Biological Data Analysis: Homework 4

Due Tuesday, September 29

You must type this and all other homework assignments. Do not e-mail the assignment to me; turn it in early (at 322 Wolf) for a foreseeable absence, or turn it in late after an unexpected absence from class.

1. Under certain conditions, animal cell lines can become "immortalized," meaning they will keep growing and dividing indefinitely in laboratory cultures. Nowak et al. (2004) looked at the effect of the pro-apoptotic protein Bax on immortalization of mouse muscle cells. They made mice without the Bax protein (Bax−/−), established cell lines from them, and compared them to cell lines from mice with the Bax protein (Bax+/− and Bax+/+). After 50 days, all 7 lines of Bax−/− cells were still growing, while only 3 out of 9 of the lines with Bax were growing. Test the data using all three tests of independence, and compare the results of the three tests.

2. McDonald (1989) collected amphipods (Platorchestia platensis) on a beach on Long Island, New York, and determined their genotype at the mannose-6-phosphate isomerase (Mpi) locus. Totalled across several dates, there were 1002 Mpi100/100, 1715 Mpi100/90, and 761 Mpi90/90 females; there were 676 Mpi100/100, 1204 Mpi100/90, and 442 Mpi90/90 males. Is the difference in genotype proportions between females and males significant? Test the data using the chi-squared and G-tests of independence, and compare the results of the two tests.

3. In 1983, I collected data on polymorphism in the gene coding for glucose-6-phosphate isomerase (GPI) in the amphipod crustacean Megalorchestia californiana (the critter shown in the banner at the top of the handbook). In 2009, I collected from six of the same locations, to see whether natural selection by changing climate had caused a change in the allele frequencies. There are two GPI alleles, "fast" and "slow"; the table below shows the number of alleles at each location in each year (it's an autosomal gene, so each individual has two alleles). Analyze the data using the Cochran-Mantel-Haenszel test, draw a graph that summarizes the data, and write a sentence interpreting the results.

                            Number of alleles
Location              Year     fast  slow
----------------      ----     ----  ----
Pt. Townsend, WA      1983        4   182 
                      2009        8   218

Neskowin, OR          1983      237   181
                      2009      376   324

Siuslaw Jetty, OR     1983     1006   780
                      2009      301   233

Winchester Bay, OR    1983      190   172
                      2009      539   457

Empire, OR            1983       62    72
                      2009      295   281

Bastendorf Beach, OR  1983      298   270
                      2009      467   387

4. Collect some measurement data. You must have one nominal variable with at least six values (such as six different biology classes) and one measurement variable (such as blood pressure). You must have at least ten observations in each of your six or more categories (such as ten students in each of the biology classes). Your data set could be a published data set, some data you've collected for your research, or some data you collect for this assignment. It must be real data, not something you made up.

Try to pick groups where the difference in the measurement variable is not so big that it's obvious the statistical test will be highly significant. For example, if you measure the weights of leaves, measure leaves from six or more trees of the same species, not different species with obviously different leaves.

Put your raw data (the individual observations) in a table. For each category, calculate the mean, median, range, standard deviation, standard error of the mean, and 95 percent confidence interval (you may use a spreadsheet, web page or computer program for this). Add these summary numbers to the table. We haven't talked about standard deviation, standard error, or confidence intervals in class yet, so read the textbook pages about them.

Keep a copy of your raw data; you'll need it for the next two homework assignments.


McDonald, J.H. 1989. Selection component analysis of the Mpi locus in the amphipod Platorchestia platensis. Heredity 62: 243-249.

Nowak, J.A., J. Malowitz, M. Girgenrath, C.A. Kostek, A.J. Kravetz, J.A. Dominov, and J.B. Miller. 2004. Immortalization of mouse myogenic cells can occur without loss of p16INK4a, p19ARF, or p53 and is accelerated by inactivation of Bax. BMC Cell Biology 5:1.

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