Instructor: John McDonald
322 Wolf Hall (office)
E-mail: mcdonald@udel.edu
Phone: 831-2007 (I don't check messages very often; e-mail is better)
Class web page: http://udel.edu/~mcdonald/geneticssyllabus.html
This schedule has links to the online lab manual for the course. The web pages will be revised throughout the semester, up until the morning of each lab, so don't print them out ahead of time.
Purpose of the course: I have two goals for this course. The first is to reinforce the genetics and evolution concepts you learned in BISC403 using laboratory work (on Drosophila melanogaster, mostly). Although much of the laboratory work may seem rather old-fashioned, I feel that there is still no better way to learn the basics of transmission and population genetics than by observing live organisms. The second goal of the course will be to introduce you to some of the computer tools that are commonly used in modern genetics research. Here I will emphasize publicly available databases and software, so that you may continue to use these resources in the future.
Office hours: There are no fixed office hours. You can make an appointment by talking to me before or after class, or by e-mailing me. If you have questions while studying or doing the homework assignments, feel free to e-mail me or drop by my office.
Textbook: We will not use a textbook or printed lab manual this fall. The individual labs for each week will be linked from this web page. The topics for each lab may change at the last minute, depending on what the flies are doing, so don't print out the labs ahead of time.
Attendance: You will not be penalized for absences, but you must make up the work you miss. If you know in advance that you will miss a class, please talk to me so we may make arrangements for you to do the work at another time. If you have an unplanned absences, please e-mail me as soon as you can so we may make arrangements.
Grading: Your grade will be based on the following:
The grades will not be curved. There are no extra credit projects. The points from the assignments will be combined and converted to letter grades as follows:
A 93-100; A- 90-92.9; B+ 87-89.9; B 83-86.9; B- 80-82.9; C+ 77-79.9; C 73-76.9; C- 70-72.9; D+ 67-69.9; D 63-66.9; D- 60-62.9; F 0-59.9.
Students who are less than 3 points below the minimum grade needed for their program (such as an undergraduate biology major with 67 to 69.9 points) will be given the opportunity to take an incomplete grade and complete an extra credit project. This project will be a lot of work, such as writing a 15-page term paper on a topic of my choice. Upon satisfactory completion of the project, you'll get the minimum grade needed for your program (such as C- for undergraduate biology majors). There will be no other extra credit.
You will do much of the lab work with a partner. The instructions for each lab report will specify which parts of the lab report can be the same as your partner's (tables of data that you collected together, for example) and which parts must be your own work (the written text). If you and a classmate have identical or nearly identical material in your lab reports that isn't specifically permitted by the instructions, you will each receive a zero for the assignment. Please ask me if you're not sure about what you can work on with your lab partner, and what you must do yourself.
Making up data, or copying someone else's data, are extremely serious offenses in science. A scientist who fabricates data will usually lose their job and have difficulty finding another job in science. In addition, fabrication is a serious violation of the University's Code of Conduct. If you make up data or copy someone else's data, you will receive a 0 for the assignment. If the fabrication is particularly extensive or egregious, you will receive a harsher penalty, up to an F for the course.
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 0 for the assignment. If the copying is particularly extensive or egregious, you will receive a harsher penalty, up to an F for the course.
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).
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 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 in your term paper.
You must follow these formatting rules for your lab reports and your term paper. They may seem picky, but following them demonstrates your ability to follow instructions exactly, an important skill for both research biologists and medical professionals.
Most of your lab reports will not need citations of scientific literature; you do not need to cite the online lab manual. When you do use citations in the text, they 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 (2008), 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 (2008), 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. 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.
Books
Sokal, R. R., and F. J. Rohlf. 1995. Biometry. W.H. Freeman, New York.
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. 2008. Animal Genome Size Database. http://www.genomesize.com
University of California Museum of Paleontology. 2007. Understanding evolution. http://evolution.berkeley.edu.
Anonymous. Undated [viewed January 28, 2007]. Frequently asked questions about creationism and evolution. http://www.talkorigins.org/origins/faqs-qa.html.
Return to John McDonald's home page
This page was last revised September 1, 2008. Its URL is http://udel.edu/~mcdonald/geneticssyllabus.html