BISC 413, Advanced Genetics Lab

Allozyme paper instructions

Your allozyme paper is due by 7 p.m. on Thursday, November 30. You must turn in a printed version at my office (322 Wolf) and you must also e-mail the paper to me. If I'm not in my office, slide your paper under my door. If you have printer problems, etc. and can't turn in the print version on time, your lateness penalty will depend on when you send the e-mail. A minimum of 1 point will be deducted if you turn it in late, with the penalty increasing by 0.1 point for each additional hour. The file can be in any format (Word, OpenOffice, Pages, pdf, plain text, etc.), and the name of the file must include your name (such as "JaneStudent allozymes.doc"). I will save the files in case someone in next year's class expands upon your project.

Content

Your paper should contain the following:

Title

The title of your paper should summarize the results, not just say what the paper was about. "Frequency of white cats in different areas of Philadelphia" would not be a good title. "Greater frequency of white cats in wealthier parts of Philadelphia" would be much better. As you look through the reference lists of papers, notice which titles give you a clear idea of whether you need to read the paper, and which titles are frustratingly vague. Try not to make yours frustratingly vague.

Abstract

Your paper must have an abstract, less than 200 words long, that summarizes the paper. The purpose of the abstract is to let busy people know whether they need to read the whole paper. It should start with a couple of sentences explaining what the goal of the research was, then a little about the methods, then the results. As with the title, it is important that the abstract says what the results were, not just what the study was about. "The frequency of white cats was surveyed in 23 neighborhoods in Philadelphia and compared with census data on average household income" would not be sufficient; it would be better to say "The frequency of white cats was surveyed in 23 neighborhoods in Philadelphia and was correlated with census data on average household income, with almost three times as many white cats in the wealthiest neighborhoods as in the lowest income neighborhoods."

Introduction

The introduction gives background information about your topic. It explains why you are doing the research--what biological questions you hope to answer. It should summarize all of the relevant literature on the topic. For the example paper on white cats in Philadelphia, you would want to explain the genetic basis of white coats in cats; summarize other papers on geographic variation in the frequency of white cats; summarize papers on geographic variation in other genetic characters in cats; and give some information about the different neighborhoods of Philadelphia and why some are rich and some are poor. You should summarize some papers in great detail, while others get only a brief mention. For the example paper, you might summarize five papers on the biochemical basis of white fur in cats in a couple of sentences, while a single paper on differences in frequency of white cats in different neighborhoods of Edinburgh, Scotland would obviously be very relevant and get half a page of detailed summary.

The proposal you wrote in September will form the basis for your introduction for your final paper. Some of you may have such a good proposal that you can use it for the introduction with little re-writing, while some of you will have to do a lot more literature research. You should get a good idea of how much more you need to do from my comments on your proposal.

Materials and methods

The general goal of a methods section is to give the methods you used in sufficient detail that someone else could do the experiment again and get the same results. You don't need to give the information about the methods that were the same for everyone: the dimensions of the gel, starch concentration, gelatin concentration and temperature, the kind of paper used for the wicks, etc. Your methods section should include a detailed map, showing exactly where you collected your samples; a table with site name, latitude and longitude, date collected, and number of individuals collected for each site; your procedure for collecting samples; how you preserved them (whole, or just a certain body part or tissue?); and any other details specific to your organism.

Results

You should have one table with the genotype counts and allele frequencies, with a separate line for each location. You should also have a bar graph showing the allele frequencies at the different locations. If you only have two alleles, you shoud only graph one of them; if there are more than two alleles, you can have bars for all of them. You should do a goodness-of-fit test of the fit of the genotype frequencies to Hardy-Weinberg proportions, and you should do tests of independence comparing allele frequencies at different locations.

If some of your gels didn't work, be sure to describe how they didn't work—did you not run the gel long enough, was it blank, did you drop it on the floor, etc.

Discussion

Your discussion section should interpret your results. Some of you have found published allozyme data from your species; you should compare your results to the published data in some detail. You may have found papers on similar species or with similar sampling designs, and you should compare your results to those. Some of you don't have any literature to compare your results to, and that's fine.

Your discussion should end with ideas for further research. If your experiment didn't work very well, you should write about ways of doing the same experiment, only better. If your experiment went well enough that you got some good data, your further research might be a completely different experiment to test your explanations of the results you got. Don't just say "collect more samples," go into more detail.

Literature Cited

Your Literature Cited section must contain all of the literature you cited in the text, and nothing else. See below for the detailed format.

Passive vs. active voice

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.

Text format

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.

Figures

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). 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. Or you can take a picture of the printed figure. If you're going to take a picture, make sure the paper is flat and exposed to a lot of light, so you'll have a nice sharp picture.

Plagiarism

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 at least 10 points off; depending on how extensive the plagiarism is, you may receive up to 40 points off (which would mean that you would fail the course). This is not an empty threat; almost every year, there are biology majors who do not graduate in the spring because they plagiarized parts of their term papers for BISC495, the class that I teach in the spring. I haven't had much problem with plagiarism in BISC413, and I hope you'll keep that streak going.

To illustrate the difference between plagiarism and 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, without blockquoting (as I've done here) or quotation marks, 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 that I helped to uncover.

Direct quotes

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.

Citation format

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 (2017), 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 (2017), 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:

There are two kinds of books you're likely to use; I'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 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, and don't worry if you're not exactly sure you're right; unlike journal articles and books, I won't be very picky about how you cite web pages. 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:

Journal articles

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.

Slater, G.J., et al. 2010. Biomechanical consequences of rapid evolution in the polar bear lineage. PLoS One 5: e13870.

Regular books

McDonald, J. H. 2009. Handbook of biological statistics, 2nd 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.

Web pages

Gregory, T. R. 2016. Animal genome size database. http://www.genomesize.com

University of California Museum of Paleontology. 2016. Understanding evolution. http://evolution.berkeley.edu/evolibrary/home.php

Anonymous. Undated [viewed February 3, 2016]. Frequently asked questions about creationism and evolution. http://www.talkorigins.org/origins/faqs-qa.html

Term paper from previous class

Lesko, J. 2011. VS construct of sprinter gene in Drosophila melanogaster inserts on second chromosome. Term paper for BISC413 (Advanced Genetics Lab), University of Delaware.


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