Principles

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CHAPTER 1

• Principles
• of Life
• (An Introduction to Life
• on Earth)

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BIOLOGY

• Greek
• BIO life
• LOGIA study of

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• Biologythe scientific study of living things
• Living thingsAll the diverse organisms
  descended from a single-celled ancestor (a single
  common ancestor)

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Define - LIFE

• Dictionary - the condition which distinguishes
  animals plants from inorganic objects dead
  organisms

• Dead (Dictionary) deprived of life

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Primary Scientific Principles

• Scientific Principles Underlie All Scientific
  Inquiry
• Natural Causality Is the Principle That All
  Events Can Be Traced to Natural Causes
• The Natural Laws That Govern Events Apply
  Everywhere and for All Time
• Scientific Inquiry Is Based on the Assumption
  That People Perceive Natural Events in Similar
  Ways
• The Scientific Method Is the Basis for Scientific
  Inquiry
• Science Is a Human Endeavor

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Scientific Principles

• Natural Causality - all events can be traced to
  natural causes
• Uniformity in Time Space - forces (natural
  laws) acting today are the same as those of past
• Common Perception - all humans perceive natural
  events in the same way (senses)

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• Common Perception does not mean or result in
  Common Interpretation.
• Interpretation is influenced by external factors,
  such as, the cultural, social, and philosophical
  background of the observer(s).
• Science focuses on quantifiable measures NOT
  abstract value systems.

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Lifes Levels of Organization

• We understand life by thinking about nature at
  different levels of organization
• Natures organization begins at the level of
  atoms, and extends through the biosphere
• The quality of life emerges at the level of the
  cell

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A Pattern in Lifes Organization

• Atoms
• Fundamental building blocks of all substances
• Molecules
• Consisting of two or more atoms
• Cell
• The smallest unit of life
• Organism
• An individual consisting of one or more cells

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A Pattern in Lifes Organization

• Population
• Individuals of the same species in the same area
• Community
• Populations of all species in the same area
• Ecosystem
• A community and its environment
• Biosphere
• All regions of the Earth where organisms live

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Levels of Organization in Nature
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Levels of Organization in Nature
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• Key Concepts
• Living Organisms Share Common Aspects of
  Structure, Function, and Energy Flow
• Genetic Systems Control the Flow, Exchange,
  Storage, and Use of Information
• Organisms Interact with and Affect Their
  Environments
• Evolution Explains Both the Unity and Diversity
  of Life
• Science Is Based on Quantifiable Observations and
  Experiments

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Characteristics shared by all living organisms

• Composed of a common set of chemical components
  and similar structures
• Contain genetic information that uses a nearly
  universal code
• Convert molecules obtained from their environment
  into new biological molecules
• Extract energy from the environment and use it to
  do biological work

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Characteristics shared by all living organisms

• Regulate their internal environment
• Replicate their genetic information in the same
  manner when reproducing
• Share sequence similarities among a fundamental
  set of genes
• Evolve through gradual changes in genetic
  information

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Complexity and Organization
Fig. 1-5e, p. 7
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Homeostasis

• Homeostasis
• Organisms use receptors to help keep conditions
  in their internal environment within ranges that
  their cells can tolerate

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What Are the Characteristics of Living Things?

• Living Things Acquire and Use Materials and
  Energy
• Living things acquire energy and nutrients from
  the environment

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Energy and Lifes Organization

• Matter (Nutrients)
• Atoms or molecules essential in growth and
  survival that an organism cannot make for itself
• Energy
• The capacity to do work

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Producers and Consumers

• Producers
• Acquire energy and raw materials from the
  environment
• Make their own food (photosynthesis)
• Consumers
• Cannot make their own food
• Get energy by eating producers and other
  organisms

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A Energy inputs from the environment ?ow through
producers, then consumers.
energy input, mainly from sunlight
B Nutrients become incorporated into the cells of
producers and consumers. Some nutrients released
by decomposition cycle back to producers.
PRODUCERS
plants and other self-feeding organisms
nutrient cycling
CONSUMERS
C All energy that enters an ecosystem eventually
?ows out of it, mainly as heat.
animals, most fungi, many protists, bacteria
energy output, mainly heat
Fig. 1-3, p. 6
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Organisms Sense and Respond to Change

• Organisms sense and respond to change both inside
  and outside the body by way of receptors
• Receptor
• A molecule or cellular structure that responds to
  a specific form of stimulation

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What Are the Characteristics of Living Things?

• Living Things Grow
• Living Things Reproduce Themselves
• Living things reproduce

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Organisms Grow and Reproduce

• Organisms grow, develop, and reproduce using
  information in their DNA, a nucleic acid
  inherited from parents
• Information encoded in DNA is the source of an
  individuals distinct features (traits)

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Instructions in DNA Guide Development
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Responding to Receptors
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What Are the Characteristics of Living Things?

• Living Things As a Whole Have the Capacity to
  Evolve

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• DNA Is the Molecule of Heredity
• DNA

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Adaptation

• Some forms of traits are more adaptive than
  others, so their bearers are more likely to
  survive and reproduce
• Over generations, adaptive traits tend to become
  more common in a population less adaptive forms
  of traits become less common or are lost

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Variation and Mutation

• Information encoded in DNA is the basis of traits
  an organism shares with others of its species
• Mutations are the original source of variation in
  traits

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Summary of Lifes Characteristics
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Evolution and Natural Selection

• Evolution is change in a line of descent
• Traits that characterize a species can change
  over generations in evolving populations
• Natural selection is an evolutionary process
• Differential survival and reproduction among
  individuals that vary in the details of their
  shared, heritable traits

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Lifes Underlying Unity

• All organisms consist of one or more cells, which
  stay alive through ongoing inputs of energy and
  raw materials
• All sense and respond to change all inherited
  DNA, a type of molecule that encodes information
  necessary for growth, development, and
  reproduction

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Unifying Concept in Biology

• EVOLUTION - the idea that modern organisms
  descended with modification from pre-existing
  organisms

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Three Natural Processes Underlie Evolution

• Genetic Variation - variation exists among
  members of a population
• Inheritance - genetic differences among members
  of a population are inheritable from parents to
  offspring
• Natural Selection - the unequal survival and
  reproduction of members of a population due to
  variation in the genetic makeup

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• Complex biological molecules possibly arose from
  random associations of chemicals in the early
  environment.
• Experiments that simulate conditions on early
  Earth show that this was possible.
• Critical step for evolution of lifeformation of
  nucleic acids
• Biological molecules were enclosed in membranes,
  to form the first cells.
• Fatty acids were important in forming membranes.

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Miller-Urey Experiment

• The Miller-Urey experiment was an experiment that
  simulated hypothetical conditions present on the
  early Earth in order to test what kind of
  environment would be needed to allow the
  development of types of organic molecules. It is
  considered by many to be the classic experiment
  on the origin of life.
• It was conducted in 1953 by Stanley L. Miller and
  Harold C. Urey at the University of Chicago.
• The experiment used water (H2O), methane (CH4),
  ammonia (NH3) and hydrogen (H2) - materials which
  were believed to represent the major components
  of the early Earth's atmosphere.

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Miller-Urey Experiment

• The chemicals were all sealed and circulated
  inside a sterile array of glass tubes and flasks
  connected together in a loop, with one flask
  half-full of liquid water and another flask
  containing a pair of electrodes. The liquid water
  was heated to add water vapour to the chemical
  mixture and the resulting gases were circulated
  around the apparatus, simulating the Earth's
  atmosphere.
• Sparks were fired between the electrodes to
  simulate lightning storms (believed to be common
  on the early earth) through the water vapors, and
  then the vapors were cooled again so that the
  water could condense (simulating the oceans).

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Miller-Urey Experiment

• At the end of one week of continuous operation,
  Miller and Urey observed, by analyzing the cooled
  water, that as much as 10-15 of the carbon
  within the system was now in the form of organic
  compounds. Two percent of the carbon had formed
  amino acids, including 13 of the 22 that are used
  to make proteins in living cells, with glycine as
  the most abundant.
• The molecules produced were simple organic
  molecules, far from a complete living biochemical
  system, but the experiment established that the
  hypothetical processes could produce some
  building blocks of life without requiring life to
  synthesize them first.

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Miller-Urey Experiment

• Other Experiments
• The Miller-Urey experiment inspired many
  experiments in a similar vein. In 1961, Joan Oró
  found that amino acids could be made from
  hydrogen cyanide (HCN) and ammonia in a water
  solution. He also found that his experiment
  produced a large amount of the nucleotide base
  adenine which is one of the four bases in RNA and
  DNA. It is also a component of ATP, which is a
  major energy releasing molecule in cells.
• Experiments conducted later showed that other RNA
  and DNA bases could be obtained through simulated
  prebiotic chemistry with a reducing atmosphere
  (an atmosphere characterized by little or no free
  oxygen .

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Miller-Urey Experiment

• Criticism of Miller-Urey Experiment
• There have been a number of objections to the
  implications derived from these experiments. Some
  scientists believe that Earth's original
  atmosphere might contain less of the methane
  (CH4) and ammonia (NH3) molecules (reducing
  molecules) as was thought at the time of
  Miller-Urey experiment.
• But other experiments maintain that the early
  atmosphere of Earth could have contained up to 40
  percent hydrogen - implying a much more
  hospitable environment for the formation of
  prebiotic organic molecules.

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Miller-Urey Experiment

• Criticism of Miller-Urey Experiment
• Another objection is that Miller-Urey Experiment
  required a tremendous amount of energy. Although
  lightning storms are thought to have been very
  common in the primordial atmosphere, they are not
  thought to have been as common as the amount of
  electricity used by the Miller-Urey experiment
  implied. These factors suggest that much lower
  concentrations of biochemicals would have been
  produced on Earth than was originally predicted
  (although the time scale would be 100 million
  years instead of a week).

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Miller-Urey Experiment
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• For 2 billion years, organisms were unicellular
  prokaryotes.
• Early prokaryotes were confined to oceans, where
  they were protected from UV light.
• There was little or no O2 in the atmosphere, and
  hence no protective ozone (O3) layer.

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Basic Unit of Life is the Cell
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• Photosynthesis evolved about 2.7 billion years
  ago.
• The energy of sunlight is transformed into the
  energy of biological molecules.
• Earliest photosynthetic cells were probably
  similar to cyanobacteria.
• O2 was a byproduct of photosynthesis, and it
  began to accumulate in the atmosphere.

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• O2 was poisonous to many early prokaryotes.
• Organisms that could tolerate O2 evolved aerobic
  metabolism (energy production using O2), which is
  more efficient than anaerobic metabolism.
• Organisms were able to grow larger. Aerobic
  metabolism is used by most living organisms today.

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• O2 also produced a layer of ozone (O3) in the
  upper atmosphere.
• This layer absorbs UV light, and its formation
  allowed organisms to move from the ocean to land.

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• Some cells evolved membrane-enclosed compartments
  called organelles.
• Example The nucleus contains the genetic
  information.
• These cells are eukaryotes.
• Prokaryotes lack nuclei and other internal
  compartments.

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• Some organelles may have originated by
  endosymbiosis, when larger cells engulfed smaller
  ones.
• Mitochondria (site of energy generation) probably
  evolved from engulfed prokaryotic organisms.
• Chloroplasts (site of photosynthesis) probably
  evolved from photosynthetic prokaryotes.

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• Multicellular organisms arose about 1 billion
  years ago.
• Cellular specializationcells became specialized
  to perform certain functions.

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Cell Types

• Prokaryotic - small and structurally simple
• Kingdom Archaea and Bacteria
• No nucleus (nucleoid)
• Has ribosomes
• Plasma membrane
• Cell wall

• Eukaryotic - more complex
• Four other kingdoms
• Have a true nucleus
• A variety of organelles
• Plasma membrane
• Some have cell walls

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• Each species has a distinct scientific name, a
  binomial
• Genus name
• Species name
• Example Homo sapiens

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• Evolutionary relationships of species can be
  determined by comparing genomes.
• A phylogenetic tree documents and diagrams
  evolutionary relationships.

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• Complete genome sequences have been determined
  for many organisms.
• Genome sequences are used to study the genetic
  basis of everything from physical structure to
  inherited diseases, and evolutionary
  relationships.

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Figure 1.4 The Tree of Life
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• Relationships in the tree of life are determined
  by fossil evidence, structures, metabolic
  processes, behavior, and molecular analyses of
  genomes.
• Three domains of life
• Bacteria (prokaryotes)
• Archaea (prokaryotes)
• Eukarya (eukaryotes)

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• Genomethe sum total of all the information
  encoded by an organisms genes
• DNA consists of repeating subunits called
  nucleotides.
• Genea specific segment of DNA that contains
  information for making a protein
• Proteins govern chemical reactions in cells and
  form much of an organisms structure.

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• Biological systems are organized in a hierarchy.
• Traditionally, biologists concentrated on one
  level of the hierarchy, but today much biology
  involves integrating investigations across many
  levels.

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Lifes Diversity

• Of an estimated 100 billion kinds of organisms
  that have ever lived on Earth, as many as 100
  million are with us today

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Biology Is Studied at Many Levels of Organization
(Part 1)
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Biology Is Studied at Many Levels of Organization
(Part 2)
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• Organisms interact
• Populationgroup of individuals of the same
  species that interact with one another
• A communitypopulations of all the species that
  live in the same area and interact
• Communities plus their abiotic environment
  constitute an ecosystem.

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Explaining Unity in Diversity

• Theories of evolution, especially a theory of
  evolution by natural selection, help explain why
  life shows both unity and diversity
• Evolutionary theories guide research in all
  fields of biology

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Categorizing the Diversity of Life?

• 1 The Domains Bacteria and Archaea Consist of
  Prokaryotic Cells the Domain Eukarya Is Composed
  of Eukaryotic Cells
• 2 Bacteria, Archaea, and the Protists Are Mostly
  Unicellular Members of the Kingdoms Fungi,
  Plantae, and Animalia Are Primarily Multicellular
• 3 Members of the Different Kingdoms Have
  Different Ways of Acquiring Energy

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Domains and Kingdoms

• Domain the broadest category of classification
• Bacteria, Archaea, and Eukarya
• Kingdom next level (taxa) in classification of
  living organisms
• Currently there are six kingdoms

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Classification Systems

• Classification systems group species by their
  shared, heritable traits
• All organisms are classified into three domains
• Bacteria, archaea, and eukaryotes
• Eukaryotes include plants, animals, protists and
  fungi

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Comparison of Lifes Three Domains
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Diversity of LifeSix Kingdom System of
Classification
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Some Characteristics of the Six Kingdoms
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The Tree of Life
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The domain Archaea
A color-enhanced electron micrograph of an
archaean. The cell wall appears red, and DNA is
scattered inside. Many archaeans can survive
extreme conditions. This Antarctic species lives
at temperatures as low as 2.5C.
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The domain Bacteria
cell wall
plasma membrane
genetic material (DNA)
1 micrometer
A color-enhanced electron micrograph of a
dividing bacterium. Bacteria are unicellular and
prokaryotic most are surrounded by a thick cell
wall. Some bacteria photosynthesize, but most
absorb food from their surroundings.
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Diversity of Life
Bacteria on skin
Magnetotactic bacterium
cyanobacteria
Lactobacillus (yogart)
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Diversity of Life
Archaea
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cell wall
Eukaryotic cell
cell membrane
organelles
nucleus
nuclear envelope
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Diversity of Life
Protists
Plants
Fungi
Animal
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A protist (domain Eukarya)
contractile vacuole
oral groove (mouth)
food vacuoles
10 micrometers
This light micrograph of a Paramecium illustrates
the complexity of these large, normally single,
eukaryotic cells. Some protists photosynthesize,
but others ingest or absorb their food. Many,
including Paramecium, are mobile, moving with
cilia or flagella.
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The kingdom Fungi (domain Eukarya)
An exotic mushroom found in Peru. Most fungi are
multicellular. Fungi generally absorb their
food, which is usually the dead bodies or wastes
of plants and animals. The food is digested by
enzymes secreted outside the fungal body. Most
fungi cannot move.
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The kingdom Plantae (domain Eukarya)
This butterfly weed represents the flowering
plants, the dominant members of the kingdom
Plantae. Flowering plants owe much of their
success to mutually beneficial relationships
with animals, such as these pearl crescent
butterflies, in which the flower provides food
and the insect carries pollen from flower to
flower, fertilizing them. Plants are
multicellular, nonmotile eukaryotes that acquire
nutrients by photosynthesis.
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The kingdom Animalia (domain Eukarya)
A wrasse rests on a soft coral. Animals are
multicellular animal bodies consist of a wide
assortment of tissues and organs composed of
specialized cell types. Most animals can move
and respond rapidly to stimuli. The coral is a
member of the largest group of animals the
invertebrates, which lack a backbone. This group
also includes insects and mollusks. The wrasse
is a vertebrate like humans, it has a backbone.
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Scientific Naming

• Each type of organism is given a two-part name
  that includes genus and species names
• Genus
• A group of species that share unique features
• Species
• Individuals that share one or more heritable
  traits and can interbreed (if sexually
  reproducing)

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How Science Works

• Scientists make and test potentially falsifiable
  predictions about how the natural world works

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Science Is Based on Reasoning

• Inductive Reasoning
• Is a type of reasoning that involves moving from
  a set of specific facts to a general conclusion.
• Used in the development of scientific theories
• A generalization is created from many
  observations
• e.g., the cell theory (all living things are made
  of one or more cells) arises from many
  observations that all indicate a cellular basis
  for life

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Science Is Based on Reasoning

• Deductive Reasoning
• Reasoning which constructs a deductive argument
  where, the truth of the conclusion is purported
  to necessarily follow from or be a logical
  consequence of the truth of the premises and
  (consequently) its corresponding conditions.
• Generating hypotheses based on a well-supported
  generalization (such as a theory)
• e.g., based on the cell theory, any newly
  discovered organism would be expected to be
  composed of cells

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• Inductive logic leads to tentative explanations
  called hypotheses.
• Deductive logic is used to make predictions.
• Experiments are designed to test these
  predictions.

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Scientific Method

• Observation
• Hypothesis
• Experimentation
• Analyze Data
• Assess hypothesis based on experimentation
• Modify hypothesis
• Present findings

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A Scientific Approach
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Scientific Explanations

• HYPOTHESIS - a plausible answer or educated
  guess concerning a question or problem
• THEORY - a reasonable explanation (based on a
  large of observations) to explain a natural
  phenomenon but lacking confirming proof
• LAW - a statement of a biological principle that
  appears to be without exception at the time it is
  made

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Scientific Methodology
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• Controlled experiments manipulate the variable
  that is predicted to cause differences between
  groups.
• Independent variablethe variable being
  manipulated
• Dependent variablethe response that is measured

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Examples of Scientific Theories
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• Comparative experiments look for differences
  between samples or groups.
• The variables cannot be controlled data are
  gathered from different sample groups and
  compared.

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• Statistical methods help scientists determine if
  differences between groups are significant.
• Statistical tests start with a null
  hypothesisthat no differences exists.
• Statistical methods eliminate the possibility
  that results are due to random variation.

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• Not all forms of inquiry into nature are
  scientific.
• Scientific hypotheses must be testable, and have
  the potential of being rejected.
• Science depends on evidence that comes from
  reproducible and quantifiable observations.

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• Religious or spiritual explanations of natural
  phenomena are not testable and therefore are not
  science.
• Science and religion are nonoverlapping
  approaches to inquiry.

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• Scientific advances that may contribute to human
  welfare may also raise ethical questions.
• Science describes how the world works it is
  silent on the question of how the world ought to
  be.
• Contributions from other forms of human inquiry
  may help us come to grips with such questions.