• E.G. NEWTONS LAWS

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THEME 10

• Science, Technology, and Society

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SCIENCE IS A SOCIAL PROCESS

• SCIENTISTS READ JOURNALS, SHARE INFORMATION AND
  PUBLISH THEIR FINDING FOR OTHER SCIENTISTS TO
  READ.
• THEY CHECK AND VALIDATE PUBLISHED FINDINGS.

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TECHNOLOGY

• A DEVELOPMENT THAT SOLVES A PROBLEM
• NOT ALL ARE SCIENCE RELATED E.G. PRIMITIVE TOOLS
• TECHNOLOGY HAS SOLVED MANY PROBLEMS BUT AT THE
  SAME TIME HAS CREATED OTHERS.

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Table 1.1 Review of Ten Unifying Themes in
Biology
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Table 1.1 Review of Ten Unifying Themes in
Biology (continued)
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Figure 1.8 Regulation by feedback mechanisms