BISC 219/F10:Questions to Guide Your Reading1

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Questions to Guide Your Reading 1

You can download and print a pdf file of Ch'ng et al's research report, Indentification of Genes that Regulate a Left-Right Aymmetric Neuronal Migration in Caenorhabditis elegans published in Genetics 164: 1355-1367 (August 2003). at: | http://www.genetics.org/cgi/content/full/164/4/1355. Please bring a pdf copy of this paper and of the Handout "The Structure of Scientific Writing" to LAB2. The Handout can be downloaded here: Media: Structure_of_Scientific_Writing219.doc

Use the following questions to help you focus on the structure of the paper as opposed to the content. We realize that it will be very difficult for you to understand the terminology and to follow the experiments, results, and conclusions found in this study since you are not neuroscientists and you are beginning genetics students. Please, don't get bogged down or overwhelmed by the technical information. We are using this paper to model scientific writing in the format of the journal Genetics. However, as with just about any paper, this one is imperfect as a model. There are some great "do's" to follow and some things about its format that deviate from the instructions in your handout "The Structure of Scientific Writing". Keep in mind that the general guidelines found in your handout are for learning scientific writing and are not "rules" that are universally followed. There are many "correct" ways to organize and present information in a research report. During our discussion of this paper in Lab2, we will focus on some of things the authors did that follow our general guidelines and why they may have made choices that deviate from common structure.

Questions To Guide Your Reading:
1. Does the title to the paper give you the main conclusion or the main research goal.
Which is preferable and why?

2. Does the abstract include all of the following: general topic and significance of the topic; general outline of experimental design (methods); specific results; conclusions that address the experimental question or goals; broader context of this study's findings?
If not, what's missing?
If so, are they found in this order?
Why might the authors have failed to include one or more of the elements that the reader expects to find in an abstract?

3. The introduction is not labeled as such, but we know which part is the introduction by its position and content. Does the author include all the elements listed in your Structure of Science Writing Handout and in the expected order?
Does the background information move from old to new and broad to narrow? How so?
All material that isn't "common knowledge" should be cited at the end of any sentence, anywhere someone else's published findings are mentioned. What does "common knowledge" mean?
Do these authors cite everything that is attribitable to specific investigators?
If not, point out a sentence that needs a citation. (Keep in mind that if you include a proper citation in a sentence and continue to refer to that cited work in the next sentence, you need not repeat the citation, IF it is obvious in the second sentence to which paper you refer. If it's not obvious, you should repeat the citation to avoid confusion and to give credit to those who made the discovery you mention.)
Are the methods summarized or outlined at the end of the introduction? These authors have chosen to summarize their main findings and conclusions in the introduction.
Do you like that structure?
Why is it more common to end with a summary of the experimental design and omit findings and conclusions?

4. The Materials and Methods section of this paper is the most problematic part, in that it doesn'f follow the expected guideline that M&M should NOT include experimental results, but should merely describe, in carefully constructed sections, how the experimental design was executed. Where do you find results included in this section?
Why do you think the authors include so many of their experimental findings here rather than to save them for the results section?
Is there material that is more commonly found in a discussion section included here as well?
(Note that these authors are describing a forward genetic study that is similar in goal and methods to the one you will conduct in Series 2, which is why we chose this paper despite its difficulty level).

5. Generally ALL figures are found in the Results section, except for a Table of strain information about the model organisms used in the study, which is included in M&M. These authors include figures or tables in every section, including the introduction and the discussion.
What is different about the type of information in the figures and tables outside the results section from those included in results?
Describe how tables are formatted differently from figures as far as the position of the figure or table number, title and legend.
Where do you find examples of the following appropriate legend information: a general description of the information including in the table or legend; how the data shown were generated; how to interpret any ambiguous symbols or terms; references to other places in the paper where you can find important information?
Do the figures have titles? Titles usually give reader the main point of the data shown.
Does the first line of figures 4 and 5 give the take home message?
Why do you think the authors composed the titles as shown?
The legend, generally, should not analyze the data for you but gives you the tools to figure out the main point for yourself. Is that true of Figures 4 and 5?
If not, why did the authors choose to include the information found in these legends?

The Results narrative portion in this paper does include citations to other work. Each section in a results narrative should begin by spelling out the specific experimental goal or question and then use the data generated to explain how that question can be answered.
In general, each paragraph should be structured, "In order to find out_____, _______ was done", where the first blank gives the specific experimental goal and the second blank summarizes what was done experimentally to answer that question or reach that goal.
Point out examples of that structure in the results section.
A results section is usually limited to explaining the experimental findings from this study; therefore, it does not cite others' work.
Why have these authors included previous work and cited it in Results?
The last sentence of each paragraph should be the main conclusion to the goal that was stated in the first sentence or early in the paragraph. Point out examples of that structure.

6. The Discussion section usually differs from Results by the use of conditional modifiers that let the reader know that the data doesn't yet "prove" anything, but that the data presented might support one explanation or refute another.
Can you find typical discussion words such as: "likely that, possible that, suggests that, speculate, might, may, could, etc."?
We have said that information moves from broad to narrow and old to new in the introduction; however, the discussion should go from the narrow conclusions in this study to their broader application in a less specific context.
Does this discussion do this?
Point out some phrases that explain that the finding are applied more widely.
Students often write papers that seem to end abruptly, rather than to conclude. Is the last paragraph a true conclusion?
What kind of information makes a conclusion?
Does the conclusion limit itself to this study?

7. What is the title of the Reference list? How are the references ordered? Is this the exact citation format as the one used in the journal Cell? How does Genetics format differ?
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