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Biology 4974/5974 D. F. Tomback Name KEY Student ID number Fall 2013 100 points Evolution Exam #1: Take Home Exam Read this before taking the exam. Please word-process your answers. You are free to use class notes, papers posted on Canvas, and information in your textbook in order to answer questions. A few things to warn you about: I expect that answers will be written in complete, well-constructed sentences, with names and terminology spelled correctly. Misspellings and writing problems will result in deducted points. Make sure that you understand what the question is asking before writing an answer. Be very careful to use your own wording for answers. Students consciously or unconsciously may plagiarize when using source materials. Plagiarism violates the UCD honor code and public ethics and will result in an F on this assignment. You can take as much space as you need for your answers. (More is not always better if you are on the wrong track.) 1. (6 pts) Evolution is regarded as a theory in science. a. What is a theory? In science, a theory is an explanation of cause and effect that that has supported by repeated observation or experimentation and an accumulating wealth of evidence. (3 pts) b. Explain the significance of the fact that evolution is a theory: what does that mean regarding this field of study? Evolution as a theory means that its basic tenets, such as descent with modification and the mechanism of natural selection have been supported by a body of scientific observation and experimentation. (3 pts) 2. (4 pts) a. Does the study of evolution follow the scientific method? Yes, the study of evolution follows the scientific method, which is based on hypothesis testing. (2 pts) b. What are at least two different approaches (sources of information) used by scientists who study evolution? (2 pts each) i. Scientists may construct hypotheses concerning the fossil record. Ii Scientists may use a comparative approach, studying organisms and their relationships. The mechanisms of evolution and adaptation, inheritance, and genetic diversity may be studied experimentally as well. 3. (4 pts) What is being defined below? a. “Unites individuals that share more characteristics (features) with one another than they do with any other organism.” Morphological Species Concept b. “Two species bearing the same phenotype caused by common ancestry for the same genotype.” Homology 2 4. (10 pts) What contribution did each of the following individuals make to the development of our understanding of biological species? (2 pts each unless noted) a. George Buffon –Believed that species were biological units, and that species were reproductively isolated from one another. b. Carl von Linné (Linnaeus) –Provided a basis for describing species, the binomial system, by noting the most important features. He also initiated a hierarchical classification system, reflecting degrees of relationships. He also noted the existence of races or varieties within a species, which acknowledges variation. c. Jean-Baptiste de Lamarck—Believed that species change over time. Provided the first biologically-based explanation for gradual change in species over time, although it was later discredited. d. Charles Darwin and Alfred Russel Wallace—Together recognized the mechanism of natural selection and presented it to the Linnaean Society. (4 pts) 5. (6 pts) Present a summary of how natural selection works, listing the step by step processes involved. Most species have high reproductive rates. Finite food and space limits numbers of individuals. Also, predation, parasitism, disease, competition, climate further weed out the susceptible or weak. Individuals vary in characteristics. Certain variation results in higher survival and/or better reproduction. Thus, relatively greater contribution of offspring from some individuals. Their offspring may in turn have similar traits because of inheritance. Thus, certain “favored” variation spreads through the species over time. Leads to “descent with modification” or evolution over time. 6. (6 pts) Mayr, in his essay, “Darwin’s influence on modern thought,” brought up many good ideas. Pick two of the following and explain their meaning: “population thinking”, “historicity” in science, “Darwin does away with determinism”, or “theory of common descent.” Population thinking: Involves a rejection of ‘typology’, which means the all members of a species are expected to follow an identical type as believed by Aristotle. But, populations consist of unique individuals who vary from each other. Historicity: Reconstruction of what led to past events. Proposed scenario is tested with information as it becomes available. Determinism: Darwin recognized that chance played a role in evolution in terms of the variation within species, but that natural selection sorts this out. This view contrasted with previous views of predictability in natural processes. Theory of common descent: Humans are descended from the same common ancestor as all organisms. Anatomical comparisons indicate the connection with living primates. Thus, man is not the product of special creation. 3 7. (10pts) Explain Darwin’s literary strategy or approach for the first four chapters of On the Origin of Species. a. Why did he begin with Chapter I, Variation under Domestication? First of all, the British public could relate to the breeding of domesticated animals and plants. (1 pt) They could understand Darwin’s discussion about the “power of selective breeding” leading to exaggerating desired traits in plants and animals.(2 pts). Secondly, this was a good way to communicate the existence of individual variation, both in physical traits but also in animal disposition, in a way the public could understand. b. Why did he then transition to Chapter II, Variation under Nature? He then pointed out that variation was well documented in natural species, and there was so much individual variation that identifying species was confusing. He is setting the stage for the next two chapters. c. What was he trying to show in Chapter III, Struggle for Existence? Given that most organisms have high reproductive rates, all individuals cannot survive. Finite food and space limit numbers; also, predation, parasitism, disease, competition, climate reduce populations. d. Why was establishing that variation exists among individuals of all species and demonstrating how selection works in domestic animals and plants so crucial to the main ideas in Chapter IV, Natural Selection? What were these ideas? The key to understanding the mechanism of natural selection is recognizing that individual variation exists among organisms within a species, resulting in differential survival and reproduction. Most people could see this most easily with practical examples. Thus, there is a relatively greater contribution of offspring from the individuals that have certain variation, and their offspring will in turn have similar traits. Thus, certain “favored” variation spreads through the species over time, which leads to “descent with modification” or evolution over time. 8. (10 pts) More questions based on On the Origin of Species 4 a. This diagram from Chapter IV, Natural Selection, depicts what process? This diagram illustrates how species may arise from other species, leading to the process of “descent with modification.” b. Referring to Chapter VII, Instinct, what does Darwin mean by “instinct”? What is his main point in this chapter? Instinct is used to mean “behavior” by Darwin. His main point is that behavior is a trait that can be sorted by selection just like morphological traits. c. Referring to Chapter XIII, Mutual Affinities of Organic Beings, what is by the statement, “By means of descent with modification, all the great facts in morphology become intelligible. “ These “great facts” include descriptions of anatomy, morphology, and embryology. So Darwin realized that common descent and degree of relatedness from the process of “descent with modification” explains similarities and differences among these features in species. The more closely related the species, the more similar. 9. (3 pts) a. What theories account for the formation of the universe and the formation of our solar system? The Big Bang theory explains the formation of the universe. The Nebular or Condensation hypothesis explains the formation of the solar system. b. What is the relative abundance of normal matter, dark matter, and dark energy in the universe? The relative abundances are: 4.6% normal (baryonic) matter, 23.3% dark matter, 72.1% dark energy. 10. (6 pts) a. What was the composition and fate of the first atmosphere on earth? The first atmosphere was composed of hydrogen and helium. The gravity was too weak to hold it, coupled with other forces such as heat radiating from the earth and the solar wind. (2 pts) b. What was the composition of the second stable atmosphere? The second atmosphere was composed of H O, CO N H CH CO NH 2 2 2 2 4 3 Cl H S. (3 pts) 2 c. What was the general chemical property of the second atmosphere (hint: redox)? Catalyzed reduction reactions: a reducing atmosphere. (1 pt) 11. (4 pts) List four possible places/conditions were organic molecules were first synthesized abiotically? (1 pt each) i. Outer space (exogenous delivery) brought in by meteors ii. Hydrothermal vent systems or volcanoes iii. Clay substrates iv. Oceans and ponds 12. (10 pts) What are two sources of data that demonstrate that simple organic molecules can readily be synthesized abiotically under roughly the conditions that existed on the young earth or in outer space? Explain both of these forms of evidence. i. One form of evidence comes from the analysis of organics on meteors that have fallen to earth, such as the Murchison meteor. This meteor carried 5 many amino acids, urea, and other simple organic molecules, indicating that these may be easily synthesized in space. Space has precursor gases and high energy sources, as existed on the early earth. (4 pts) ii. The other form of evidence includes laboratory synthesis of organics under conditions believed to have existed on early earth. These conditions were replicated in the laboratory experiments of Stanley Miller. He circulated ammonia, methane, hydrogen gas, and water in an apparatus with an electric spark discharged every few seconds but all day for an entire week. Circulating cool water condensed gases, and samples were taken from liquid water at the bottom of the apparatus and analyzed. The experiment generated simple organics similar to those from the Murchison meteor. (6 pts) Also, molecules from the five basic groups of organic molecules—Aldehydes, sugars, purines and pyrimidines, fatty acids, and pyrroles and porphyrin rings— have been synthesized in the laboratory under conditions simulating the early earth and reducing atmosphere more recently. More complex macromolecules can be synthesized from these. 13. (3 pts) Explain what is meant by the principle of self-assembly when it comes to the structure of protocells. The proposed models for protocells are composed of somewhat complex structures that spontaneously self-assemble from simple organic molecules, because of basic chemical interactions. 14. (10 pts) Briefly describe the structure and function of the following protocell models in terms of self-assembly and chemical organization. Which have the most potential, in your opinion, as an ancestral protocell? a. coacervate: These form spontaneously in water. They form from clumps or aggregations of macromolecules with a rigid shell of water, and can be very stable over time. They are selectively permeable and capable of conducting metabolic reactions, if proteins have enzymatic activity. They can grow and fragment, giving rise to more coacervates. (3 pts) b. proteinoid microsphere: These microspheres form when dry mixtures of amino acids are heated to high temperatures and cooled in water. They have double membranes, and a composition that departs from the original mixture. The membranes are selectively permeable. The microspheres can bud off. ( 3 pts) c. liposome: These are biphosplipid layers, like cell membranes, that have formed vesicles. The layers can capture proteins within, which can have function and determine permeability. (2 pts). d. clay vesicle: Clay-coated bubbles can form vesicles after the bubbles pop. Montmorillonite clay in particular can catalyze reactions such as polypeptide bonds and nucleotide bonds. (2 pts) 6 15. (8 pts) Given that the protocells are not living organisms, explain how a sort of natural selection could function and improve their efficiency. Use the following parallels to develop your argument. variation within populations: Protocells differ in type and structure. (1 pt) population growth: The number of protocells have grown over time by protocells accumulating and budding and fragmenting from taking in materials from the surrounding medium. (1 pt) struggle for existence: With so many protocells, organic molecules and salts in the medium become scarce. This slows growth and reproduction. (2 pts) natural selection: The protocells best able to take in materials, or those that can catalyze reactions and synthesize scarce molecules are those that prevail by continuing to grow and “reproduce” where the others cannot. (2 pts) descent with modification: Every step in improvement of function and efficiency within a protocell results in its increase and the replacement of other protocells. Changes occur over time in the protocell structure and function.