Paper: You must choose an article on a topic in evolutionary genetics. You will then research the literature on the topic of the article, and write a paper about it, summarizing the relevant literature.
The paper is due one week before the presentation (unless you're presenting on April 9, in which case it's due April 7). I'll grade it and get it back to you at the next class, so you have time to make revisions to your presentation based on my suggestions. The paper is worth 30 percent of your grade. Papers turned in late without a valid excuse will be penalized one point for each day late.
Your paper should identify the major question the article was trying to answer, summarize any previous papers which posed that question or tried to answer it, and summarize what more recent papers (if any) have said about the paper under discussion. If appropriate, you should also describe any techniques used in the paper that are new to the class and are important for understanding the paper. You should do a thorough job of researching the literature; see the Guide to Biological Literature for help.
The paper must be typed and have at least 15 full pages (i.e., to the bottom of page 15) of double-spaced text, not including figures or the reference list. Do not use unusually wide margins, large font, increased line spacing, etc. to make the 15-page limit; just grit your teeth and write some more. Figures are useful, and you should definitely have them, but they don't count towards the 15 pages; thus if you have four half-page figures, your paper must be at least 17 pages long.
Do not use jargon that your classmates would not understand without explaining it. In particular, do not use phrases that you have read if you don't understand them. If you can't figure something out, ask me and I'll try to help.
The reference list must include at least 25 references, strictly following the format shown below. You may include web pages, but they don't count towards the minimum of 25. You may not cite Wikipedia; it can be a useful first step in researching some topics, but for this paper, you should look at the original references cited by the Wikipedian rather than trusting their interpretation.
One of the key things I'll be looking at is the thoroughness of your literature research. I will pick one or two key references on your topic, then take a quick look at their reference lists, and the papers that have cited them. If I find some papers that you didn't cite that are very relevant to your topic, you'll get points off.
You must follow these formatting rules. They may seem picky, but following them demonstrates your ability to follow instructions exactly, an important skill for both research biologists and medical professionals.
You should include figures that illustrate the main points of your paper. Because this is a student paper, and not something that you're going to publish, you may copy figures from books, articles, and the Internet without asking for permission from the authors. You must, however, cite the original source of the figure in the figure legend. You must write your own, original figure legend; don't just copy the figure legend from the source of the figure.
Copying someone else's writing and pretending that it is yours is a serious violation of the University's Code of Conduct. If you copy text from a book, article, web page, or other source, you will receive a 0 for the final draft. If the copying is particularly extensive or egregious, you will receive an F for the course.
Here's a passage from Hudson et al. (1987):
The presence of a balanced polymorphism in the coding region of Adh could explain the relatively high level of polymorphism observed in that region. The existence of a balanced polymorphism at a single site can lead to higher levels of neutral polymorphism at linked sites (Strobeck 1983). The reason this can occur is that during the time that the balanced polymorphism is maintained by selection, new mutations will tend to accumulate in the region tightly linked to the selected site.
Copying these words exactly is plagiarism, even if you put "(Hudson et al. 1987)" at the end. It's also plagiarism if you just change a few words, like this:
A balanced polymorphism in the coding region of Adh could explain the high level of polymorphism in that region. The existence of a balanced polymorphism at a single site can cause higher levels of neutral polymorphism at linked sites (Strobeck 1983). This is because during the time that the balanced polymorphism is maintained by selection, new mutations will accumulate in the region tightly linked to the selected site (Hudson et al. 1987).
Instead of copying or trying to rewrite a passage, you should paraphrase it, summarizing the information in your own words:
There is an area around an amino acid polymorphism in Adh that has a relatively high level of silent polymorphism. This may be caused by balancing selection (Hudson et al. 1987).
If you find yourself staring at a sentence in a paper, struggling to think of a way to rearrange the words in that sentence just enough to keep it from being plagiarism, you're going down the wrong path. Read several paragraphs, set them aside, then write down a summary of the main points. Don't try to write about things you don't understand.
For more examples of plagiarism, see this report on a paper in a major scientific journal that was retracted due to plagiarism.
In papers in other fields, such as English or history, it is common to use many direct quotes, putting phrases or sentences from sources in quotation marks. This is because the exact words are important; if you're writing a paper on "The meanings of dust in Kafka's Metamorphosis," it's important to quote exactly what Kafka wrote about dust; his words are your "data," and you want to represent the data accurately. As long as you cite the source correctly, using quotes in quotation marks is not plagiarism.
In scientific writing, however, we rarely use direct quotes. Partly, this is just a cultural tradition; partly, it's because when scientists cite another paper, it's because they're writing about the information in the paper, and the exact words used to convey that information are not important. You may use a quotation or two, if you come across a particularly pithy statement of an important concept, but you will get points off for excessive use of direct quotes.
Citations in the text must follow the author, year format: (Lewontin and Hubby 1966; Kreitman 1983; Hudson et al. 1987). Use "et al." for three or more authors. If the authors' names are part of the sentence, they are not in parentheses: "Lewontin and Hubby (1966) surveyed allozyme polymorphism in Drosophila pseudoobscura."; "The fly species Drosophila pseudoobscura has extensive allozyme polymorphism (Lewontin and Hubby 1966)." If there are multiple citations in a single set of parentheses, they are in chronological order from oldest to most recent.
Do not give the article title or journal name in the body of the paper. Don't say, for example, "Richard Hudson, Martin Kreitman and Montserrat Aguadé, in a paper titled 'A test of neutral molecular evolution based on nucleotide data,' published in Genetics in 1987, developed a method to detect selection using variation in the ratio of polymorphism to divergence." Instead, say "Hudson et al. (1987) developed a method to detect selection using variation in the ratio of polymorphism to divergence."
Web pages should be cited using the author and year, if that information is available; this page would be cited as McDonald (2009), for example. If the web page does not say when it was written, say "undated." If there's an institutional author, list that; UD's home page could be cited as University of Delaware (2009), for example. If there's no apparent author of any kind, say Anonymous.
The Literature Cited section must include all of the literature cited in the text, alphabetically by first author, in the following format. If there are more than one paper with the same first author, they go alphabetically by the second author's last name, etc. If there are multiple papers by the exact same author or set of authors, they go from oldest to most recent. If there are multiple papers by the same author from the same year, they are distinguished by an a, b, c, etc. after the year in both the Literature Cited and the in-text citations.
For journal articles, the format consists of the following, in order:
Books are cited the same as journal articles, except instead of the journal, volume and page numbers, you give the publisher and the publisher's city. Do not abbreviate book titles. Book chapters are the same as journal articles, except instead of the journal, volume and page numbers, you give the pages, the editors of the book, the title of the book, publisher and city.
Web pages can be tricky to cite, as it's often not clear what the author, title, and year are. Follow the format shown below as best you can.
Here are some examples of citation format:
Journal articles
Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
Methe, B. A., K. E. Nelson, J. W. Deming et al. (24 co-authors). 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. USA 102: 10913-10918.
McDonald, J. H., and M. Kreitman. 1991a. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
McDonald, J. H., and M. Kreitman. 1991b. Scientific correspondence. Nature 354: 116.
Books
McDonald, J. H. 2008. Handbook of biological statistics. Sparky House Publishing, Baltimore.
Book chapters
Hall, B. G. 1983. Evolution of new metabolic functions in laboratory organisms. Pp. 234-257 in M. Nei and R. K. Koehn, eds. Evolution of genes and proteins. Sinauer Associates, Sunderland, Mass.
Web pages
Gregory, T.R. 2009. Animal genome size database. http://www.genomesize.com
University of California Museum of Paleontology. 2008. Understanding evolution. http://evolution.berkeley.edu.
Anonymous. Undated [viewed February 5, 2009]. Frequently asked questions about creationism and evolution. http://www.talkorigins.org/origins/faqs-qa.html.
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This page was last revised February 8, 2008. Its URL is http://udel.edu/~mcdonald/evolpaper.html