Mowshowitz                                                                PAPER QUESTIONS                                                    Last update 06/03/2010

The following questions are designed to help you read and analyze scientific papers. The basic questions apply to all papers. Specific examples are drawn from two Nature papers in different areas of biology. The paper by Parmesan & Yohe (P & Y) was discussed in Frontiers of Science, 2004. The paper by Baron et al. (B) was discussed in an earlier genetics course. Here are the complete references to the papers:

P & Y = Parmesan, C, & Yohe, G, A globally coherent fingerprint of climate change impacts across natural systems. Nature 421:37-42 (2003)

B = Baron et al, Nature 326:289-292 (87). Genetic Linkage between X-chromosome markers and bipolar affective illness.

Nature = Name of journal; 421  or 326 = volume number; 37-42 = page numbers; 2003 = year

When you read each of the assigned articles for a course you should try to answer all of the questions before class. You are not expected to figure out all the answers but you are expected to think about the questions and to know what information you are missing.

Here are the actual questions. Sometimes the questions need to be asked only once for each paper, but often they need to be repeated for each experiment.

1. Why did they do this set of experiments?

A. What are the authors trying to settle, prove or demolish? To put it another way, what is the question(s)? For P & Y: Is climate change responsible for significant changes in biological systems? For B: Is bipolar illness sex linked in any or all of these families?

B. How did this issue come up? For P & Y: Why do the authors think climate change is responsible for changes in timing & location of biological populations? Why do others think it may not be?

C. Why is it worth the effort to settle this issue? For P & Y: So what if biological changes are caused by climate changes? For B:  So what if bipolar illness IS sex linked?

Note: Believe it or not, it is sometimes easier to figure out why they did it (Q1) AFTER you figure out what they did (Q2). So if in doubt about "why," attack "what" first.

2. How were the experiments actually done?

A. What number or quantity was actually measured? In other words, what did the scientists write down on the data paper or paper towel? This is a little difficult in the paper by P & Y, as the authors are summarizing the results of others. For B, to get G6PD activity (as in figure 1), they wrote down absorbance and time. Sometimes the raw data are pictures, not numbers as, for example, if the authors are making karyotypes or doing autoradiography.

B. How was the number in (A) obtained, i.e., what did they actually do? For P & Y: Did they sit out in the bush and count animals? Check everyday for time of first flowering? For B: How did they do the G6PD assay? What did they put in the test tube?

C. What numbers are really wanted, i.e., must be calculated? For P& Y: In Table 1, For each species, amount of change in distribution, timing, etc. For Table 2, want P values in addition to simple summary of info in Table 1. Also meta-analyses of changes in timing and position. For B: In fig. 1 they wanted G6PD levels; in table 1 they wanted Lod scores.

D. What information is necessary to calculate the numbers in (C) and where did they (or you) get the information? Is it from a table or experimental control or is it "common knowledge." For P& Y: How do you calculate a P value? How do you do a meta-analysis? For B: How did they convert absorbance vs time into G6PD levels? Once they used the G6PD levels to make the pedigree in figure 1, how did they use the pedigree to calculate the Lod values in table 1?

3. What are the results?

What is the translation into English of the data in their figures, tables and/or pictures? From P & Y: What does figure 1 mean? Table 3?
 From B: The last line of table 1 can be translated " In the non-Ashkenazi family shown in pedigree 009, there is a probability of about 1000:1 that the locus for G6PD is closely linked to a locus causing bipolar illness; the distance between the 2 loci is probably less than 5 map units."

4. What can you conclude from the results?
Assume for the time being that you can take the results at face value -- in other words, assume they did both the experiments and calculations correctly. Whether or not they really "did it right" is Q5.

  A. Do the results support the stated conclusions or interpretation of the authors?: For P & Y: Are the results  consistent with the   hypothesis (statement?) that biological changes are caused by climate change? For B: Are the results consistent with the  hypothesis that there is a form of bipolar illness linked to G6PD locus?

B. Do the results prove the stated conclusion, i.e., do they rule out any of the stated or unstated alternative? For P & Y: What else could explain the observed changes? For B: Could the locus for bipolar illness in the non-Ashkenazi families be on an autosome? To check this point consider what the figures and tables would look like if an alternative interpretation were correct. Could you really tell the difference?

5. Did they do everything correctly?

A. Could anything be wrong with their experimental methods? Did they measure their variables correctly? For B: Did they measure G6PD levels correctly? Diagnose bipolar illness accurately?

B. Could anything be wrong with their theoretical methods? Did they use the right formulas, make reasonable assumptions, etc.?

In the beginning it is usually better to concentrate on the first 3 questions. Once you can answer them easily you can start worrying about the last two questions about the interpretation and/or validity of the results.