BIO 172W - Introduction to Organismal Biology and Principles of Evolution

1. Demonstrate an understanding about the modern levels of taxonomic classification of organisms.
   1. List the levels of taxonomic classification. 
   2. Produce several examples using the levels of taxonomic.
   3. Compare and contrast placement of humans in reference to other common organisms.
2. Demonstrate an understanding of the history of evolutionary thought.
   1. Name several people who are important in the history of evolutionary biology (ex: Charles Darwin, Jean Baptiste Lamarck, George Cuvier, James Hutton, Thomas Malthus, and Charles Lyel).
   2. List the steps created by Charles Darwin with his theory of Natural Selection and it's effects on population characteristics.
   3. Describe the importance of the fossil record, comparative anatomy, embryology, biogeography, and molecular biology data as possible avenues for explaining evolution.
   4. List three major types of selection for traits (ex: Stabilizing, Directional, Diversifying).
   5. Describe the major types of fossils (ex: Amber, Imprint, Caste, Petrified) and how radioactive dating applies to them.
   6. Predict and describe how each of these individuals would respond to modern evolutionary data.
   7. Compare these individuals and show if their work was later scientifically substantiated.
   8. Propose possible applications of types of selection resulting in the creation of new species.
   9. Predict the age of a fossil when given proper data.
   10. Apply Darwin’s hypothesis to new data that is provided.
3. Demonstrate an understanding of the history of life on Earth.
   1. Describe the four major eras in geological time with beginning and ending dates (ex: Cenozoic, Mesozoic, Paleozoic, and Precambrian).
   2. Describe when major biological events occurred in the past (ex: solidification of the crust, appearance of microbes, primitive atmosphere, appearance of the modern atmosphere, changes in the major life forms on the Earth).
   3. List the major people who are important in our understanding of the formation of cellular life (ex: Oparin, Haldane, Miller, Urey, and Fox).
   4. Describe the ecosystem of the Earth at any point in it’s early history, with specific reference to life forms.
   5. Determine the application of early theories to the appearance of cellular life and it’s subsequent evolution.
   6. Differentiate between chemical and biological evolution, and their importance in the appearance of life on the early Earth.
4. Describe the characteristics of major groups in the Kingdom Monera.
   1. List the two major groupings of bacteria (ex: Archaebacteria and Eubacteria).
   2. List the subgroupings of bacteria, based on Bergey’s Manual (ex: Halophiles, Thermoacidophiles, Methanogens,Actinomycetes, Chemoautotrophs, Cyanobacteria, Endospore-formers, Enterics, Myxoplasmas, Myxobacteria, Nitrogen-fixators, Phototrophs, Pseudomonads, Rickettsias, Chlamydias, and Spirochetes).
   3. List the taxonomic subgroupings of protists (ex: Algae, Protozoa, Fungal-like).
   4. List the taxonomic subgroupings of algae (ex: Chlorophyta, Rhodophyta, Phaeophyta, and Chrysophyta).
   5. List the taxonomic subgroupings of protozoa (ex: Rhizopoda, Actinopoda, Zoomastigophora, Ciliophora, Foraminifera, and Apicomplexa).
   6. List the taxonomic subgroupings of fungal-like protists (ex: Myxomycota, Acrasiomycota,Oomycota, Chytridiomycota).
   7. Describe the interaction between the various bacterial groups during the stabilization of the early Earth.
   8. Describe the basic forms of bacterial life-styles and how they may have played a part in bacterial evolution.
   9. Describe several theories which could explain the appearance of eukaryotic cells from prokaryotic beginnings (ex: Autogenous and Endosymbiotic Theories).
   10. Describe how the oxygen atmosphere could have arisen and relate this occurrence to the evolution of eukaryotes.
   11. Describe the basic characteristics which differentiate the early eukaryotes from the prokaryotes (ex: mostly aquatic aerobes with diverse nutrition, cilia/flagella in their life-cycles, and cyst formation).
   12. Relate the appearance of the various forms of bacteria with formation of the three basic protistal groupings based on metabolism (ex: Plant-like, Animal-like, and Fungal-like), and the subsequent appearance of the multicellular kingdoms that share these characteristics.
   13. Place these organisms in their proper context when describing the evolution of the early Earth (using the geological time scale).
5. Describe major events in the life cycle of four divisions of plants.
   1. List the four major groupings of modern plants (ex: Nonvascular, Vascular Spore-producers, Vascular Naked-seeds, and Vascular True Seeds).
   2. List the divisions of nonvascular plants (ex: Bryophytes, Hepatophytes, and Anthocerophytes).
   3. List the divisions of vascular spore-producing plants (ex: Pterophytes, Lycophytes, Sphenophytes, and Psilophytes).
   4. List the divisions of vascular naked seed plants (ex: Coniferophyta, Cycadophyta, Gnetophyta, and Ginkophyta).
   5. State the one division of vascular true seed plants (ex: Anthophyta).
   6. List the portions of an anthophyte’s flower and their importance in reproduction.
   7. List the major adaptations of the plant kingdom as a whole (ex: vascular tissues, reduction in gametophyte size, protection of embryos, and protection against dessication).
   8. Describe the alternation of generations in plants (ex: gametophyte and sporophyte).
   9. List many of the problems created by the plant kingdom (ex: weedy plants, destruction of wood and other products, competition for water supplies, allergies, etc.).
   10. List many of the benefits created by the plant kingdom (ex: foods, competition with bacteria and protists, building supplies, energy sources, oxygen production, etc.).
   11. Place the major plant groupings into a historical context using the geological time scale.
   12. Describe how the adaptations of the plant divisions led to changes in the evolution of the plant kingdom as a whole.
   13. Describe how the appearance of the anthophytes changed the evolution of other organisms on the early Earth.
   14. Compare/contrast the Gymnosperms and Angiosperms.
   15. Compare/contrast the Monocots and Dicots.
   16. Relate the organisms within the plant kingdom and the organisms within the two earlier kingdoms (ex: bacteria are needed by most plants in order to fix nitrogen, plants create oxygen and most protists are aerobic, etc.).
6. Describe major events in the life cycle of four division of Fungi.
   1. List the four major groupings of modern fungi (ex: Zygomycetes, Ascomycetes, Basidiomycetes, and Deuteromycetes.
   2. List the major characteristics of fungi (ex: yeasts, hyphae, mold/mildew, mycelia, septate/aseptate, haustoria, lichens, mycorrhizae, etc.).
   3. List the three major groupings of lichens (ex: crustose, foliose, and fruticose).
   4. List the major characteristics for each of the fungal groups (ex: Zygomycetes are normally coenocytic spore producers that form mycorrhizae with many plants).
   5. List many of the problems created by the fungal kingdom (ex: plant pathogens, human disorders, allergies, destruction of food, destruction of wood products, etc.).
   6. List many of the benefits created by the fungal kingdom (ex: antibiotics, foods, competition with bacteria, etc.).
   7. Place the major fungal groupings into a historical context using the geological time scale.
   8. Describe how the appearance of the fungi changed the evolution of other organisms on the early Earth (ex: antibiotics and their effects).
   9. Compare/contrast the true fungi and the deuteromycetes.
   10. Relate the organisms within the fungal kingdom and the organisms within the three earlier kingdoms (ex: mycorrhizae allowed plants to venture into new areas, lichens produce soil for plants, fungi compete with bacteria and thus accelerate their evolution, etc.).
7. Describe the characteristics of major phyla of Parazoa and Eumetazoa in the Kingdom Animalia.
   1. List the major characteristics of the animal kingdom (ex: prey ingestion, glycogen energy storage, intercellular junctions, 2-4 tissues in embryo development, and dominant diploid forms).
   2. List the major groupings in the animal kingdom (ex: Parazoa and Eumetazoa, Radiata and Bilateria, Acoelomates,  Pseudocoelomates,  Protostomates, and Deuterostomates).
   3. List the major phyla of the animal kingdom (ex: Porifera, Cnidaria, Platyhelminthes, Rotifera, Nematoda, Mollusca, Annelida, Arthropoda, Echinoderms, and Chordates).
   4. List the major classes within the phyla of the animal kingdom (ex: Hydrazoans, Scyphozoans, and Anthozoans in the Phylum Cnidaria).
   5. List the major characteristics of the chordate embryo (ex: cartilagenous notochord, dorsal hollow nerve cord, respiratory slits, and a post-anal tail).
   6. List examples of prosimians, new world monkeys, old world monkeys, and great apes.
   7. Be able to list the two forms of hominids (ex: Homo and Australopithecus).
   8. List many of the problems created by the animal kingdom (ex: parasitism, competition with mankind for resources, etc.).
   9. List many of the benefits created by the animal kingdom (ex: food products, work animals, companionship, etc.).
   10. Place the major animal groups into a historical context using the geological time scale.
   11. Describe how the appearance of the animals changed the evolution of other organisms on the early Earth (ex: food supplies, changes in dominant life-forms, etc.)
   12. Create a flow-chart showing the major adaptations within the animal kingdom (ex: importance of coelom formation, mouth-to-anus formation, body symmetry, etc.).
   13. Create a flow-chart showing the major adaptations within the chordates (ex: jaws, armor, cartilagenous skeletons, bones, skin breathers, leathery eggs, calcified eggs, internalized maturation of young, etc.
   14. Compare/contrast the acoelomates and the coelomates.
   15. Compare/contrast the protostomates and deuterostomates.
   16. Compare/contrast the echinoderms and the chordates.
   17. Compare/contrast the prosimians, monkeys, and the great apes.
   18. Compare/contrast the new world and old world monkeys.
   19. Compare/contrast the Homo and Australopithecine lines of hominids.
   20. Relate the organisms within the animal kingdom and the organisms within the four earlier kingdoms (ex: inter-relationship between plants and animals, CO₂/O₂ cycling, energy cycling, colonization of all of the Earth, predator/prey relationships, parasitism, etc.).
   21. Describe how various adaptations within the primate group were correlated with changes in the terrestrial ecosystems of the Earth in the past (ex: drying of the African continent and shifts from arboreal life-styles, specialization vs. generalization of feeding requirements in the primates, pack behavior, etc.).
8. Describe major adaptations of Gymnosperms in the Kingdom Planae.
   1. List the major characteristics of monocots and dicots (ex: cotyledon number, vein type, vascular bundle arrangement, root type, floral part number, and woody growth). 
   2. List the major portions of the modern plant embryo and the tissues that are used to make them.
   3. List the major adaptations of plant roots (ex: winter energy storage, adventitious support, mycorrhizae, nitrogen nodules, root hairs, etc.).
   4. List the major adaptations of plant stems (ex: bulbs, stolons, rhizomes, tubers, and xenophobes, etc.).
   5. List the major adaptations of plant leaves (ex: deciduous/evergreen, tendrils, spines/thorns, succulents, animal traps, petals, etc.).
   6. Diagram the progression of embryonic development in seeds (ex: triploblastic embryo, formation of bark, progression of ground tissue,  cambium formation of xylem and phloem, secondary woody growth, etc.).
   7. Describe the major characteristics of xylem and phloem (ex: cell types, transpiration, source-to-sink sugar movement, flow rates, ionic control of stoma, etc.).
   8. Describe the major characteristics involved in anthophyte reproduction (ex: germination, pollination, fertilization, flower part uses, pollen formation and use, egg formation and use, double fertilization of the seed, etc.).
   9. List the four major groupings of seeds (ex: simple dry, simple fleshy, aggregate, and multiple).
   10. List the five major forms of hormones controlling plant development (ex: auxins, cytokinins, gibberellins, abscisic acid, and ethylene).
   11. List several tropisms seen in plants (ex: prototropism, apical dominance, fruit ripening, anti-aging effects, winter dormancy, gravitropism, leaf abscission, thigmotropism, etc.).
   12. Compare/contrast the monocots and the dicots in reference to human uses.
   13. Compare/contrast plant root, stem, and leaf adaptations in reference to human uses of the plants.
   14. Compare/contrast the various forms of plant fruits and their uses to mankind.
   15. Compare/contrast the life history strategies of monocots and dicots.
   16. Compare/contrast the life history strategies of deciduous and evergreen plants.
   17. Analyze the reproductive method seen in the anthophytes and formulate possible pros and cons of this system.
   18. Describe the functions of the five major groupings of hormones in the control of plant tropisms (ex: aging, seed dormancy, fruit development, apical dominance, phototropism, etc.).
   19. Relate the adaptations of the plant kingdom and the rise of the hominids (ex: winter food storage, adaptations to the ice ages, movement of hominids on the Earth, shift from nomadic to agricultural life-styles, etc.).
   20. Describe how the various adaptations in plant reproductive styles and fruit development may have correlated with the development of insects, bats, and other forms of animals.
9. Describe the major tissues seen in the Sub-Kingdom Vertebrat.
   1. List the four major forms of modern animal tissues (ex: epithelial, connective, muscular, and nervous).
   2. List examples of epithelial tissues (ex: simple squamous, simple cuboidal, simple columnar, pseudostratified ciliated columnar, stratified squamous, etc.)
   3. List examples of connective tissues (ex: adipose, loose fibrous, blood, dense fibrous, cartilage, osseous, etc.).
   4. List examples of muscular tissues (ex: skeletal, smooth, and cardiac).
   5. List the two major cell types seen in nervous tissue (ex: neurons and neuroglia).
   6. Compare/contrast the forms of epithelia and their uses in animals.
   7. Compare/contrast the forms of connective tissues and their uses in animals.
   8. Compare/contrast the forms of muscle tissues and their uses in animals.
   9. Describe how nervous tissue cells function in relationship to other tissues.
   10. Relate the appearance of various forms of tissues and the subsequent success of various taxonomic groups containing those tissues in the fossil history of the Earth.
10. Demonstrate an understanding of anatomy and physiology of animal nutrition.
    1. Describe different feeding mechanisms of animal nutrition.
    2. Define stages of nutrition such as ingestion, digestion, absorption, and elimination.
    3. Explain how food is processed by animals in relation to their structural complexity.
    4. Describe structures and functions of digestive systems of major animal phyla.
    5. Define intracellular digestion and extracellular digestion.
    6. Name different categories of organic molecules in terms of macromolecules and their monomers.
    7. Name major digestive enzymes needed in food processing (humans).
    8. Explain how macromolecules are broken down into their monomers by enzymatic hydrolysis (carbohydrates-> simple sugar, proteins-> amino acids, lipids ->fatty acid and glycerol, nucleic acids-> nucleotides).
    9. Describe where each type of macromolecule is broken down in the digestive tract.
    10. Explain what is meant by “healthy diet”.
    11. Explain the roles of vitamins in digestion and enzymatic reactions.
11. Demonstrate an understanding of animals’ respiratory systems.
    1. List different respiratory systems in major animal phyla.
    2. Name parts and components of these organ systems.
    3. Define characteristics of parts and components within each system.
    4. Define diffusion of gas exchange in this organ system.
    5. Describe the functions of respiratory systems in animals as either being gastrovascular (both digestion and distribution of  nutrients) or cardiovascular.
    6. Explain general evolutionary trends found in the respiratory system of animals (ex: increase in surface area, internalization of respiratory surface, move from water - aquatic environment - to air medium - terrestrial environment, use of concurrent exchange and countercurrent exchange in different animals).
    7. Describe the following respiratory modifications as feature of adaptation in different animals (ex: skin, external gills, internal gills, internal lungs).
    8. Compare and contrast all possible adaptive features found in respiratory systems of major animal phyla.
12. Demonstrate an understanding of animals’ circulatory systems.
    1. List different circulatory and respiratory systems in major animal phyla.
    2. Name parts and components of these organ systems.
    3. Define characteristics of parts and components within each system.
    4. Define diffusion of gas and liquid conditions.
    5. Distinguish between open and closed circulatory systems.
    6. Describe the functions of circulatory systems in animals as either being gastrovascular (both digestion and distribution of nutrients) or cardiovascular.
    7. Explain why most animals need a circulatory system and some do not.
    8. Explain the role of osmotic pressure and hydrostatic pressure in regulating the exchange of fluid and slute across capillaries.
    9. Analyze different adaptations of the cardiovascular systems in vertebrates.
    10. Compare and contrast all possible adaptive features found in circulatory systems of major animal phyla.
    11. Compare and contrast the circulatory schemes of birds, amphibians, reptiles, and mammals.
13. Demonstrate an understanding about the body defense system of major animal groups.
    1. Define the function of the body defense system.
    2. List the nonspecific lines of defenses in the vertebrate body.
    3. List components of specific defenses.
    4. Define immunity: (active and passive).
    5. Categorize different lines of the body defense system and provide an example for each case.
    6. Explain mechanisms of nonspecific defenses (ex: first line of defense - integumentary and mucous membranes, second line of defense - nonspecific macrophages, inflammation, and  protein compliments).
    7. Explain mechanisms of specific defenses (ex: the role of MHC makers and helper T-cells in the humoral mediated response with antibodies and the cell-mediated response).
    8. Explain sequential response to antigens (ex: entry of pathogen, interaction with  macrophages, binds with helper T-cell, activation at subcellular or cell levels, monoclonal selection, primary and secondary immune responses).
    9. Evaluate the consequences of over-reaction and under-reaction of the immune system in relation to the following: autoimmune disorders, immunodeficient individuals, susceptibility to cancer, allergic reaction and the role of IgE.
    10. Characterize the following in relation to the immune system: interleukins with cancer treatments, tissue typing - ex. blood, septic shock - ex. bee stings.
    11. Compare and contrast the structure and function of an enzyme’s active site and an antibody’s antigen-binding site.
14. Demonstrate an understanding about mechanisms controlling animals’ internal environment.
    1. Distinguish between osmoregulator and osmoconformers.
    2. Name different excretory systems found in different animals (ex: planaria – protonephridia, earthworms – metanephridia, insects – malpighian tubules, vertebrates – kidneys).
    3. List components of different excretory systems in animals.
    4. Define internal environment and state where is it found in insects and vertebrates.
    5. Discuss the problems with respect to homeostasis which face organisms living in different environments, and then describe the major types of fossils (ex: Amber, Imprint, Caste, Petrified) and how radioactive dating applies to them.
    6. Describe the functions of the following: protonephridia, metanephridia, malpighian tubules.
    7. Describe the structure and function of the kidney in humans: Structure - cortex (glomerulus and convoluted tubules) and medulla (loop of Henle and collecting tubules), Function (general physiology of the nephron): filtration, secretion, and reabsorption.
    8. Discuss mechanisms involved in water balance with respect to the following three major forms of nitrogenous wastes produced by the metabolism of proteins and nucleic acid, in different animals: ammonia NH₃ – invertebrates, most fish, and some amphibians, urea – (CO (NH₂)₂₎ – all mammals, many amphibians, sharks, and some fish, uric acid (C₅ H₄ N₄ O₃) – birds, insects, reptiles, terrestrial snails.
    9. Discuss physiological adaptations in the kidneys of non-mammalian species that are beneficial in different environments.
15. Demonstrate an understanding of how animals exhibit coordination.
    1. Define terms related to the concept of chemical coordination (ex: hormones, endocrinology, endocrine glands, exocrine glands, receptors, and pheromones).
    2. List different levels of chemical communications between the cells (local level: synaptic and  paracrine, long distance level: pheromones,  neurosecretory, and hormones).
    3. List the three types of hormones and provide examples of each (ex: steroid  hormones/testosterone, hormones derived from amino acids/oxytocin, peptide hormones/insulin).
    4. Describe different levels of cell communication (ex: local level, long distance pheromones in moths, dogs, humans, neurosecretory hormones - protein/amino acid hormones like insulin, glucagon, oxytocin, ADH, calitonin, and growth hormones, steroid hormones like FSH, aldosterone, testosterone, estrogen, and progesterone).
    5. Describe the relationships among the following in chemical signaling systems: hormones, endocrine glands, target cells, target cell receptors.
    6. Explain the evolutionary significance of the two levels of synaptic effects at the local level: monosynaptic reflex, polysynaptic response.
    7. Determine the relationships between the endocrine and nervous system in terms of their structure, function, and chemical component.
16. Demonstrate an understanding about animal reproduction.
    1. Distinguish between asexual and sexual reproduction.
    2. Name different modes of reproduction and distinguish among parthenogenesis, hermaphroditic reproduction, and sequential hermaphroditicism.
    3. Name the parts of the reproductive systems seen in major animal phyla (including humans).
    4. Describe the importance of sexual reproduction.
    5. Describe the function of each component of the reproductive system of the human male and  female.
    6. Discuss the hormonal control of reproduction in male and female mammals.
    7. Compare and contrast spermatogenesis and oogenesis.
    8. Explain the mode of function for various methods of contraception and their relative effectiveness: ovulation barriers (pill, patch, implants)-barriers to sperm (coitus interruptus, condom, sponge, diaphragm, vasectomy, tubal ligation), implantation barriers (IUD, RU-486).
    9. Determine the evolutionary relationships among different modes of reproduction in major animal phyla: hermaphroditic vs. parthenogenesis, and sequential parthenogenesis vs.population dynamics.
17. Demonstrate an understanding of the basic ecological concepts.
    1. List all the domains of ecology and describe them (ex: organism, population, community, ecosystem, and biosphere). 
    2. List the structure and function of ecosystems and their interactions (ex: abiotic factors like temperature, light intensity, nutrients, wind, gas, and other physical factors, versus biotic factors like competition, predator/prey relationships, and parasite loads).
    3. Describe the relationship between ecology and evolution.
    4. Explain how global effects influence ecosystems (ex: latitude and light intensity, global air cells, and latitude vs altitude).
    5. Explain the following responses of organisms to environmental changes (ex: behavioral response, physiological response, morphological response, and adaptation over evolutionary time).
    6. Describe terrestrial ecosystems with respect to their diversity (ex: tropical forests, desert, temperate forests, coniferous forests, and tundra).
    7. Describe aquatic ecosystems with respect to their diversity (ex: marine - abyssal/pelagic/photic zones, coral reefs, estuaries, freshwater - riparian, and lakes).
    8. Identify the various biomes (terrestrial and aquatic) by using a diagram or a map of the region or the world and associate them with dominant life forms from the multicellular kingdoms.
18. Demonstrate an understanding of factors regulating species population size.
    1. Define the scope of both population and community ecology.
    2. Distinguish between density and dispersion.
    3. List the major population parameters and define them.
    4. List major properties of a community and importance of each.
    5. Distinguish between the habitat and the niche of a species.
    6. Define carrying capacity of a given environment.
    7. Describe types of survivorship curves and provide an example for each (ex: Type I, Type II, and Type III).
    8. Explain how ecologists measure density of a species with a capture-mark-recapture formula.
    9. Explain how different population parameters affect population growth and provide examples (ex: intrinsic rate of growth and carrying capacity, exponential growth, and logistic growth).
    10. Describe a theoretical community structure using the individualistic hypothesis and the interactive hypothesis.
    11. Explain all possible community interactions and provide examples (ex: competition, competitive exclusion principle, predator/prey relationships, parasitism, commensalism, ammensalism, mutualism, neutral interaction).
    12. Explain Island Biogeography Theory in relation to species colonization and dispersal in both real islands and areas that act like islands in the mainland situation.
    13. Explain both primary and secondary successions and give examples of each.
    14. Explain the structure and function of the ecosystems in terms of structure (abiotic vs. biotic), primary producers, consumers (primary consumers, secondary consumers, and tertiary), function (energy flow (thermodynamics), food chain and food web, chemical recycling and trophic structure (water, carbon, nitrogen, and phosphorous).
    15. Determine productivity of various ecosystems on the earth and relate them to different human environmental concerns (ex: human population growth, environmental pollution, habitat destruction, genetic diversity, and species and ecosystem utilization).
    16. Compute population size, growth capacity, and type of community interactions when given appropriate novel data.
19. Perform writing tasks to promote learning.
20. Demonstrate the learning of concepts through writing.