Biological Principles
1. The Organization of Life
    a. Origin of Life
        i. Abiotic Production of Organic Molecules
            1. Hypotheses on Origin of Macromolecules
            2. Making Organic Compounds: The Stanley Miller Experiment & Others
            Chemosynthesis: The use of inorganic substances such as carbon dioxide to make carbohydrates from the energy released by chemical reactions.
        ii. Macromolecules to Living Cells
            1. Prebionts: Nonliving structures that evolved into the first living cells
            2. Coacervates: Colloidal aggregation containing a mixture of organic compounds.
                The formation of coacervates in the primeval soup was a step towards the development of cells.
                Organic molecules surrounded by a film of water molecules
                Selectively absorb materials from surrounding water
                Incorporate them into their structure
                Not a random arrangement of molecules
            3. Microsphere
                Organic molecules surrounded by a double membrane
                Can be formed from Proteinoids, when placed in boiling water & cooled.
        iii. Microspheres = Protocells!!
        iv. Earliest Evidence of Life
            1. Stromatolites

2. Hypotheses for where Life Originated
    1. Vent Hypothesis: Chemosynthetic, external source of energy for earliest (anaerobic) autotrophs were chemical reactions (not sun).
    2. Tidal Pool Hypothesis: Hot tidal pools of seawater concentrated chemicals and provided energy for origin of amino acids and DNA.
    3. Panspermia: Life originated on Mars, and rode to Earth in meteorites.Image source: http://library.thinkquest.org

3. Classification of Organisms: Typological (base on the type specimen)
    a. The Species Concept
        i. Biological
        ii. Paleontological
    b. Basis for classification = Evolution
        i. Hierarchy of classification
            1. Domain> Kingdom> Phylum (or Division)> Class> Order> Family> Genus (pl. Genera)> Species
        ii. Classification of humans
            1. Domain: Eucarya
            2. Kingdom: Animalia
            3. Phylum: Chordata(Plants use Division instead of Phylum)
            4. Class: Mammalia
            5. Order: Primates
            6. Family: Hominidae
            7. Genus: Homo
            8. Species: Homo sapiens
        iii. Domains:
            1. Bacteria: heterotrophic, cyanobacteria (stromatolites)
            2. Archaea: halophiles, thermophiles
            3. Eucarya
                a. Kingdom Protista
                b. Kingdom Fungi
                c. Kingdom Animalia
                d. Kingdom Plantae
        iv. Taxonomy: the study of the composition and relationships of those groups. Taxon individual group (pl. taxa)
        v. Species: group of individuals that can interbreed.

4. The basic dichotomy of life
    a. Cell: is a membrane-bounded module with a variety of distinct features, including structures in which certain chemical reaction take place.
    b. Prokaryotic Cells (Domains Bacteria and Archaea
        Cells of the most primitive organisms have cells that lack a nucleus.
        Monerans (bacteria and related organisms) are prokaryotes.
        Prokaryotes also lack other membrane-bound internal structures.
    c. Eukaryotic Cells
        All organisms, other than monerans, have cells with nuclei.
        Cells with nuclei = eukaryotic cells, and the organisms made of such cells are eukaryotes.Eukaryotic cells have membrane-bound internal structures (organelles) in addition to the nucleus.Endosymbiosis: for the origin of the eukaryotic

5. Characteristics of Animals
    a. Features Used to Classify the Animal Kingdom
        1. Grade of organization of cells
            a. Cellular Level
            b. Tissue Level
            c. Organ Level
        2. Body symmetry
                a. Bilateral
                b. Radial or spherical
                c. Asymmetrical
        3. Number of skin cell layers in early development
            a. Primitive simplest animals lack differentiated dermal layers
            b. More advanced forms
            c. Ectoderm (outer skin)
            d. Mesoderm (middle skin)
            e. Endoderm (inner skin)
        4. Presence or Absence of Coelom (internal fluid-filled cavity in the body, See table 2.1)
            a. Acoelomates
            b. Pseudoacolemates
            c. Eucoelomates
            d. Lophophorates
            e. Schizocoels = protostromes (first mouth)
            f. Enterocoels = deuterostomes (second mouth)
        5. Presence or absence of segmentation: Divisions of the body

6. Characteristics of Plants
            a. The Organization of Life (Plant Kingdom)
                i. Eukaryotic organisms
                ii. Manufacture their own food
                    1. photosynthesis
                    2. autotrophs (self-feeding)
            b. Division of Plants
                i. Presence or absence of vascular tissue and Habitat
                    1. Algae: aquatic (marine and fresh water), lack vascular tissue
                    2. Tracheophytes (have vascular tissue = true land plants)
                    3. Bryophytes (mosses and liverworts) do not have vascular tissue (live on land)

7. The theory of organic evolution: Evolution is the central, unifying theory of modern biology.
Darwin and the Origin of Species by Natural Selection:
         1.- Life is old: Was not created but evolved from previously existing organisms
         2.- Life started with simple organisms and became more complex with time
         3.- Natural Selection is the force that drives evolution

    a. Natural Selection
    b. The Genetic Basis of Evolution: Mutations
    c. The level at which evolution takes place
        i. Species (interbreeding)
        ii. Population (genetic variation)
        iii. Individuals (single)
    d. The Mechanisms of Evolution:
        i. Variation
        ii. Natural Selection
        iii. Isolation: Geographic distribution of organisms
    e. Modes of speciation
        i. Phyletic evolution: Gradualism, slow change; evol. horses -MICROEVOLUTION
        ii. Punctuated equilibrium: Rapid change
    f. Extinctions
        i. Causes of extinction
            1. Physical:
                a. local environmental change
                b. climate change
                c. extraterrestrial causes
            2. Biological:
                a. increased predation
                b. new predator or disease
                c. humans
    g. Patterns of Evolution
        i. Divergence: new species (speciation)
        ii. Convergence: groups develop similar-looking characteristics
            1. Homologous (structure evolves from similar ancestral feature)
            2. Analogous structures (similar functions, dissimilar origins)
        iii. Parallel evolution: unrelated lineages undergo similar evolutionary changes through time.
        iv. Speciation: Adaptive radiation and mass extinction. Speciation is caused by reproductive barriers
            1. Physical reproductive barriers:
                a. mountain range
                b. boundary between ocean layers
            2. Biological reproductive barriers:
                a. differences in mating behavior
                b. incompatibility of egg and sperm
                c. differences in reproductive timing
        v. Radiation: rapid origin of many new species from a single ancestral group

8. Environments of Life: Some Concepts
    a. Habitat: Setting on or close to the Earth’s surface that are inhabited by life.
        i. Aquatic
            1. Marine (oceans and seas
            2. Freshwater (lakes, rivers, and streams)
        ii. Terrestrial
    b. Ecology: the study of the factors that govern the distribution and abundance of organisms in natural environments
    c. Niche: relations between a given species and it environment
    d. Life Habitat: the way a species lives within its niche.
        i. Limiting factors: physical and chemical conditions that restrict every species to its niche.
    e. Population: group of individuals that belong to a single species
    f. Community: populations of several species living together in a habit. Some species feed on others
        i. Producers: the foundation of the system, photosynthesizing organisms or bacteria that harness the energy of chemical reactions
        ii. Consumers: herbivores which feed on producers
        iii. Carnivores, feed on other consumers
    g. Ecosystem: Organisms of an ecological community and the physical environment they occupy. Come in all sizes
        i. Fauna: The animals and protozoans (Protists) of an ecosystem
        ii. Flora: Plants and plantlike Protists of an ecosystem
        iii. Biota: Flora and fauna living together
        iv. Food Chain: sequence of species from producer to top carnivore
        v. Diversity: designate the number of species that live together within a community
        vi. Opportunistic species: species that specialize in invading newly vacated habitats, e.g, land cleared by fire, or shore areas formed along rivers that change course at flood stage.
    h. Biogeography: Distributions and abundances of organisms on a broad geographic scale.
        i. Realms: a primary marine or terrestrial biogeographic division of the earth's surface
            1. Terrestrial
            2. Marine
                a. Plankton: organisms that drift in water
                    i. Phytoplankton
                    ii. Zooplankton
                b. Nekton: Animals that move through the water primarily by swimming
                c. Pelagic: plankton and nekton in the open ocean
                d. Benthos: immobile and mobile organisms that populate the seafloor.
                e. Benthic herbivores graze on plantlike forms like algae
                    i. Suspension feeders: strain phytoplankton and plan debris from the water.
                    ii. Deposit feeders: Consume sediment and digest organic mater mixed in with mineral grains.
Source: <http://www.bigelow.org/virtual/bath_sub1.html#margin>