Homework answers / question archive / Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight Laboratory Assignment (READ THIS!) For this assignment you will be finding scientific literature using literature search tools that relate to the role of microhabitat variation in structuring insect communities

Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight Laboratory Assignment (READ THIS!) For this assignment you will be finding scientific literature using literature search tools that relate to the role of microhabitat variation in structuring insect communities

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Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight Laboratory Assignment (READ THIS!) For this assignment you will be finding scientific literature using literature search tools that relate to the role of microhabitat variation in structuring insect communities. You will then choose one of these papers to read critically and for which you will submit a brief (structured) summary. The purpose of this assignment is therefore twofold: (1) learn how to find relevant literature on a topic; and (2) begin to learn how to read the scientific literature. Primary scientific literature includes peer-reviewed scientific papers presenting primary research, reviews, or communications. Note that this DOES NOT include websites (including Wikipedia), magazines, or newspapers. While these are often good places to start when searching for primary literature, they do not represent peer-reviewed, scientifically vetted articles. If, through the course of this assignment, you turn in citations that include these as references you will lose points. Part one of this laboratory exercise is meant to introduce you to the process of searching for literature. It will subsequently aid you in doing a rather more complete and developed literature search for your independent projects. Part two of this laboratory is to introduce you to the construction of a scientific paper. This generally has a very structured form and is intended to allow rather consistent information retrieval for the reader. But reading the scientific literature takes skill, practice, and patience. Knowing what to look for when reading will not only help you access the scientific literature, but it will also help you frame and articulate your own independent project. Practicing scientists must relate their research to that of other workers in the field. In planning research, one must survey the information that others have obtained on the topic, and design work that will go beyond current knowledge. Likewise, in interpreting research results, one should compare and contrast one's own findings with those of others. Many students entering science, however, do not realize how much information is available on a topic that arouses their interest, and are unfamiliar with techniques for locating this information in the enormous scientific literature. The ability to use library and literature resources, particularly those accessed and managed by computer systems, is an essential skill for anybody entering a career in science/medicine. This exercise is a brief introduction to the use of resources for searching the primary literature. Its primary objective is to aid you in locating books and articles pertinent to course research activities, special study or seminar topics, and thesis research projects. The techniques of literature research and library use are in very rapid flux as these procedures have become computerized. You will need to explore the databases that are available for searching for topics. RECORDING REFERENCES References on a particular topic should be recorded in a fashion that enables them to be filed logically and retrieved easily. Once upon a time, most biologists traditionally stored reference citations in card files, but computer software for storing and managing such information is now state-of-the-art. I highly recommend using Mendeley (www.mendeley.com). This is free software and works on multiple platforms including Mac, Windows, Linux, and iOS devices. The instructions and tutorials for using this are readily available via the website. This has a plug-in for Microsoft Word and will allow you to insert citations and will include them, fully formatted, in the bibliography section of your paper. Given your future accumulation of literature in different courses, it is a good idea to get started on this now. Even if you do not use a reference manager, you will need to provide reference for your scientific writing. References must include all information required for a bibliographic reference, as well as the source of the reference itself (in case you have to check it again). Examples of references for different types of publications are given below. The following formats are quite stylized and you should use these for this course. If you are struggling with this, go to any issue of the journals Ecology or Evolution and you will get a good sense of what to do. The most important thing is that you are CONSISTENT. If you have some references with given names written out and some with them abbreviated, you will lose points. If you have some references with the journal name abbreviated and some with them written out, you will lose points. 1 Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight Book • Zar, J. H. 1999. Biostatistical analysis. 3rd ed. Prentice-Hall, Upper Saddle River, New Jersey, USA. o This would be cited in text as (Zar, 1999); or “as discussed in Zar (1999).” Journal articles • Single author: o Will, K.W. 2011. Taxonomic review of the Pterostichini and Loxandrini fauna of New Caledonia (Coleoptera, Carabidae). Zookeys 147: 337-397. o This would be cited in text as (Will, 2011); or “Will (2011) found that…” • Two authors: o Makarkin, V.N., and S.B. Archibald. 2014. An unusual new fossil genus probably belonging to the Psychopsidae (Neuroptera) from the Eocene Okanagan Highlands, western North America. Zootaxa 3838: 385–391. o This would be cited in text as (Makarkin and Archibald, 2014); or “Makarkin and Archibald (2014) state that…” • More than two authors (note that in the references cited ALL authors are included): o Archibald, S.B., G.E. Morse, D.R. Greenwood, and R.W. Mathewes. 2014. Fossil palm beetles refine upland winter temperatures in the Early Eocene Climatic Optimum. Proceedings of the National Academy of Sciences (USA) 111: 8095-8100. o This would be cited in text as (Archibald et al., 2014); or “Archibald et al. (2014) found that…” Article in a symposium or edited volume • Hanski, I., and D. Simberloff. 1997. The metapopulation approach, its history, conceptual domain, and application to conservation. Pages 5-26 in (I. Hanski and M. Gilpin, eds.) Metapopulation Biology. Academic Press, San Diego, California, USA. A few things to note here! Note that the format is consistent. Do not include the author(s) first names, only their initials. Note that the year follows the Authors and is separated from them and the subsequent citation by a period. Some journals have the year in parentheses, some use commas. Regardless, BE CONSISTENT in your application. Always italicize Latin binomials. Do not use Title Case in the title of the journal article (i.e. note above that the journal article title is NOT “Species Diversity and Biomass Stability”). See the comments under “Journal articles” above for when you cite within text. In addition, if you cite multiple references at once, you should first order them by year and then alphabetically. For example, you might have cited all of the above authors like this (Hanski and Simberloff, 1997; Zar, 1999; Will, 2011; Archibald et al. 2014; Makarkin and Archibald, 2014). Note that the final two were both in 2014 so they were placed in alphabetical order. Current Periodicals Stacks, Book Stacks and Microforms Books, monographs, and most scientific journals are still maintained in unbound or bound form. Unbound current issues of periodicals are held on shelves near a reading area until a series suitable for binding has accumulated. For many periodicals, especially those that are bulky or subject to rapid deterioration, such as newspapers and news magazines, back issues are retained only in electronic format, or in some cases on microfiche or microfilm. Abstracting and Indexing Services There are a number of very useful indexes and guides to the periodical literature; some of these also cover material published in book form. These guides provide references and, in some cases, abstracts of the current literature. To survey the publications on a given topic fully, these guides must be utilized. They also provide one of the most efficient ways for obtaining a list of useful current references relating to a 2 Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight topic. We will focus on the Science Citation Index and Google Scholar, but there are numerous other scientific databases for you to explore, and you may make use of them as you see fit: • Google Scholar (http://scholar.google.com/) This is a fairly recently available resource and provides access to primary literature articles. Note that this is quite different from the standard Google in that it does not take you to the nonscientific literature nor to other websites. ASSIGNMENT: Reading assignment & literature search • • You will type up this assignment using this Word document and submit it through the Assignment link on-line. Save your work as either a Word document or a PDF file (if you use Pages, please use the “Print to a PDF” function in your computer), and submit electronically via the link on Blackboard. Also submit a PDF of the paper that you read for this assignment. It is due by Tuesday, February 25th at midnight. Literature Search 1. Begin by finding a paper using the Science Citation Index that relates to the role of microhabitat variation in structuring insect communities. You should make sure that the university has electronic access to it. Record the citation for this article and by reading the abstract, 3 Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight • provide a brief annotation as to how you think the paper relates to this topic. One to three sentences is sufficient. Citation 1: • Brief annotation: 2. Examine the bibliography of the article from step 1, and select two more references that are most similar in their content to the article itself. Locate these references using any of the tools discussed above. Record the citations for each of these articles and (as above) provide a brief annotation as to how it relates to this topic. One to three sentences is sufficient. • Citation 2: • Brief annotation: • Citation 3: • Brief annotation: 3. Examine Science Citation Index for more recent papers that cite these references. Record complete citations for two articles that seem most similar to the article you have just read and (as above) provide a brief annotation as to how it relates to this topic. One to three sentences is sufficient. Provide the URL for each paper. • Citation 4: • Brief annotation: • URL: • Citation 5: • Brief annotation: • URL: 4. Using Google Scholar, locate two additional papers that discuss the topic. Record the citations for each of these articles and (as above) provide a brief annotation as to how it relates to this topic. One to three sentences is/are sufficient. Provide the URL for each paper. • Citation 6: • Brief annotation: 4 Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight • URL: • Citation 7: • Brief annotation: • URL: You should now have 7 recent references on the role of microhabitat variation in structuring insect communities. Each citation should be complete and follow the format provided at the beginning of this handout. In addition, each resource should have a brief explanatory annotation and you should indicate in which resource you found the article (e.g. items 1-4 above). Reading the Scientific Literature Once you have compiled the literature, you should pick ONE of these articles, read it carefully and do the following assignment. Reading the Scientific Literature Assignment. Scientific papers tend to have a very structured format and in many ways this follows the conventions of the scientific method. Introductions will often identify observations that lead to questions about those observations. These observations become hypotheses from which are derived explicit and testable predictions. The methodology for testing these predictions are then set out in the Methods section. It is important to remember that this section, while being rather straightforward, is the make-or-break part of the paper. Do the methods really test the predictions? Note that the methods are written in paragraph form. They are not written as a recipe or a series of instructions. They tell what the authors did. The Results then present the data that have been collected based on the methods in summarized form. This includes graphical representation of the data and results of statistical analyses. The Discussion then relates the results (derived from the methods) back to the original hypotheses to explain the introduced observations. The following worksheet is an excellent starting point for figuring out the important points of a scientific paper. It is structured according to the scientific method. Please fill in the worksheet based on the paper that you have chosen. 1. Citation. Write the entire citation to your paper, using the format provided in the previous handout. 2. Observation that led to research (look in abstract and introduction). • Describe 2-3 observations. 3. Question (try rewording the title). • • • Identify the model organism/system State why the model is an appropriate choice State why the question is important (what did the authors hope to learn about the field?) 5 Biology 348, Laboratory Assignment #2, due Friday, 5th March at midnight 4. Hypotheses (usually not stated but implied in abstract or introduction; look for phrases like “this research shows…”) • Explain why these hypotheses make sense based on current knowledge (introduction) 5A. Experiment (look at the figures to determine what they did) • • • • • Choose 2-3 key figures that directly address the hypotheses. Restate the model organism/system (figure legend). Describe the general experimental design; what was measured/compared and how? Describe the methods (draw a flow diagram). Explain why the choice of controls was appropriate (if present: many ecological experiments do not include controls). 5B. Results (look at the figures first) • • • • Explain the 2-3 key figures that you chose clearly; restate what is being compared to what for each one. Look for trends; e.g., what is increased over what? Identify the controls and how they validate the trends. Look for statistical analyses (figure legend or results) that validate the data. 5. Conclusions (based on the data, not the discussion) • • • • • • Do the data support the hypotheses? Are there other possible explanations for the data? Is the data convincing (statistics)? How could the experiment be improved? Why are the data interesting; how does it contribute to our understanding of the field? What is the next logical step in the research?