Dr. Adam Safer

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BIO 1107
Dr. Adam Safer BS Armstrong Atlantic State
University MS Georgia Southern University PhD
Florida Institute of Technology
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About Me

• B.S. in 1998 from Armstrong Atlantic State
  University
• M.S. in 2001 from Georgia Southern University
• Thesis Natural history and ecology of the
  flatwoods salamander (Ambystoma cingulatum) on
  the Atlantic Coastal Plain.
• Ph.D. 2007 from Florida Tech
• Dissertation Mechanisms of infrared imaging in
  snakes.

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The Science of Biology

• Chapter 1

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Properties of Life

• Living organisms
• are composed of cells
• are complex and ordered
• respond to their environment
• can grow and reproduce
• obtain and use energy
• maintain internal balance
• allow for evolutionary adaptation

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How to Define Life

• Living Things Are Organized
• Organization of living systems begins with atoms,
  which make up basic building blocks called
  elements.
• The cell is the basic structural and functional
  unit of all living things.
• Different cells combine to make up tissues (e.g.,
  myocardial tissue).
• Tissues combine to make up an organ (e.g., the
  heart).
• Specific organs work together as a system (e.g.,
  the heart, arteries, veins, etc.).
• Multicellular organisms (each an individual
  within a particular species) contain organ
  systems (e.g., cardiovascular, digestive,
  respiratory, etc.).
• A species in a particular area (e.g., gray
  squirrels in a forest) constitutes a population.
• Interacting populations in a particular area
  comprise a community.
• A community plus its physical environment is an
  ecosystem.
• The biosphere is comprised of regions of the
  Earths crust, waters, and atmosphere inhabited
  by organisms.
• Each level of organization is more complex than
  the level preceding it.
• Each level of organization has emergent
  properties due to interactions between the parts
  making up the whole all emergent properties
  follow the laws of physics and chemistry.
• Emergent property quality that appears as
  biological complexity increases

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Levels of Organization

• Cellular Organization
• cells
• organelles
• molecules
• atoms
• The cell is the
• basic unit of life.

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Levels of Organization

• Organismal Level
• organism
• organ systems
• organs
• tissues

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Levels of Organization

• Population Level
• ecosystem
• community
• population

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Levels of Organization

• Each level of organization builds on the level
  below it but often demonstrates new features.
• Emergent properties new properties present at
  one level that are not seen in the previous level

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• Living Things Acquire Materials and Energy
• Maintaining organization and conducting
  life-sustaining processes require an outside
  source of energy, defined as the capacity to do
  work.
• The ultimate source of energy for nearly all life
  on earth is the sun plants and certain other
  organisms convert solar energy into chemical
  energy by the process of photosynthesis.
• Food provides nutrient molecules used as building
  blocks for energy.
• Metabolism is all the chemical reactions that
  occur in a cell.
• All organisms must maintain a state of biological
  balance, or homeostasis. Temperature, moisture
  level, pH, etc. must be maintained within the
  tolerance range of the organism. Organisms have
  intricate feedback and control mechanisms to
  maintain homeostatic balance.

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• Living Things Respond
• Living things interact with the environment and
  with other living things.
• Response often results in movement of the
  organism (e.g., a plant bending toward the sun to
  capture solar energy, a turtle withdrawing into
  its shell for safety, etc.).
• Responses help ensure survival of the organism
  and allow the organism to carry out its
  biological activities.
• The collective responses of an organism
  constitute the behavior of the organism.

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• Living Things Reproduce and Develop
• Reproduction is the ability of every type of
  organism to give rise to another organism like
  itself.
• Bacteria, protozoans, and other unicellular
  organisms simply split in two (binary fission).
• Multicellular organisms often unite sperm and
  egg, each from a different individual, resulting
  in an immature individual which develops into the
  adult.
• The instructions for an organisms organization
  and development are encoded in genes.
• Genes are comprised of long molecules of DNA
  (deoxyribonucleic acid) DNA is the genetic code
  in all living things.

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• Living Things Have Adaptations
• Adaptations are modifications that make organisms
  suited to their way of life.
• Natural selection is the process by which species
  become modified over time.
• A species is a group of interbreeding
  individuals.
• In natural selection, members of a species may
  inherit a genetic change that makes them better
  suited to a particular environment.
• These members would be more likely to produce
  higher numbers of surviving offspring.
• Evolution is defined as descent with
  modification over time.
• The fact that all life forms are composed of
  cells, contain genes comprised of DNA, and
  conduct the same metabolic reactions suggests all
  living things have a common ancestor.
• One species can give rise to several species,
  each adapted to to a particular set of
  environmental conditions.
• Evolution is responsible for the great diversity
  of life on Earth.

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How the Biosphere is Organized

• Levels of Complexity
• The biosphere is the zone of air, land, and water
  where organisms exist.
• A population consists of all members of one
  species in a particular area.
• A community consists of all of the local
  interacting populations.
• An ecosystem includes all aspects of a living
  community and the physical environment (soil,
  atmosphere,
  etc.).
• Interactions between various food chains make up
  a food web.
• Ecosystems are characterized by chemical cycling
  and energy flow.
• Ecosystems stay in existence because of a
  constant input of solar energy and the ability of
  
  photosynthetic organisms to absorb it.

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• The Human Population
• The human population modifies existing ecosystems
  for its own purposes.
• Two biologically diverse ecosystems, rain forests
  and coral reefs, are severely threatened by the
  human population.
• Human beings depend on healthy working ecosystems
  for food, medicines, and raw materials.

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The Nature of Science

• Science aims to understand the natural world
  through observation and reasoning.
• Science begins with observations, therefore, much
  of science is purely descriptive.
• Science uses both deductive and inductive
  reasoning.

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The Nature of Science

• Deductive reasoning uses general principles to
  make specific predictions.
• Inductive reasoning uses specific observations to
  develop general conclusions.

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Inductive and Deductive Reasoning

• Deductive Reasoning
• Proceeds from generalities to specifics
• Adds nothing new to knowledge, but makes
  relationships among data more apparent
• Ex
• GENERAL RULE All birds have wings
• SPECIFIC EXAMPLE Robins are birds
• CONCLUSION (based on deductive reasoning) All
  Robins have wings

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Inductive and Deductive Reasoning

• Inductive Reasoning
• Used to discover general principles
• Seeks a unifying explanation for all the data
  available
• Ex
• FACT Gold is a metal heavier than water
• FACT Iron is metal heavier than water
• FACT Silver is a metal heavier than water
• CONCLUSION (based on inductive reasoning) All
  metals are heavier than water
• Conclusions reached with inductive reasoning may
  changed with new information

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The Nature of Science

• Scientists use a systematic approach to gain
  understanding of the natural world.
• -Observation
• -Hypothesis formation
• -Prediction
• -Experimentation
• -Conclusion

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The Nature of Science

• A hypothesis is a possible explanation for an
  observation.
• A hypothesis
• -must be tested to determine its validity
• -is often tested in many different ways
• -allows for predictions to be made

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The Nature of Science

• The experiment
• -tests the hypothesis
• -must be carefully designed to test only one
  variable at a time
• -consists of a test experiment and a control
  experiment

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The Nature of Science

• If the hypothesis is valid, the scientist can
  predict the result of the experiment.
• Conducting the experiment to determine if it
  yields the predicted result is one way to test
  the validity of the experiment.

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The Nature of Science

• Scientists may use
• reductionism - to break a complex process down
  to its simpler parts
• models to simulate phenomena that are
  difficult to study directly

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• A Controlled Study
• A controlled study ensures that the outcome is
  due to the experimental (independent) variable,
  the factor being tested.
• The result is called the responding (dependent)
  variable because it is due to the independent
  variable.
• The Experiment
• Hypothesis pigeon pea/winter wheat rotation will
  increase winter wheat production as well as or
  better than the use of nitrogen fertilizer.
• Prediction wheat biomass following the growth of
  pigeon peas in the soil will surpass wheat
  biomass following nitrogen fertilizer treatment.
• Control group winter wheat that receives no
  fertilizer.
• Test groups winter wheat treated with different
  levels of fertilizer winter wheat grown in soil
  into which pigeon pea plants had been tilled.
• Environmental conditions and watering were
  identical in control and test groups.
• Results all test groups produced more biomass
  than control group, but high level of nitrogen
  fertilizer produced more biomass than pigeon pea
  test group. Thus, hypothesis is not supported.

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• Continuing the Experiment
• To test the hypothesis that pigeon pea residues
  will build up over time and will increase winter
  wheat production compared to nitrogen fertilizer,
  the study is continued for another year.
• The fertilizer-only treatment no longer exceeded
  biomass production with the use of pigeon peas
  biomass in the pigeon pea-treated test group was
  highest.
• Conclusion at the end of two years, the yield
  of winter wheat is better in the pigeon
  pea-treated test group. Hypothesis supported.
• Continuation of the study for another year showed
  that the soil was continuously improved by the
  pigeon peas compared to the nitrogen fertilizer
  test groups.
• Results were reported in a scientific journal.

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The Nature of Science

• A scientific theory
• -is a body of interconnected concepts
• -is supported by much experimental evidence and
  scientific reasoning
• -expresses ideas of which we are most certain

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Charles Darwin

• Served as naturalist on mapping expedition around
  coastal South America.
• Used many observations to develop his ideas
• Proposed that evolution occurs by
• natural selection

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Voyage of the Beagle
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Evolution

• The cumulative genetic changes that occur in a
  population of organisms over time
• Current theories were proposed by Charles Darwin,
  a 19th century naturalist
• Evolution occurs through natural selection
• Natural Selection
• Individuals with more favorable genetic traits
  are more likely to survive and reproduce
• Frequency of favorable traits increase in
  subsequent generations

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Natural Selection

• Based on four observations about the natural
  world
• Overproduction
• Each species produces more offspring than will
  survive to maturity
• Variation
• Individuals in a population exhibit variation
• Some traits improve the chances of survival.
  Others do not.
• Limits on Population Growth
• Resource limitations will keep population in
  check
• Differential Reproductive Success
• Individuals with most favorable traits are more
  likely to reproduce

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Darwins Evidence

• Similarity of related species
• - Darwin noticed variations in related species
  living in different locations

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Darwins Evidence

• Population growth vs. availability of resources
• -population growth
• is geometric
• -increase in food
• supply is arithmetic

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Darwins Evidence

• Population growth vs. availability of resources
• - Darwin realized that not all members of a
• population survive and reproduce.
• -Darwin based these ideas on the writings of
  Thomas Malthus.

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Post-Darwin Evolution Evidence

• Fossil record
• - New fossils are found all the time
• - Earth is older than previously believed
• Mechanisms of heredity
• - Early criticism of Darwins ideas were resolved
  by Mendels theories for genetic inheritance.

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Post-Darwin Evolution Evidence

• Comparative anatomy
• - Homologous structures have same evolutionary
  origin, but different structure and function.
• - Analogous structures have similar structure and
  function, but different evolutionary origin.

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Homologous Structures
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Post-Darwin Evolution Evidence

• Molecular Evidence
• - Our increased understanding of DNA and protein
  structures has led to the development of more
  accurate phylogenetic trees.

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Natural Selection Fossils and Comparative Anatomy
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Unifying Themes in Biology

• Cell theory
• - All living organisms are made of cells, and all
  living cells come from preexisting cells.
• Molecular basis of inheritance
• - DNA encodes genes which control living
  organisms and are passed from one generation to
  the next.

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Unifying Themes in Biology

• Structure and Function
• -The proper function of a molecule is dependent
  on its structure.
• -The structure of a molecule can often tell us
  about its function.

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Unifying Themes in Biology

• Evolutionary change
• - Living organisms have evolved from the same
  origin event. The diversity of life is the
  result of evolutionary change.
• Evolutionary conservation
• - Critical characteristics of early organisms are
  preserved and passed on to future generations.

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Unifying Themes in Biology

• Cells - information processing systems
• - Cells process information stored in DNA as well
  as information received from the environment.
• Emergent properties
• - New properties are present at one level of
  organization that are not seen in the previous
  level.

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How Living Things Are Classified

• Taxonomy
• discipline of identifying and classifying
  organisms according to certain rules.
• Taxonomic classification changes as more is
  learned about living things, including the
  evolutionary relationships between species

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• Categories of Classification
• From smaller (least inclusive) categories to
  larger (more inclusive), the sequence of
  classification categories is species, genus,
  family, order, class, phylum, kingdom, domain.
• The species within one genus share many specific
  characteristics and are the most closely related.
• Species in the same kingdom share only general
  characteristics with one another

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• Domains
• Biochemical evidence suggests that there are
  three domains Bacteria, Archaea, and Eukarya.
• The domains Bacteria and Archaea contain
  unicellular prokaryotes organisms in the domain
  Eukarya have a membrane-bound nucleus.
• The prokaryotes are structurally simple but are
  metabolically complex.
• Archaea can live in water devoid of oxygen, and
  are able to survive harsh environmental
  conditions (temperatures, salinity, pH).
• Bacteria are variously adapted to living almost
  anywhere (water, soil, atmosphere, in/on the
  human body, etc.).

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• Kingdoms
• The domains Archaea and Bacteria are not yet
  categorized into kingdoms.
• Eukarya contains four kingdoms Protista, Fungi,
  Plantae, and Animalia.
• Protists (kingdom Protista) range from
  unicellular forms to multicellular ones.
• Fungi (kingdom Fungi) are the molds and
  mushrooms.
• Plants (kingdom Plantae) are multicellular
  photosynthetic organisms.
• Animals (kingdom Animalia) are multicellular
  organisms that ingest and process their food.

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Archaea Bacteria-like unicellular
prokaryotes Extreme aquatic environments
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Bacteria Microscopic unicellular prokaryotes
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• Scientific Name
• A binomial name is a two-part scientific name
  the genus (first word, capitalized) and the
  specific epithet of a species (second word, not
  capitalized).
• Binomial names are based on Latin and are used
  universally by biologists.
• Either the genus name or the specific epithet
  name may be abbreviated.

Lampropeltis getula eating Crotalus atrox
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Levels of Classification
Corn
Human
Taxon
Eukarya
Eukarya
Domain
Plantae
Animalia
Kingdom
Anthophyta
Chordata
Phylum
Liliopsida
Mammalia
Class
Commelinales
Primates
Order
Poacae
Hominidae
Family
Zea
Homo
Genus
Z. mays
H. sapiens
Species