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.
I'd like to have the paper one week before the presentation, so that I can 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. You can turn it in any time up to the day of your presentation, but I can't guarantee that I'll read it in time to give you suggestions for your presentation; as a result, you might end up saying something stupid and embarrassing in front of your classmates. If you turn it after your presentation, I will penalize you two points per day. The paper is worth 32 percent of your grade.
In addition to turning in the printed version of the paper, you must e-mail it to me. The file can be in any format (Word, OpenOffice, Pages, pdf, plain text, etc.), and the name of the file must be your name (such as "JaneStudent.doc"). Unfortunately, I have had several cases of plagiarism in the past in this assignment. If I suspect your paper is plagiarized, the file will make it easier to search the web for matching sentences.
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 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. The best way to flesh out your paper is to write about how different papers did their experiments; if your paper is about elephant genetics, don't just say "Woolly mammoths were more closely related to Asian elephants than to African elephants (Krause et al. 2006)," talk about where Krause et al. (2006) found their mammoth specimens, how they extracted the DNA, the precautions they used to prevent contamination, the statistical techniques they used to draw their phylogeny, etc.
You must include some figures, 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 Wikipedians 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 must 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.
To copy a figure from a web page, control-click on the figure (Mac) or right-click on the figure (Windows) and choose "Copy Image" from the menu. Then go to your document and Paste. To resize, click on the image, then drag a corner to make it smaller or larger.
Copying from a pdf is a little more complicated; you'll have to do a screen capture, copying the image as it is shown on your computer screen:
Macintosh: While viewing the pdf, zoom in until the figure you want fills as much of the screen as possible (this will make it look less pixellated when you copy and paste it). Then hit the Control, Command, Shift, and 4 keys simultaneously. The cursor will change from an arrow to a crosshairs. Drag the crosshairs from one corner of the region you want to copy to the other corner. When you release the mouse, the area of screen that you dragged across will be copied to the clipboard. Paste it into your document and resize it.
Windows: While viewing the pdf, zoom in until the figure you want fills as much of the screen as possible. Get the cursor out of the way. Then hit the Print Screen key (it may say PrtScn) on your keyboard. The entire screen is now copied to the clipboard. Open up a graphics program, such as Microsoft Paint (this should come with Windows). Paste the image of the screen into Paint. Choose the rectangular select tool (the dashed rectangle) and select the area you want. Copy it, then Paste it into your document, then resize it.
If you want to use a figure from a printed book or journal, you can use a scanner; there is one you can use in the basement of the Morris library. As a last resort, you can take a picture of the printed figure, but try to do a good job and don't use a dim, blurry, slanted picture.
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, or from another student or former student, you will receive a severe penalty, ranging from 15 points off up to an F for the course, depending on how extensive and egregious your plagiarism is. This is not an empty threat; unfortunately, there have been several students over the years who did not graduate in the spring because they plagiarized parts of their term papers for BISC656.
To illustrate the difference between plagiarism and acceptable paraphrasing, 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).
Sometimes students tell me that they're worried that they might inadvertently plagiarize. Trust me, if you're copying from an article and pasting it into your paper, you'll know it; if you copy, paste, and change a few words, you'll know that too.
For more examples of plagiarism, see this report on a paper in a major scientific journal that was retracted due to plagiarism that I helped to detect.
In papers in other fields, such as English or history, it is common to use 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 "Entomological ambiguities in Kafka's Metamorphosis," it's important to quote exactly what Kafka wrote about Gregor Samsa's carapace. 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 we'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 in your term paper (because it can be a lazy way to fill up space).
Most scientific papers are written in the passive voice: "Two cm was cut from the end of each mouse tail, DNA was extracted from the tail segment, and the FOX2P gene was sequenced." Some people hate the passive voice and prefer the active voice: "I cut two cm from the end of each mouse tail, then I extracted DNA from the tail segment and I sequenced the FOX2P gene." The active voice is livelier and more interesting to read; it creates a more vivid word picture, it's easier to imagine the razor blade slicing through the poor mouse's tail in the second sentence. However, the active voice can be difficult to use accurately. Most scientific papers have multiple authors, so the active voice would use "we." However, if Johnson, Hussein, Ramachandran and Xie write "We cut two cm from the end of each mouse tail, then we extracted DNA from the tail segment and we sequenced the FOX2P gene," it could be a little inaccurate. Hussein may have cut the mouse tails, Johnson and Ramachandran may have extracted the DNA, and someone at a core DNA sequencing facility (whose name isn't even on the paper) may have done the DNA sequencing. Xie may have gotten the grant money and helped write the paper, but never actually touched a mouse or its DNA. It may seem trivial, but any hint of inaccuracy in a scientific paper is a big, big deal.
You may use either the passive or active voice for your paper. If you use the active voice, you must be accurate: don't say "we" if you mean "I", don't say "I" if you mean "we", and don't say "we" without explaining who the "we" are.
Citations in the text must follow the author, year format: (Lewontin and Hubby 1966; Kreitman 1983; Hudson et al. 1987). There is no comma between the author and year, and multiple citations are separated by semicolons. 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 (2015), 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 (2015), for example. If there's no apparent author of any kind, say Anonymous. Remember that while you may cite web pages, they do not count towards the minumum number of references.
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:
There are two kinds of books you're likely to use; we'll call them "regular books" and "edited collections." A "regular book" has a single author or set of authors for the whole book. It counts as a single reference for the term paper. A regular book is cited the same as a journal article, except instead of the journal, volume and page numbers, you give the publisher and the publisher's city. Do not abbreviate book titles. "Edited collections" have one or more editors for the whole book, but each chapter has a different author or authors. Each chapter that you cite counts as a separate reference for the term paper. You cite a book chapter the same as a journal article, 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. Remember that while you should cite web pages that you use as sources, they don't count towards the minimum number of references needed for the paper.
Here are some examples of citation format:
Hudson, R. R., Kreitman, M., and Aguadé, M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
Methe, B. A., Nelson, K. E., Deming, J. W., 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 Kreitman, M. 1991a. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
McDonald, J. H., and Kreitman, M. 1991b. Scientific correspondence. Nature 354: 116.
McDonald, J. H. 2014. Handbook of biological statistics, 3rd ed. Sparky House Publishing, Baltimore.
Book chapters in edited volumes
Hall, B. G. 1983. Evolution of new metabolic functions in laboratory organisms. Pp. 234-257 in Nei, M., and Koehn, R. K., eds. Evolution of genes and proteins. Sinauer Associates, Sunderland, Mass.
Gregory, T. R. 2015. Animal genome size database. http://www.genomesize.com
University of California Museum of Paleontology. 2015. Understanding evolution. http://evolution.berkeley.edu.
Anonymous. Undated [viewed February 7, 2015]. 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 7, 2015. Its URL is http://udel.edu/~mcdonald/evolpaper.html