BSCI 1511L Statistics Manual: 3.2 Components of a scientific paper

Nearly all journal articles are divided into the following major sections: abstract, introduction, methods, results, discussion, and references or literature cited.  Usually the sections are labeled as such, although often the introduction (and sometimes the abstract) is not labeled.  Sometimes alternative section titles are used.  The abstract is sometimes called the "summary", the methods are sometimes called "materials and methods", and the discussion is sometimes called "conclusions".   Some journals also include the minor sections of "key words" following the abstract, and "acknowledgments" following the discussion.  In some journals, the sections may be divided into subsections that are given descriptive titles.  However, the general division into the six major sections is nearly universal.

The abstract is a short summary (150-200 words or less) of the important points of the paper.  It does not generally include background information.  There may be a very brief statement of the rationale for conducting the study.  It describes what was done, but without details.  It also describes the results in a summarized way that usually includes whether or not the statistical tests were significant.  It usually concludes with a brief statement of the importance of the results.  Abstracts do not include references.  When writing a paper, the abstract is always the last part to be written.

The purpose of the abstract is to allow potential readers of a paper to find out the important points of the paper without having to actually read the paper.  It should be a self-contained unit capable of being understood without the benefit of the text of the article. It essentially serves as an "advertisement" for the paper that readers use to determine whether or not they actually want to wade through the entire paper or not.  Abstracts are generally freely available in electronic form and are often presented in the results of an electronic search.  If searchers do not have electronic access to the journal in which the article is published, the abstract is the only means that they have to decide whether to go through the effort (going to the library to look up the paper journal, requesting a reprint from the author, buying a copy of the article from a service, requesting the article by Interlibrary Loan) of acquiring the article.  Therefore it is important that the abstract accurately and succinctly presents the most important information in the article.

The introduction section of a paper provides the background information necessary to understand why the described experiment was conducted.  The introduction should describe previous research on the topic that has led to the unanswered questions being addressed by the experiment and should cite important previous papers that form the background for the experiment.  The introduction should also state in an organized fashion the goals of the research, i.e. the particular, specific questions that will be tested in the experiments.  There should be a one-to-one correspondence between questions raised in the introduction and points discussed in the conclusion section of the paper.  In other words, do not raise questions in the introduction unless you are going to have some kind of answer to the question that you intend to discuss at the end of the paper. 

You may have been told that every paper must have a hypothesis that can be clearly stated.  That is often true, but not always.  If your experiment involves a manipulation which tests a specific hypothesis, then you should clearly state that hypothesis.  On the other hand, if your experiment was primarily exploratory, descriptive, or measurative, then you probably did not have an a priori hypothesis, so don't pretend that you did and make one up.  (See the discussion in the introduction to Experiment 5 for more on this.)  If you state a hypothesis in the introduction, it should be a general hypothesis and not a null or alternative hypothesis for a statistical test.  If it is necessary to explain how a statistical test will help you evaluate your general hypothesis, explain that in the methods section. 

A good introduction should be fairly heavy with citations.  This indicates to the reader that the authors are informed about previous work on the topic and are not working in a vacuum.  Citations also provide jumping-off points to allow the reader to explore other tangents to the subject that are not directly addressed in the paper.  If the paper supports or refutes previous work, readers can look up the citations and make a comparison for themselves. 

"Do not get lost in reviewing background information. Remember that the Introduction is meant to introduce the reader to your research, not summarize and evaluate all past literature on the subject (which is the purpose of a review paper). Many of the other studies you may be tempted to discuss in your Introduction are better saved for the Discussion, where they become a powerful tool for comparing and interpreting your results. Include only enough background information to allow your reader to understand why you are asking the questions you are and why your hypotheses are reasonable ones. Often, a brief explanation of the theory involved is sufficient.

Write this section in the past or present tense, never in the future. " (Steingraber et al. 1985)

In other words, the introduction section relates what the topic being investigated is, why it is important, what research (if any) has been done prior that is relevant to what you are trying to do, and in what ways you will be looking into this topic.

An example to think about:

This is an example of a student-derived introduction.  Read the paragraph and before you go beyond, think about the paragraph first.

"Hand-washing is one of the most effective and simplest of ways to reduce infection and disease, and thereby causing less death.  When examining the effects of soap on hands, it was the work of Sickbert-Bennett and colleagues (2005) that showed that using soap or an alcohol on the hands during hand-washing was a significant effect in removing bacteria from the human hand.  Based on the work of this, the team led by Larsen (1991) then showed that the use of computer imaging could be a more effective way to compare the amount of bacteria on a hand."

There are several aspects within this "introduction" that could use improvement.  A group of any random 4 of you could easily come up with at 10 different things to reword, revise, expand upon.

In specific, there should be one thing addressed that more than likely you did not catch when you were reading it.

The citations: Not the format, but the logical use of them.

Look again. "...the work of Sickbert-Bennett...(2005)" and then "Based on the work of this, the team led by Larsen (1991)..."

How can someone in 1991 use or base their work on something from 2005?

They cannot.  You can spend an entire hour using spellcheck and reading through and through again to find all the little things to "give it more oomph", but at the core, you still must present a clear and concise and logical thought-process.

The function of the methods section is to describe all experimental procedures, including controls. The description should be complete enough to enable someone else to repeat your work. If there is more than one part to the experiment, it is a good idea to describe your methods and present your results in the same order in each section. This may not be the same order in which the experiments were performed -it is up to you to decide what order of presentation will make the most sense to your reader.

1. Explain why each procedure was done, i.e., what variable were you measuring and why? Example:

Difficult to understand: First, I removed the frog muscle and then I poured Ringer’s solution on it. Next, I attached it to the kymograph.

Improved: I removed the frog muscle and poured Ringer’s solution on it to prevent it from drying out. I then attached the muscle to the kymograph in order to determine the minimum voltage required for contraction.

Better: Frog muscle was excised between attachment points to the bone. Ringer's solution was added to the excised section to prevent drying out. The muscle was attached to the kymograph in order to determine the minimum voltage required for contraction.

2. Experimental procedures and results are narrated in the past tense (what you did, what you found, etc.) whereas conclusions from your results are given in the present tense.

3. Mathematical equations and statistical tests are considered mathematical methods and should be described in this section along with the actual experimental work. (Show a sample calculation, state the type of test(s) performed and program used)

4. Use active rather than passive voice when possible.  [Note: see Section 3.1.4 for more about this.]  Always use the singular "I" rather than the plural "we" when you are the only author of the paper (Methods section only).  Throughout the paper, avoid contractions, e.g. did not vs. didn’t.

5. If any of your methods is fully described in a previous publication (yours or someone else’s), you can cite work that instead of describing the procedure again.

Example: The chromosomes were counted at meiosis in the anthers with the standard acetocarmine technique of Snow (1955).

Below is a PARTIAL and incomplete version of a "method".  Without getting into the details of why, Version A and B are bad.  A is missing too many details and B is giving some extra details but not giving some important ones, such as the volumes used.  Version C is still not complete, but it is at least a viable method. Notice that C is also not the longest....it is possible to be detailed without being long-winded.

In other words, the methods section is what you did in the experiment and has enough details that someone else can repeat your experiment.  If the methods section has excluded one or more important detail(s) such that the reader of the method does not know what happened, it is a 'poor' methods section.  Similarly, by giving out too many useless details a methods section can be 'poor'.

You may have multiple sub-sections within your methods (i.e., a section for media preparation, a section for where the chemicals came from, a section for the basic physical process that occurred, etc.,).  A methods section is NEVER a list of numbered steps.

The function of this section is to summarize general trends in the data without comment, bias, or interpretation. The results of statistical tests applied to your data are reported in this section although conclusions about your original hypotheses are saved for the Discussion section. In other words, you state "the P-value" in Results and whether below/above 0.05 and thus significant/not significant while in the Discussion you restate the P-value and then formally state what that means beyond "significant/not significant".

Tables and figures should be used when they are a more efficient way to convey information than verbal description. They must be independent units, accompanied by explanatory captions that allow them to be understood by someone who has not read the text. Do not repeat in the text the information in tables and figures, but do cite them, with a summary statement when that is appropriate.  Example:

Incorrect: The results are given in Figure 1.

Correct: Temperature was directly proportional to metabolic rate (Fig. 1).

Please note that the entire word "Figure" is almost never written in an article.  It is nearly always abbreviated as "Fig." and capitalized.  Tables are cited in the same way, although Table is not abbreviated.

Whenever possible, use a figure instead of a table. Relationships between numbers are more readily grasped when they are presented graphically rather than as columns in a table.

Data may be presented in figures and tables, but this may not substitute for a verbal summary of the findings. The text should be understandable by someone who has not seen your figures and tables.

1. All results should be presented, including those that do not support the hypothesis.

2. Statements made in the text must be supported by the results contained in figures and tables.

3. The results of statistical tests can be presented in parentheses following a verbal description.

Example: Fruit size was significantly greater in trees growing alone (t = 3.65, df = 2, p < 0.05).

Simple results of statistical tests may be reported in the text as shown in the preceding example.  The results of multiple tests may be reported in a table if that increases clarity. (See Section 11 of the Statistics Manual for more details about reporting the results of statistical tests.)  It is not necessary to provide a citation for a simple t-test of means, paired t-test, or linear regression.  If you use other more complex (or less well-known) tests, you should cite the text or reference you followed to do the test.  In your materials and methods section, you should report how you did the test (e.g. using the statistical analysis package of Excel). 

It is NEVER appropriate to simply paste the results from statistical software into the results section of your paper.  The output generally reports more information than is required and it is not in an appropriate format for a paper. Similar, do NOT place a screenshot.  

Should you include every data point or not in the paper?  Prior to 2010 or so, most papers would probably not present the actual raw data collected, but rather show the "descriptive statistics" about their data (mean, SD, SE, CI, etc.). Often, people could simply contact the author(s) for the data and go from there.  As many journals have a significant on-line footprint now, it has become increasingly more common that the entire data could be included in the paper.  And realize why the entire raw data may not have been included in a publication. Prior to about 2010, your publication had limited paper space to be seen on.  If you have a sample of size of 10 or 50, you probably could show the entire data set easily in one table/figure and it not take up too much printed space. If your sample size was 500 or 5,000 or more, the size of the data alone would take pages of printed text.  Given how much the Internet and on-line publications have improved/increased in storage space, often now there will be either an embedded file to access or the author(s) will place the file on-line somewhere with an address link, such as GitHub.  Videos of the experiment are also shown as well now.

• Do not repeat information in a table that you are depicting in a graph or histogram; include a table only if it presents new information.
• It is easier to compare numbers by reading down a column rather than across a row. Therefore, list sets of data you want your reader to compare in vertical form.
• Provide each table with a number (Table 1, Table 2, etc.) and a title. The numbered title is placed above the table.
• Please see Section 11 of the Excel Reference and Statistics Manual for further information on reporting the results of statistical tests.

• These comprise graphs, histograms, and illustrations, both drawings and photographs. Provide each figure with a number (Fig. 1, Fig. 2, etc.) and a caption (or "legend") that explains what the figure shows. The numbered caption is placed below the figure.  Figure legend = Figure caption.
• Figures submitted for publication must be "photo ready," i.e., they will appear just as you submit them, or photographically reduced. Therefore, when you graduate from student papers to publishable manuscripts, you must learn to prepare figures that will not embarrass you. At the present time, virtually all journals require manuscripts to be submitted electronically and it is generally assumed that all graphs and maps will be created using software rather than being created by hand.  Nearly all journals have specific guidelines for the file types, resolution, and physical widths required for figures.  Only in a few cases (e.g. sketched diagrams) would figures still be created by hand using ink and those figures would be scanned and labeled using graphics software.  Proportions must be the same as those of the page in the journal to which the paper will be submitted. 
• Graphs and Histograms: Both can be used to compare two variables. However, graphs show continuous change, whereas histograms show discrete variables only.  You can compare groups of data by plotting two or even three lines on one graph, but avoid cluttered graphs that are hard to read, and do not plot unrelated trends on the same graph. For both graphs, and histograms, plot the independent variable on the horizontal (x) axis and the dependent variable on the vertical (y) axis. Label both axes, including units of measurement except in the few cases where variables are unitless, such as absorbance.
• Drawings and Photographs: These are used to illustrate organisms, experimental apparatus, models of structures, cellular and subcellular structure, and results of procedures like electrophoresis. Preparing such figures well is a lot of work and can be very expensive, so each figure must add enough to justify its preparation and publication, but good figures can greatly enhance a professional article, as your reading in biological journals has already shown.

The function of this section is to analyze the data and relate them to other studies. To "analyze" means to evaluate the meaning of your results in terms of the original question or hypothesis and point out their biological significance.

1. The Discussion should contain at least:

• the relationship between the results and the original hypothesis, i.e., whether they support the hypothesis, or cause it to be rejected or modified
• an integration of your results with those of previous studies in order to arrive at explanations for the observed phenomena
• possible explanations for unexpected results and observations, phrased as hypotheses that can be tested by realistic experimental procedures, which you should describe

2. Trends that are not statistically significant can still be discussed if they are suggestive or interesting, but cannot be made the basis for conclusions as if they were significant.

3. Avoid redundancy between the Results and the Discussion section. Do not repeat detailed descriptions of the data and results in the Discussion. In some journals, Results and Discussions are joined in a single section, in order to permit a single integrated treatment with minimal repetition. This is more appropriate for short, simple articles than for longer, more complicated ones.

4. End the Discussion with a summary of the principal points you want the reader to remember. This is also the appropriate place to propose specific further study if that will serve some purpose, but do not end with the tired cliché that "this problem needs more study." All problems in biology need more study. Do not close on what you wish you had done, rather finish stating your conclusions and contributions.

5. Conclusion section.  Primarily dependent upon the complexity and depth of an experiment, there may be a formal conclusion section after the discussion section. In general, the last line or so of the discussion section should be a more or less summary statement of the overall finding of the experiment.  IF the experiment was large enough/complex enough/multiple findings uncovered, a distinct paragraph (or two) may be needed to help clarify the findings.  Again, only if the experiment scale/findings warrant a separate conclusion section.

The title of the paper should be the last thing that you write.  That is because it should distill the essence of the paper even more than the abstract (the next to last thing that you write). 

The title should contain three elements:

1. the name of the organism studied;

2. the particular aspect or system studied;

3. the variable(s) manipulated.

Do not be afraid to be grammatically creative. Here are some variations on a theme, all suitable as titles:

THE EFFECT OF TEMPERATURE ON GERMINATION OF ZEA MAYS

DOES TEMPERATURE AFFECT GERMINATION OF ZEA MAYS?

TEMPERATURE AND ZEA MAYS GERMINATION: IMPLICATIONS FOR AGRICULTURE

Sometimes it is possible to include the principal result or conclusion in the title:

HIGH TEMPERATURES REDUCE GERMINATION OF ZEA MAYS

Note for the BSCI 1510L class: to make your paper look more like a real paper, you can list all of the other group members as co-authors.  However, if you do that, you should list you name first so that we know that you wrote it.

Please refer to section 2.1 of this guide.