Class Assignments

Assignment for Friday 1 September 2006:

Write a brief (250-500 word) essay or discussion on one of the following topics. This can be turned in on Blackboard, by e-mail, or in hard-copy by the due date. By far the best method is via Blackboard.

1. Discuss a scientific advance that was not seen to have any practical application when it was first discovered, but was later found to have substantial practical application.

2. Argue with me. Construct an alternative definition of science and explain why you believe it to be more useful than the one I have presented in these notes.

3. Look through recent issues of Scientific American or American Scientist (available in the library). Find an article that describing a scientific advance on the interface between two of the traditional scientific disciplines. Describe how the insights of the two disciplines combine to provide understanding.

Summarize, in 350-600 words, the first five essays (chapters) in Trefil's book, 101 things you don't know about science and no one else does either. Provide details of what the author says on these topics. By this date you should have read all of the first ten essays.

Assignment for Friday 15 September 2006:

Do one of the following:

1. Extend the list given on 1-6 September of tools of science to include one or more additional items. Present a convincing argument that your additions to the list are as important as the existing items.
2. Access the world-wide web via a browser. Find the Protein Data Bank at http://www.rcsb.org/ and find at least two structures in it for which M. Whitlow was one of the authors. Name the two structures you found. Examine the protein sequence for one of the structures and count how many methionine residues are present in the structures. Turn in the results of your search.
   n.b.: A residue is one of the amino-acid building blocks from which a protein is made; that is, a protein built up from 210 amino acids is said to contain 210 residues. There are several atoms in a methionine residue. Count residues, not atoms! If you don't understand how this works, talk to me about it. "I didn't understand what you meant by a residue" is not an acceptable excuse for getting this wrong, unless you asked me and I refused to answer.

Assignment for Friday 22 September 2006:

Investigate career opportunities in physics, chemistry, biology, or applied mathematics as research fields. Please do not investigate medical career opportunities, even if you're pre-med; the point of this assignment is to understand the realities of a career in research science. Bear in mind issues like (1) what kinds of personality traits and intellectual strengths are particularly well-suited to a career in the field you choose to write about; (2) how large the field is (i.e., how many people work in the field, or how many people enter the field in a given year, or both); (3) what typical salaries for starting professionals are; and (4) how students can look for employment. Write a roughly 300-word description of what you find out; include an indication of whether it makes you feel more or less motivated to pursue a career in the sciences, and why. Include discussions of all four of the issues just listed.
In particular, if you choose physics, you may want to examine a website developed by the American Institute of Physics, and a resource site and a statistics site accessible from there.
If you choose biology, check out a site maintained by the Federation of American Societies of Experimental Biology: http://www.bls.gov/ and follow the instructions to get to http://data.bls.gov/labjava/outside.jsp?survey=nc and then follow the directions.
If you choose chemistry, check out the career information available from the American Chemical Society's website, including their http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=chemjobs A particularly useful resource is a PDF file containing a statistical survey on graduates of the class of 2002. If you do not have a PDF reader on your computer, you'll need to get it in order to read this PDF file. I can help you with that.

Assignment for Friday 29 September 2006:

Examine the course website developed by Bernhard Rupp at Lawrence Livermore National Laboratory on macromolecular crystallography. Dr. Rupp's site occasionally goes down for internal maintenance, so be prepared to try checking it more than once. Come to me for help in finding this if you encounter difficulties. Read over the overviews of the four sections of the crystallography course, all of which appear on the frame on the lefthand side of the page:

• Experimental Setup
• About Symmetry and Space Groups
• Structure Factors and Phase Problem
• Phasing Techniques

• Does the website appear to provide a comprehensive overview of the subject?
• Does it provide a motivation to learn more about macromolecular crystallography?
• Does it convince you that there are practical applications for this particular field of science?

Assignment for Friday 6 October 2006:

Below are four lists of scholarly journals--one list each for physics, chemistry, biology, and molecular biochemistry and biophysics. Pick the list that applies to your own major. Go to Galvin Library and determine which of these journals are:

1. Available in hard-copy up through the current issue at Galvin;
2. Available by Internet download at Galvin;
3. Available for some number of back-issues in hard-copy, but not up through the current issue;
4. Unavailable at Galvin Library except through Interlibrary loan.

Assignment for Friday 13 October 2006:

No assignment: this is fall break week.

Assignment for Friday 20 October 2006:

Do EITHER of the following:

1. In considering income for a group of people, which is the more meaningful central measure: the mean or the median? Why?

2. Describe an algorithm for computing the median of a group of measurements without sorting them into increasing or decreasing order. You don't have to actually code the algorithm in software (although you can!), but if you don't you should describe the algorithm in detail.

Do both of the following:

1. Calculate the coefficients a and b in the linear equation y = ax+b that best fits the following points in the least-squares sense, using equations [25] and [26] from the lecture on least-squares fitting:

   x	1.2	2.1	3.3	4.2	5.4	6.4	7.5	8.4	9.5	10.7	11.6	12.9	13.8	14.8	16.0	17.2
   y	9.2	8.5	7.0	6.5	5.1	4.9	4.1	3.0	2.3	1.8	1.3	0.4	-0.7	-1.3	-2.1	-2.9

2. Determine which point in the list of data above deviates most from the calculated value, i.e. calculate
       max |y(calc) - y(obs)|
   where y(calc) = ax + b and y(obs) is the observed y value. Recalculate the least-squares line, omitting that one point. For full credit you should do the recalculation without starting from scratch (hint: fiddle with the definitions [17]).

Assignment for Friday 3 November 2006

Find a Materials Safety Data Sheet for any two of the following substances:

• Isopropyl alcohol (isopropanol, 2-propanol)
• uranyl acetate
• bismuth subsalicylate
• acrylamide
• dimethyl sulfoxide
• 2-methyl-2,4-pentanediol

Provide a summary and a critique of the the sixth through tenth chapters or essays in Trefil's book. Your summary should be similar to that provided in the September assignment, but it should be supplemented with a critique. Concentrate on critiquing how effectively Trefil communicates information and ideas. Remember what we discussed early in the semester: a critique must include an analysis of how effective the author is at getting his or her points across. By this date you should have read the first sixty of the essays in the book.

Deliver your group oral presentation to the class as described in the course syllabus. Note that some of the Thursday group may be presenting on Tuesday 14 November or Tuesday 21 November

Research the career of any scientist. Write a brief essay on his or her life, scientific accomplishments, and place in scientific history. At minimum, write a substantial paragraph on the scientist's life; another substantial paragraph on his or her scientific achievement; and another that explores the degree to which he or she was ahead of rather than riding the crest of the scientific accomplishments of the era.

By this date you should have read all the essays in Trefil's book.

n.b. This assignment is due during Thanksgiving weekend. This should not cause a problem, even if you're traveling over the holiday: you can submit the assignment before you leave, or you can submit it from your remote location.

Turn in a rough draft of your semester-project book review or other special project. We will grade it and e-mail comments to you in time for you to make revisions prior to the final due date of Saturday 2006. The specific instructions for this rough draft are found at http://csrri.iit.edu/~howard/itp/roughdraft.html.

Summarize in your own words the scientific focus of two of the Collaborative Access Teams at the Advanced Photon Source. You can derive the information for your summary either from the things you see on the tour or from the CATs' websites, or both. The CAT websites are all accessible from http://www.aps.anl.gov/cats/cathome.html. Don't pick SER-CAT, since it's hard for me to be objective about it!

Turn in the final version of your semester-project book review or other special project by 5 pm.