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SCIENCE: A WAY OF KNOWING
- The Definition of Science 1.1. A Way of Knowing (Epistemology) 1.2. Elements of a Better Definition: Method, Predictive, Quantitative, Theory, Rational, Cause- Effect, Natural
- Distinctions 2.1. Observation vs. Fact 2.2. Induction vs. Deduction 2.3. Idealism vs. Empiricism (Materialism) 2.4. Hypothesis, Theory, Paradigm 2.5. Reality, Truth, & Proof vs. Tested Hypotheses 2.6. Worldviews, the Role of the Observer
- The Practice of Science 3.1. Discovery (Exploratory) vs. Experimental vs. Historical Science 3.2. The Scientific (Hypothetico-Deductive) Method: OHEC and its More Realistic Expansions 3.3. Alternative Hypotheses, with/without Null Hypothesis 3.4. Testability of Hypotheses 3.5. Data (Qualitative, Quantitative), Measurement (Accuracy, Precision, Resolution), Analysis 3.6. Experimental Control, Experimental Error, Precise Expressions of Certainty/Uncertainty, (Measurement Error, Statistical Significance, Biological Significance) 3.7. Peer Review, Acceptance & Rejection 3.8. Unacceptable: Personal Bias, a priori Conclusions, Supernatural Mechanisms 3.9. The Human Side of Science = Scientists 3.9.1.1. Individual Worldviews, Cultural Contexts, Constraints on Perspective 3.9.1.2. The Politics of Science: Careers, Prestige, Influence, Publication, Funding 3.9.1.3. Scientific Revolutions (Thomas Kuhn, 1970’s) Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
STUDY GUIDE: SCIENCE - A WAY OF KNOWING
______________________________________________________________________________
READINGS
Text: Section 1. ______________________________________________________________________________ IMPORTANT TERMS AND PHRASES Knowledge Epistemology Observation Fact Induction Deduction Idealism Empiricism Materialism Hypothesis Theory Paradigm Reality Truth Proof Exploratory science Experimental science Historical science Scientific method Hypothetico-deductive method OHEC Null hypothesis Alternative hypothesis Testability Data Qualitative data Quantitative data Measurement Accuracy Precision Experiment Experimental design Experimental control Experimental error Measurement error Statistics Uncertainty Descriptive statistics Inferential statistics Statistical significance Biological significance Scientific community Peer review Worldview Personal bias A priori conclusion Scientific revolution ______________________________________________________________________________ TRUE/FALSE/RATIONALE STATEMENTS
- Scientific paradigms are usually reinforced during scientific revolutions.
- The term “precision” is used by scientists to mean the level of resolution of the measurement.
- Scientists are materialists, not idealists.
- Induction is a process of arriving at a general predictive statement by observing repeatable patterns among particular observations. Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
EVOLUTION AND WORLDVIEWS BEFORE DARWIN
(Supplemented by videotape from the series The Day the Universe Changed )
- Ionian & Athenian Greeks (611-322 B.C.) 1.1. Plato – Infinitely old universe, Fixed species, Idealist (ideal types), No evolution 1.2. Aristotle – Infinitely old universe, Fixed species, Empiricist, scala naturae , No evolution
- Natural Theology & the Newtonian Universe (<1600-1860) 2.1. Natural history reveals the creator, Argument from Design 2.2. Newtonian Universe – clockwork precision, run by laws, set in motion by the Creator 2.3. Carolus Linnaeus (1707-1788) – Hierarchical taxonomy, Binomial nomenclature, Fixed species, no evolution
- Diverse Ideas about Organic Change, the Fossil Record, and Geologic Time 3.1. Georges Comte de Buffon (1707-1788) – Degeneration Theory of Species Change, Older Earth 3.2. Jean Baptiste Lamarck (1744-1829) – First Coherent Explanation for Evolution 3.2.1. Dynamic scala naturae , progression up the great chain 3.2.2. Mechanisms: felt needs, use/disuse, inheritance of acquired characteristics 3.3. Georges Cuvier (1769-1832) 3.3.1. Comparative anatomy, paleontology, reconstruction from partial remains 3.3.2. Catastrophism to explain fossil record, no evolution 3.4. James Hutton (1726-1797) – Gradualism, large scale geological change by everyday processes 3.5. William Smith (1769-1839) 3.5.1. Geologist, canal engineer, no constraining biases about evolution 3.5.2. Fossil correlations with rock strata; simple-to-complex progression; newest fossils like modern species; extinctions 3.6. Charles Lyell (1797-1875) – the “Father of Geology” 3.6.1. Strong evidence for gradualism and for slow biological change over millions of years 3.6.2. Uniformitarianism – extreme view of gradualism, unvarying geological process rates
- Insight and Synthesis: Alfred Russell Wallace (1823-1913), Naturalist, tropical traveler, Independently conceived of natural selection as a mechanism for adaptation and speciation Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
STUDY GUIDE:
EVOLUTION & WORLDVIEWS BEFORE DARWIN
READINGS
Text, Chapters 1 (pp. 4-10) and 23 (pp. 494-503); The Beak of the Finch , chs. 1- IMPORTANT TERMS & PHRASES Plato Idealist Scala naturae Aristotle Empiricist Scala naturae Linnaeus, Carolus Binomial nomenclature Hierarchical taxonomy Argument from design Natural theology Newton, Isaac Newtonian universe de Buffon, Georges Comte Degeneration theory Lamarck, Jean Baptiste Dynamic scala naturae Felt needs Use/disuse Inheritance of acquired characteristics Cuvier, Georges Comparative anatomy Paleontology Catastrophism Hutton, James Gradualism Smith, William Charles Lyell Uniformitarianism Wallace, Alfred Natural selection TRUE/FALSE/RATIONALE STATEMENTS
- Plato was an idealist who do not believe in evolution, while Aristotle was an empiricist who did believe in evolution.
- Lyell’s work on canal engineering in England led to the first expression of the theory of gradualism.
- Lamarck’s hypothesized mechanism for evolution involved inheritance of acquired characteristics and the scala naturae.
- Cuvier developed the science of comparative anatomy and used it to explain how evolution had occurred in the vertebrates.
- Catastrophism and gradualism are two opposed theories of geological change over long periods of time. Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
intellect and your scientific evidence but realizing that you were on to something entirely new, indeed a new worldview of deep time that would contradict centuries of belief about the stability or earth and the length of its history. What do you decide to do? ANSWERS TO T/F/R STATEMENTS: True: 3, 5, 7, 8, 12 False: 1, 2, 4, 6, 9, 11 True or False: 10 Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
THE DARWINIAN REVOLUTION
- Charles R. Darwin (1809-1882) and the Road to The Origin of Species 1.1. 1826-30 – Young Man with an Uncertain Future 1.2. 1831-36 – The Voyage of the Beagle 1.3. 1837+ – Return to England, Discusses Collections, Begins Notebook on Origin of Species 1.4. 1838 – Reads Malthus, Essay on Human Population, Food Supply, and Looming Famine: Key Insight on the Struggle for Existence, develops Central Argument for Natural Selection 1.5. 1838-58 – Struggles with Three Major Problems: Heredity, Maintenance of Variation, Speciation 1.6. 1846-54 – Focuses on Barnacles, Publishes Major Four-Volume Treatise 1.7. >1854 – Refocuses on Natural Selection, Develops Analogy of Artificial Selection in Domestic Species, Continues to Struggle with Heredity, Develops Model for Speciation 1.8. 1856 – Darwin Begins the “Big Book” 1.9. 1858 – Wallace’s Letter Arrives, Darwin Prompted to Act, Essays Published Jointly 1.10. 1859 – Darwin Publishes an “Abstract” of his Work, The Origin of Species 1.11. >1859 – After The Origin
- Important Features of Darwin’s Synthesis 2.1. Broad, Unifying, Explanatory Power 2.2. Fact (Evolution has occurred) vs. Theory (Natural Selection as the Mechanism ) 2.3. Microevolution, Speciation, Macroevolution: A Continuum of Evolutionary Change 2.4. Critical Roles of Variation and Environmental Pressure 2.5. Favorable Traits Arise Randomly, though Natural Selection is not Random 2.6. Not Purposeful or Inherently Progressive
- Response to The Origin of Species and the Darwinian Revolution Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
STUDY GUIDE:
THE DARWINIAN REVOLUTION
READINGS
Text, Chapter 23; The Beak of the Finch , chs. 1- IMPORTANT TERMS & PHRASES Galapagos Islands Galapagos finches Microevolution Macroevolution Neo-Darwinian synthesis Artificial selection Natural selection Evolution Descent with modification Progressive Teleological Incipient speciation Speciation Adaptation Varieties (in a Darwinian sense) Malthus, Thomas Wallace, Alfred Homology Blending inheritance Struggle for existence Central argument for natural selection
TRUE/FALSE/RATIONALE STATEMENTS
- Darwin suspected that evolution had occurred before he went on the voyage of the Beagle, and the Galapagos finches confirmed his suspicions.
- Darwin illustrated his concept of natural selection by referring to domesticated animals.
- Darwin demonstrated that natural selection can occur but could only speculate that it can result in speciation.
- Thomas Malthus disagreed with Darwin over the struggle for existence.
- The central argument of natural selection can be summarized as eight observations that logically lead to one major inference that natural selection must occur.
- The initial response to The Origin of Species was positive both among scientists and among non- scientists in European society.
- The Neo-Darwinian synthesis confirmed that natural selection could account for adaptive evolution.
- Microevolution refers to natural selection on small geographic scales (e.g., on the Galapagos Islands), while macroevolution refers to natural selection on larger scales (e.g., across a continent). Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
- Darwin waited for 20 years to publish his ideas on natural selection and speciation because he was concerned about the response they would receive.
- Darwin’s primary mechanism for evolution, natural selection, is progressive (leads to better adaptation) and purposeful (because it preserves traits that have useful purposes). QUESTIONS TO PONDER
- The Copernican Revolution (the earth is not the center of the universe) and the Darwinian Revolution strongly altered human worldviews. In what ways were their effects similar?
- How do you think the response to The Origin of Species could have been different if the basic principles of inheritance were already understood at the time the book was published?
- What is random about natural selection? Does this make it a disorderly process?
- Why do you think Darwin begins The Origin of Species with a chapter on domestic pigeon varieties?
- Why is the central argument for natural selection so powerful? Why do you think it took so long for someone to think of it?
- Do you think Darwin would have conceived of natural selection if Malthus had not written his essay on population size and food supply? ANSWERS TO T/F/R STATEMENTS: True: 2, 3, 7, 9 False: 1, 4, 5, 6, 8, 10 Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
- Reproduction and Life Cycles 6.1. Why reproduce? 6.2. Asexual Reproduction 6.3. Sexual Reproduction, Somatic Cells vs. Reproductive Cells (Gametes) 6.5. Meiosis & Syngamy 6.6. Life Cycles, Alternation of Generations, Differences Across Kingdoms 6.7. Why does sexual reproduction exist? 6.7.1. Inherent Fitness Advantage of Asexual Reproduction 6.7.2. Possible Reasons for Sexual Reproduction
- Meiosis: One Replication, Two Divisions, and a Surprise 7.1. Overview, Reduction in Chromosome Number 7.2. Meiosis I, Separation of Homologs 7.3. Meiosis II, Separation of Sister Chromatids 7.4. Crossing Over, Genetic Recombination 7.5. Contrasts Between Mitosis & Meiosis 7.6. Meiotic Errors, Consequences
- Genetic Variation in Sexual Life Cycles: Three Mechanisms 8.1. Independent Assortment 8.2. Crossing Over 8.3. Random Fertilization 8.4. The Significance of Genetic Variation Produced by Meiosis & Syngamy Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
STUDY GUIDE:
CELL CYCLE, MEIOSIS, GENETIC VARIATION
READINGS
Text, Chapters 11 and 12, plus additional review material described below. It is not absolutely necessary to know how DNA works in order to superficially track the major events in mitosis and meiosis. However, it is much easier to understand the processes of somatic and sexual cell division, and the reasons for them, if you know how chromosomes are organized, and this ultimately means knowing something about the molecular structure of DNA, the genetic code, and how proteins are made. We will not dwell on the molecular details in this course. But the processes we will dwell on – e.g., natural selection – depend on understanding the sources of genetic variation in populations and the general features of inheritance, so it makes sense to review DNA structure. The chain of understanding we are striving for is as follows: DNA and the Genetic Code Structure of Chromosomes Chromosomal Behavior during Mitosis and Meiosis Mendelian Principles of Inheritance Genetic Variation in Populations Evolution You have all studied DNA and its expression into proteins, mitosis and meiosis, and the basic principles of inheritance in high school. Our emphasis in class will mostly be at a higher level – why cell division occurs, regulation of the cell cycle, the pros and cons of asexual versus sexual reproduction, and how meiosis and syngamy contribute to genetic variation in populations and thus to evolution. So you will need to work on your own or with study partners to refresh your knowledge of how the genetic material is organized in organisms, especially in eukaryotes. This includes the following concepts (page numbers and references to figures and tables are for the Freeman text): DNA Strand (Fig. 4.1, 4.3, 4.9), Double Helix (Fig. 4.10), Chromosome (Fig. 11.2, 11.7, 12.1), Genome Prokaryotic vs. Eukaryotic Genome Differences (pp. 129-133, 383-384) Nuclear vs. Extranuclear DNA in Eukaryotes (p. 291) Chromosome Number, Ploidy, Haploid, Diploid, Homologous Pairs (Table 12.2) Autosomes vs. Sex Chromosomes (pp. 281-282, Table 12.2) DNA Replication (Fig. 4.12) DNA Expression: Transcription and Translation (Fig. 15.4, 15.5, 15.10, 16.8, 18.1) The Genetic (Triplet) Code (Fig. 15.6, 15.8) Locus, Gene, Allele Character, Trait (pp. 249, 273-274, Fig. 12.8) Many of the terms in the list below are also part of this review. I will use the terms freely in framing questions for the exam from the lecture outline. Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
TRUE/FALSE/RATIONALE STATEMENTS
- Mitosis and meiosis exist for different reasons.
- Bacteria do not have homologous chromosomes.
- Sexual reproduction is more advantageous than asexual reproduction.
- Sexual life cycles differ in the timing of meiosis and fertilization such that the dominant phase of the life cycle is diploid in some cases and haploid in others.
- Chromatids and synapsis are involved in crossing over.
- Independent assortment cannot produce genetic variation in offspring unless crossing over occurs.
- Cytokinesis is the last step of mitosis.
- The somatic cell cycle is controlled by internal cues.
- Prokaryotic and eukaryotic genomes are organized differently.
- Cyclins regulate the somatic cell cycle.
- Because crossing over is so difficult to regulate, eukaryotic organsms try to avoid it.
- Humans show alternation of generations.
- Synapsis occurs during syngamy.
- Transcription and translation refer to important processes in Meiosis I. QUESTIONS TO PONDER
- Meiosis is sometimes called “reduction division”. Why does this term make sense?
- Bacteria are not diploid and do not do meiosis, and thus do not enjoy the benefits of sexual reproduction. Do bacterial populations show genetic variation? Where does the variation come from?
- Why would Darwin have been overjoyed to read Figure 12.4 in your text?
- Why is genetic variation among offspring so important?
- Why do the kingdoms show such marked differences overall in sexual life cycles? Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
ANSWERS TO T/F/R STATEMENTS:
True: 1, 2, 4, 5, 9, 10 False: 6, 7, 11, 12, 13, 14 T or F: 3, 8 Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
- Mendel’s Explanation (Model) 6.1. Alleles – Alternative Versions of a Gene that Account for Different Phenotypes 6.2. Genotype – Alleles Possessed by an Individual for a Given Trait (or set of Traits) 6.3. Each Individual has two Alleles for each Gene (symbolized by letters) 6.4. Allele Pairs Differ in their Phenotypic Expression due to Dominance/Recessiveness: Homozygous Dominant, Heterozygous, Homozygous Recessive 6.5. Segregation of Alleles Occurs during Gamete Formation, Results in the 3:1 Ratio in the F Generation 6.6. Punnett Square – Graphical Method for Predicting Results of Crosses 6.6.1. Structure 6.6.2. Assumptions 6.6.3. Why it Works: Probabilistic Basis of Inheritance, Rules of Probability
- Question #4: Does the model work when parents differ in two traits? 7.1. Hypotheses 7.2. Experimental Setup: a Dihybrid Cross (P, F1, F2) 7.3. Predictions 7.4. Results 7.5. Conclusion: Principle of Independent Assortment
- Testcross: a Tool for Determining Unknown Genotype of a Dominant Phenotype
- Using Statistics (Chi-Square) to Determine Inheritance Patterns
- The Fate and Significance of Mendel’s Work
- Chromosomal Basis for Mendel’s Laws Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
STUDY GUIDE:
MENDELIAN GENETICS I – PARTICULATE THEORY, SEGREGATION,
INDEPENDENT ASSORTMENT
READINGS
Text, Chapter 13, esp. 269- IMPORTANT TERMS & PHRASES Heredity Preformation Blending inheritance Particulate (discrete) inheritance Allele Gene Trait Character Factor (Mendel’s term) Genetic cross Monohybrid cross Dihybrid cross Hybridization Testcross Reciprocal cross Pure line True-breeding P generation F1 generation F2 generation Dominant (allele) Recessive (allele) Genotype Phenotype Genotypic ratio Phenotypic ratio Heterozygous Homozygous Segregation Dependent assortment Independent assortment Chi-square Punnett square Probability Probability rules Genetic model Model organism Transmission genetics TRUE/FALSE/RATIONALE STATEMENTS
- Because inheritance is a probabilistic process involving chance events, it is impossible to predict what offspring will look like.
- Mendel succeeded in discovering some of the most important rules of heredity because he quantified the results of his crosses.
- F1 and F2 generations always have different phenotypic ratios.
- Segregation and independent assortment both occur during Meiosis I.
- A gene can have more than one allele, but an allele cannot have more than one gene. Biology 110, Spring 2010, Lecture Outlines and Study Guides, T.W. Sipe
