Vertebrate Zoology

Research Paper for Biology 301: Vertebrate Zoology—Fall 2018 Successful completion of a term paper that serves as a literature review will constitute 15% of your overall grade for this course. The term paper will be of a scholarly style and format, and must be on an approved topic relating to vertebrate zoology (sign up for an approved topic on Canvas Discussions as discussed in class). Writing of the research paper serves to acquaint the student with literature searching, the breadth and depth of the primary literature, the synthesis and extrapolation of ideas, and the styles of scientific writing and formatting. 1. Look over the topics posted in lab during the first week, and consider which one(s) might interest you most. I’m happy to meet with you during office hours to discuss possible topics before you sign up, but bear in mind that topic selection opens for everyone on Canvas Discussions on Friday, Sept. 7 at 3 pm. Once you have signed up for a topic, start your search by looking for any associated summary review articles or other introductory literature. In many cases, the most recent review article will be several years old, and you will need to do additional literature searches to determine if there are newer, more recently published papers on your topic. Your goal for this paper is to review, summarize and synthesize the results of a minimum of 7 recent primary literature papers (i.e., within the last 10 years) related to your topic. One of these papers may be a summary review paper; the other 6 papers should be standard original papers presenting original data. The structure and form of such standard papers may vary a bit depending on the topic of interest, so if you have any concerns about whether your selected papers are appropriate, please ask me in advance of the final paper due date. 2. The list of citations in your review paper can serve as a guide for locating additional primary sources on your topic. The Mercer library system maintains a limited number of subscriptions to scientific journals, so it is quite likely that you will not find all (or even many) of the articles you need on the shelf or by e-journal access. Nevertheless, pdf scans are readily available through the interlibrary loan (ILL) system. Don’t procrastinate–it takes time (usually a few days, but sometimes up to several weeks) to receive materials through ILL. I will talk more about using Tarver’s electronic resources, especially the excellent online portal Web of Science. 3. Rough Drafts: You will need to bring three copies of your rough draft to your respective lab class on Monday, Oct. 15 or Wednesday, Oct. 17. This rough draft should include at least three pages of text that reflects your introduction, discussion, and/or conclusions relevant to your topic. During lab that week, you will perform peer-review editing in class, exchanging your paper with each of two other students who will in turn receive yours. Additional information on the peer-editing process (including the rubric you will use) will be provided the week of Sept. 24/26, in advance of the peer-editing labs three weeks later. After editing, students will return the drafts they have edited to their partners and receive those they have edited; at least one should be returned the same day to its author, and both should be returned no later than the following week. In addition, I will provide comments on one copy of your own draft and return it to you during lab on Oct. 29/31. It is then up to each student to decide whether changes recommended by peer-editors should be adopted, in conjunction with any suggestions and comments I make on your individual drafts.

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4. Final Paper: A single hard copy of your paper, along with all required accessory materials (see below) must be turned in to me no later than 5 pm on Friday, Nov. 16 for all students. All papers are considered late after that point, and the penalty is one letter grade per regular school day (Monday-Friday). An electronic copy of the term paper (exclusive of cited articles and peer-review drafts and completed rubrics) is also due by 5 pm on Nov. 16. 5. The final draft will include all of the following, in the following order: a. a title page with your paper’s title, student name, date, course name and

number. This page must also include your declared major (e.g., B.A. in Biology);

b. an abstract page with a complete abstract, and a signed notation at the bottom of this page noting that the Mercer Honor Code has been observed;

c. 5-7 pages of text;

d. a reference page(s) (properly formatted–see below); e. photocopies or printouts of the actual first page (i.e., that includes title and abstract) of every article cited, taken as a representation of the actual article you possess in its entirety; f. both copies of peer-edited rough drafts with their completed rubrics; g. a copy of the term paper grade sheet.

Additional requirements:

• Photocopies must be from the relevant published article. Pages of titles and abstracts printed from Galileo or other literature search engines are not acceptable.

• Do not add a running header (or footer) of your name or paper title on each page.

• Number each page except the title page, i.e., there is no page number on the title page, the abstract page is page 2, and other pages (including reference pages) are numbered consecutively after that. In Microsoft Word this can be set by going to Insert ® Page Numbers, and then unchecking the box “Show number on first page”. Page numbers should be centered at the bottom of each page.

6. Your paper should follow the reference format of the Journal of Experimental Biology. Instructions that the editors for this journal have provided to authors is given below, and are published in full at: http://jeb.biologists.org/site/author/manuscript_preparation.xhtml#references.

3.3.3. References 3.3.3.1. References in text References in the text should be cited using the Harvard (name, date) referencing system.

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Each reference cited in the text (including those cited in supplementary information) must be listed in the Reference list and vice versa: please check these carefully.

Literature citations in text are as follows. • One author – (Jones, 1995) or (Jones, 1995; Smith, 1996). • Two authors – (Jones and Kane, 1994) or (Jones and Kane, 1994; Smith, 1996). • More than two authors – (Jones et al., 1995) or (Jones et al., 1995a,b; Smith et

al., 1994, 1995). • Manuscripts accepted for publication but not yet published: list in Reference list

and cite as (Jones et al., in press). • Manuscripts posted on preprint servers but not yet published: list in Reference list

and cite as (Smith et al., 2016 preprint). • Citation of unpublished work: we discourage citation of unpublished data; if it

is necessary, use the format (S. P. Jones, unpublished observations/data). Unpublished data cannot be included in the Reference list.

• PhD theses: cite in the text but do not list in the Reference list; use the format (Arthur R. Goode, Title of thesis, PhD thesis, Institute, Year).

• Website URLs: cite in the text but do not list in the Reference list; provide the URL and, if the website is frequently updated, the date that the site was accessed.

• Personal communications (i.e. the unpublished observations of other scientists): when a person who is not an author on the paper is the source of unpublished data, those data should be cited as a personal communication using the format (full name, institution, personal communication). Personal communications should not be cited in the Reference list and will only be published when substantiated by written permission (e.g. email) from the scientist cited.

• Dataset: we recommend that all publicly available datasets are fully referenced in the reference list with an accession number or unique identifier such as a DOI. Include author surnames in the text citation, e.g. (Jones and Jane, 1994).

3.3.3.2. Reference List References are listed in alphabetical order according to surname and initials of first author. • Use the following style:

Journal Rivera, A. R. V., Wyneken, J. and Blob, R. W. (2011). Forelimb kinematics and motor patterns of swimming loggerhead sea turtles (Caretta caretta): are motor patterns conserved in the evolution of new locomotor strategies? J. Exp. Biol. 214, 3314-3323.

Book Hochachka, P. W. and Somero, G. N. (2002). Biochemical Adaptation: Mechanism and Process in Physiological Evolution. Oxford, UK: Oxford University Press.

Book chapter Feller, G. (2008). Enzyme function at low temperatures in psychrophiles. In Protein Adaptation in Extremophiles (ed. K. S. Siddiqui and T. Thomas), pp. 35-69. New York: Nova Science Publishers, Inc.

Preprint server

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Baillie-Johnson, P., van den Brink, S. C., Balayo, T., Turner, D. A. and Martinez Arias, A. (2014). Generation of aggregates of mouse ES cells that show symmetry breaking, polarisation and emergent collective behaviour in vitro. bioRxiv doi:10.1101/005215.

Dataset with persistent identifier Zheng, L.-Y., Guo, X.-S., He, B., Sun, L.-J., Peng, Y. and Dong, S.-S. (2011). Genome data from sweet and grain sorghum (Sorghum bicolor). GigaScience Database. http://dx.doi.org/10.5524/100012.

Kingsolver, J. G., Hoekstra, H. E., Hoekstra, J. M., Berrigan, D., Vignieri, S. N., Hill, C. E., Hoang, A., Gibert, P. and Beerli, P. (2001). Data from: The strength of phenotypic selection in natural populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.166.

• If there are more than 10 authors, use ‘et al.’ after the 10th author. • Within a group of papers with the same first author, list single author papers first,

then papers with two authors, then et al. papers. If more than one reference exists for each type, arrange in date order. Use a and b for papers published in the same year.

• ‘In press’ citations must have been accepted for publication and the name of the journal or publisher included.

7. Other Information

• If your citation material does not fall into any of the above categories, please see me in advance of the due date for guidance.

• Note that the Journal of Experimental Biology requires journal titles of articles

listed in the References section to be abbreviated. You can find standard abbreviations for most journals at one or both of the following sites:

• https://www.library.caltech.edu/journal-title-abbreviations • http://images.webofknowledge.com/WOKRS54B7/help/WOS/A_abrvjt.html

• DO NOT USE DIRECT QUOTATIONS IN YOUR PAPER. This paper should make clear what has been done in your set of research papers by using your own words. A synthesis of your subset of literature is the goal for your work, not simply parroting what each study says. As you develop your work, remember that some appropriate conclusions should also be drawn at the end of the paper.

• Not including your Title page, Abstract page, References, and other required materials, your paper should be 5 full pages, but not more than 7 pages, double-spaced, with 12-point font (Times New Roman only) with 1-inch margins. Note: You will not need (or be able to) to write all of the various section types normally found in the primary literature. For example, you will not have methods or results sections as part of your paper. You should, however, include an abstract, introduction section,

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body/discussion section (i.e., that you can title in a way that corresponds to your topic) and conclusion section. How you handle titling of the discussion section (or subsections) will vary widely depending upon your topic and specific approach, and I am happy to offer thoughts on this problem as needed.

• Your Reference page(s) should have a minimum of 7 primary [= peer- reviewed] references. Book citations (among other possible sources) do not count towards the 7 citations, unless they are part of an edited volume of papers. If you are not sure about the status of your source(s) ask me in advance. You must turn in photocopies of the first page (including abstract) of all articles cited in your paper. Citing of the textbook is strongly discouraged, but is permissible on a very limited basis (1-2 in-text citations at the most) if approved by me in advance; note that doing so will not count towards your required 7 primary sources.

• The abstract describes the focus of the paper and the significance of your findings. It comprises a summary of your whole paper in 300 words or less.

• The paper should contain a brief introduction (2 pages maximum) that provides pertinent background information as well as the thesis statement.

• Paragraphs should be arranged in a logical order with logical transition statements connecting them. Emphasis should be placed on the synthesis of ideas from your primary sources as opposed to a simple summary of the literature.

• Computer/printer/software difficulties are not considered sufficient grounds for submitting papers late. Give yourself time to print out your paper before the deadline.

• Papers will be graded on the quality of the scientific content, the clarity of your writing, use of the English language, the logical flow of ideas and data presented, and the originality of your thinking about the topic.

• Papers that do not adhere to length and format requirements will be penalized one or more letter grades.

• Plagiarism: Plagiarism is a form of cheating, and represents a major violation of the Honor Code. In addition to the university’s Honor Council policy (see the syllabus for a link), please review each of several documents posted on Canvas, and see me if you have any questions. Papers will be examined for plagiarism and other forms of cheating in several ways including, but not limited, to:

1. close comparison between writing samples taken from each individual during the semester (e.g., on tests) and the submitted term paper;

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2. comparison of the term paper to the text of the original sources;

3. submission to an electronic clearinghouse for comparison of each paper to a) other papers in the class, b) papers from previous submissions for this class, and c) papers on similar topics available electronically.

Any situation deemed to constitute plagiarism will receive an automatic zero, and the material in question will be submitted to the Honor Council for further possible action.