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wk3-DiversityHmwk - Bio 124L Dissect a Scientific Paper (H2...

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Unformatted text preview: Bio 124L Dissect a Scientific Paper (H2 – 5 points) Due Feb 8-12, 2010 Spring 2010 Directions: Type answers to the following questions on the answer sheet provided. ONLY TURN IN THE ANSWER SHEET. Homework not on the answer sheet provided, missing the name of the owner, or including any extra attachments will not be graded and will result in zero credit. No second chances; no late homework. You will write, proof-read, edit, and turn in 3 scientific papers for Biology 124 this semester. The quality of these papers will determine nearly one-quarter of your final course grade. This assignment is designed to help you understand what a formal scientific paper is, what type of information is included in a scientific paper, and how that information is traditionally presented. Let’s get started! For this assignment, you must first read the scientific paper. Just skim the paper or read the abstract so you understand what the paper is talking about, then go back and answer the following questions. If you get stuck, it might help to review “Appendix B: Writing Scientific Papers” on page 139 of your lab manual and/or McMillan’s Writing Papers in the Biological Sciences available on reserve at the CSEL. Complete sentence answers are not necessary except where indicated. Begin: Using the skills we practiced at the CSEL during the first week of classes, find this article: Journal Title: Applied And Environmental Microbiology Article Title: Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities Date Published: April 2009, Volume 75, Number 7 Page Numbers: 2192–2199 1. An abstract is a short summary of the entire scientific paper. It is not considered part of the paper itself. Therefore, the first section of a scientific paper would be the Introduction. What are the labeled sections of this paper? 2. How does the order of sections in this paper differ from how you will order the sections in your scientific papers? Introduction 3. In the Introduction section, the authors include interesting background information that helps explain their experiment. One piece of background information included in this article’s unlabeled Introduction section is the work that had been done to date. What data has not been evaluated? 4. In addition to background information about the experiment, the Introduction section of a scientific paper includes the author’s hypotheses and predictions. What is their hypothesis? 5. The authors include very specific predictions about the results they should find if their hypothesis is to be supported. What is considered the most important prediction? 1 Materials and Methods 6. Is the Methods section written in future, present, or past tense? 7. The point of the Materials and Methods section is to explain how the experiment was performed so that anyone could repeat it exactly as it was performed by the authors. Sometimes results seem too good to be true, so scientists do this—they repeat experiments to see if they get the same results. Notice the level of detail used to describe the experiment. Do the authors tell us the exact way the samples were transported to the laboratory? If so, how were the samples transported? 8. What were the samples of? How many high quality sequences were assembled from the samples? 9. What was the resulting product of the DNA extraction, amplification and sequencing? Results 10. The Results section is often called the “dry facts.” It presents the findings of the experiment. The majority of clones from the UBA 18S rRNA gene library were from what kingdom and what percentage? 11. The results are presented in complete sentences. What else is used to explain the results? 12. Are the tables and figures referred to in the Results section? 13. According to the Results section, what information is presented in Figure 2? 14. What types of information are NOT included in the results section? Name two. Discussion 15. The first part of the Discussion section explains the authors’ conclusions. While the Results section presents dry facts, the Discussion section explains what the facts mean. The data in the Results section are interpreted in the Discussion section. Looking back at the hypothesis, what is the main conclusion of this study? (One complete sentence please.) 16. An important part of the Discussion section is the authors’ suggestion for future studies. Future studies are suggestions to explore the findings further in order to understand questions that were developed during the study. Name a suggestion for a future study, which will provide additional information on this particular study. 17. Another important part of the Discussion section is confounding variables. A confounding variable could be a result that was not expected or the lack of results in an expected area. Name one confounding variable mentioned by the authors. What was the proposed reasons for this result? Literature Cited 18. This paper calls the Literature Cited section “References.” The manner in which references are cited varies based on the Journal in which the scientific paper is published. According to Appendix B in your lab manual, how should you cite this article if you want full credit on a future scientific paper in Biology 124? 19. What information is included for each reference? For example, all the authors’ names are given for each reference. Authors’ names are listed in the same order that they are under the paper title (not by alphabetical order). This gives the most credit to the “first author,” who is the person that did the most work leading up to the paper. S/he is the lead scientist on this experiment. What other information is given in each reference? Tables and Figures 20. Examine the tables and figures in the article. A table presents rows and columns of numerical data while a figure is what? 2 Bio 124L – Sp10 Name: ___Elisabeth Gonzalez Section: ___134__ Answer Sheet: Dissect a Scientific Paper (H2 – 5 points) Each box is worth 0.25 points (all or nothing—no partial credit). 1. 2. 3. 4. 5. 6. 7. 8. 9. 10 . 11 . 12 . 13 . 14 . 15 . 16 . 17 . 18 . Introduction, materials & methods, results, discussion, acknowledgements, footnotes, and references The order is similar, except this paper has a few more sections than the one that will be used for lab, for example—acknowledgements and footnotes The eukaryotic sequences in the three communities in the mine have not been evaluated. “Protists isolated from AMD graze on acidophilic bacteria, suggesting that they likely play a predatory role and influence the abundances of various community members.” “Eukaryotes likely play a large role in the cycling of carbon within AMD communities.” past stored on wet ice and then they were transported to the laboratory of DNA; 176 86 18S rRNA genes. fungi; >99 There are charts, graphs and tables to help explain the results of the scientific paper. The tables and figures referred to were in the Results section. The percentages of clones assigned to the various groups, in protists and fungi. The information not present in the results section is the discussion and materials and methods. The conclusion of the study was that protists play a predatory role and influence the amount of variety in a community, and that eukaryotes play a large role in cycling of carbon within AMD communities. “how widespread the lineage is in the environment and what makes these organisms uniquely suited to life in AMD” “number of N. gruberi genomic sequences is very low and very few 18S rRNA genes” and “low cell numbers compared to archaea and bacteria.” The volume number 3 19 . 20 . A link to the article A picture or a diagram relevant to the study 4 ...
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