HOW DO I WRITE A SCIENTIFIC PAPER?

Adapted with permission from a text developed by the Applied Ecology Research Group at
the University of Canberra Australia, and prepared with the aid of 'How to Write and
Publish a Scientific Paper' by Robert Day (ISI Press, Philadelphia, 1979).

A scientific paper is a written report describing original research results whose format has
been defined by centuries of developing tradition, editorial practice, scientific ethics and the
interplay with printing and publishing services. The result of this process is that virtually
every scientific paper has a title, abstract, introduction, materials and methods, results and
discussion.

It should, however, be noted that most publications have rules about a paper's format: some
divide papers into these or some of these sections, others do not, and the order may be
different in different publications. So be prepared to revise your paper in to a publication's
format when you are ready to submit.

One general points to remember is the need to avoid jargon and acronyms as much as
possible. A second is the fact that some journals like papers to be written in the active voice
- i.e. "we carried out a test..." rather than " test was carried out to..." — but that this is not
always the case.

Title

A title should be the fewest possible words that accurately describe the content of the paper.
Omit all waste words such as "A study of ...", "Investigations of ...", "Observations on ...",
etc. Indexing and abstracting services depend on the accuracy of the title, extracting from it
keywords useful in cross-referencing and computer searching.

An improperly titled paper may never reach the audience for which it was intended, so be
specific. If the study is of a particular species or chemical, name it in the title. If the study
has been limited to a particular region or system, and the inferences it contains are similarly
limited, then name the region or system in the title.

Keyword List

The keyword list provides the opportunity to add keywords, used by the indexing and
abstracting services, in addition to those already present in the title. Judicious use of
keywords may increase the ease with which interested parties can locate your article.

Abstract

A well-prepared abstract enables the reader to identify the basic content of a document
quickly and accurately, to determine its relevance to their interests, and thus to decide
whether to read the document in its entirety. The abstract concisely states the principal
objectives and scope of the investigation where these are not obvious from the title. More
important, it concisely summarizes the results and principal conclusions. Do not include
details of the methods used unless the study is methodological, i.e. primarily concerned
with methods.

The abstract must be concise; most journals specify a length, typically not exceeding 250
words. If you can convey the essential details of the paper in 100 words, do not use 200. Do
not repeat information contained in the title. The abstract, together with the title, must be
self-contained as it is published separately from the paper in abstracting services such as
Biological Abstracts or Current Contents. Omit all references to the literature and to tables
or figures, and omit obscure abbreviations and acronyms even though they may be defined
in main body of the paper.

Introduction

The introduction begins by introducing the reader to the pertinent literature. A common
mistake is to introduce authors and their areas of study in general terms without mention of
their major findings. For example: "Parmenter (1976) and Chessman (1978) studied the diet
of Chelodina longicollis at various latitudes and Legler (1978) and Chessman (1983)
conducted a similar study on Chelodina expansa" compares poorly with: "Within the
confines of carnivory, Chelodina expansa is a selective and specialized predator feeding
upon highly motile prey such as decapod crustaceans, aquatic bugs and small fish (Legler,
1978; Chessman, 1984), whereas C. longicollis is reported to have a diverse and
opportunistic diet (Parmenter, 1976; Chessman, 1984)". The latter is a far more informative
lead-in to the literature, but more importantly it will enable the reader to clearly place the
current work in the context of what is already known.

Try to introduce references so they do not interfere with the flow of your argument: first
write the text without references so that it reads smoothly, then add in the references at the
end of sentences or phrases so they do not interrupt your flow. Note that not all journals use
author's names in references, some use numbers in the text with a list of citations at the end
of the article. Check the publication's style when you are ready to submit your paper.

An important function of the introduction is to establish the significance of your current

work: Why was there a need to conduct the study? Having introduced the pertinent
literature and demonstrated the need for the current study, you should state clearly the
scope and objectives.

Avoid a list of points or bullets; use prose.

The introduction can finish with the statement of objectives or, as some people prefer, with
a brief statement of the principal findings. Either way, the reader must have an idea of
where the paper is heading to follow the development of the evidence.

Materials and Methods

The main purpose of the 'Materials and Methods' section is to provide enough detail for a
competent worker to repeat your study and reproduce the results. The scientific method
requires that your results be reproducible, and you must provide a basis for repetition of the
study by others.

Equipment and materials available off the shelf should be described exactly (e.g. Licor
underwater quantum sensor, Model LI 192SB) and sources of materials should be given if
there is variation in quality among supplies. Modifications to equipment or equipment
constructed specifically for the study should be carefully described in detail. The method
used to prepare reagents, fixatives, and stains should be stated exactly, though often
reference to standard recipes in other works will suffice.

The usual order of presentation of methods is chronological. However, related methods

may need to be described together and strict chronological order cannot always be
followed. If your methods are new (i.e. unpublished), you must provide all the detail
required to repeat them. However, if a method has been previously published, only the
name of the method and a literature reference need be given.

Be precise in describing measurements and include errors of measurement. Ordinary

statistical methods should be used without comment; advanced or unusual methods may
require a literature citation. Show your materials and methods section to a colleague. Ask if
they would have difficulty in repeating your study.

Results

In the results section you present your findings: display items (figures and tables) are
central in this section. Present the data, digested and condensed, with important trends
extracted and described. Because the results comprise the new knowledge that you are
contributing to the world, it is important that your findings be clearly and simply stated.

The results should be short and sweet. Do not say "It is clearly evident from Fig. 1 that bird
species richness increased with habitat complexity". Say instead "Bird species richness
increased with habitat complexity (Fig. 1)".

However, don't be too concise. Readers cannot be expected to extract important trends from
the data unaided. Few will bother. Combine the use of text, tables and figures to condense
data and highlight trends. In doing so be sure to refer to the guidelines for preparing tables
and figures below.

Discussion

In the discussion you should discuss what principles have been established or reinforced;
hat generalizations can be drawn; how your findings compare to the findings of others or to
expectations based on previous work; and whether there any theoretical/practical
implications of your work.
When you address these questions, it is crucial that your discussion rests firmly on the
evidence presented in the results section. Refer briefly to your results to support your
discussion statements. Do not extend your conclusions beyond those that are directly
supported by your results.

A brief paragraph of speculation about what your results may mean in a general sense is
usually acceptable, but should not form the bulk of the discussion. Be sure to address the
objectives of the study in the discussion and to discuss the significance of the results. Don't
leave the reader thinking "So what?". End the discussion with a short summary or
conclusion regarding the significance of the work.

References

Whenever you draw upon information contained in another paper, you must acknowledge
the source. All references to the literature must be followed immediately by an indication of
the source of the information that is referenced, e.g. "A drop in dissolved oxygen under
similar conditions has been demonstrated before (Norris, l986)."

If two authors are involved, include both surnames in this reference. However if more
authors are involved, you may use 'et al.l, an abbreviation of Latin meaning 'and others'. In
general you should not use the abbreviation in the full reference at the end of the article,
although some journals permit this. If two more more articles written by the same author in
the same year are cited, most journals ask you to add suffixes 'a', 'b' etc in both the text and
the reference list.

If you include in your report phrases, sentences or paragraphs repeated verbatim from the
literature, it is not sufficient to simply cite the source. You must include the material in
quotes and you must give the number of the page from which the quote was lifted. For
example: "Day (l979: 3l) reports a result where '33.3% of the mice used in this experiment
were cured by the test drug; 33.3% of the test population were unaffected by the drug and
remained in a moribund condition; the third mouse got away'".

A list of references ordered alphabetically by author's surname, or by number, depending

on the publication, must be provided at the end of your paper. The reference list should
contain all references cited in the text but no more. Include with each reference details of
the author, year of publication, title of article, name of journal or book and place of
publication of books, volume and page numbers.

Formats vary from journal to journal, so when you are preparing a scientific paper for an
assignment, choose a journal in your field of interest and follow its format for the reference
list. Be consistent in the use of journal abbreviations.

Appendices
Appendices contain information in greater detail than can be presented in the main body of
the paper, but which may be of interest to a few people working specifically in your field. .
Only appendices referred to in the text should be included.

Formatting conventions

Most publications have guidelines about submission and manuscript preparation, for online
or mailed submissions. Most journals require the manuscript to be typed with double
spacing throughout and reasonable margins. Make sure you read the guide to authors before
submitting your paper so that you can present your paper in the right format for that
publication (refer to submission of paper article in this series).

Finally — and perhaps most importantly — ALWAYS read the journal's guide to authors
before submitting a paper, and ALWAYS provide an informative cover letter to your
submission.

Constructing tables

DO include a caption and column headings that contain enough information for the reader
to understand the table without reference to the text. The caption should be at the head of
the table.

DO organize the table so that like elements read down, not across.

DO present the data in a table or in the text, but never present the same data in both forms.

DO choose units of measurement so as to avoid the use of an excessive number of digits.

DON'T include tables that are not referred to in the text.

DON'T be tempted to 'dress up' your report by presenting data in the form of tables or
figures that could easily be replaced by a sentence or two of text. Whenever a table or
columns within a table can be readily put into words, do it.

DON'T include columns of data that contain the same value throughout. If the value is
important to the table include it in the caption or as a footnote to the table.

DON'T use vertical lines to separate columns unless absolutely necessary.

When constructing figures

DO include a legend describing the figure. It should be succinct yet provide sufficient
information for the reader to interpret the figure without reference to the text. The legend
should be below the figure.

DO provide each axis with a brief but informative title (including units of measurement).
DON'T include figures that are not referred to in the text, usually in the text of the results
section.

DON'T be tempted to 'dress up' your report by presenting data in the form of figures that
could easily be replaced by a sentence or two of text.

DON'T fill the entire A4 page with the graph leaving little room for axis numeration, axis
titles and the caption. The entire figure should lie within reasonable margins (say 3 cm
margin on the left side, 2 cm margins on the top, bottom and right side of the page).

DON'T extend the axes very far beyond the range of the data. For example, if the data
range between 0 and 78, the axis should extend no further than a value of 80.

DON'T use colour, unless absolutely necessary. It is very expensive, and the costs are
usually passed on to the author. Colour in figures may look good in an assignment or thesis,
but it means redrawing in preparation for publication.

The 10 Commandments for Regression

Tables
These commands are organized according to how controversial I think they might be. If
you are my student or I am your referee these commands are not optional.

1. Report the number of observations, the r-squared, and the root mean squared error
for each regression.
2. Report the dependent variable and the estimation method in the table's caption if it
is common to all specifications or as a column heading if it varies across
specifications.
3. Use self-explanatory labels for your explanatory variables. Cryptic abbreviations or
symbols from the model section force the reader to page back and forth to
understand your results. With five or six columns of regression results there should
be enough room to use words to describe each regressor. Put the symbol used in the
model in parentheses below this.
4. Choose sensible units for variables The coefficients should not be very small (e.g.
0.000032) or very large (e.g. 75432.8). As a rule of thumb, coefficients should only
use the first two or three places to the left or right of the decimal point. One
exception is the case where variables are unit-free because you are estimating a log-
log model. In that case coefficient size is inherently meaningful.
5. The presentation version of the table should be in large type. Don't show a table full
of tiny numbers and say "I know you can't read this but..." If necessary, place some
of you control variables in an auxiliary table so you can focus attention on the
variables of interest.
 6. Put standard errors in the same column as the coefficients. Regression packages put
standard errors along side coefficients as separate columns but you should put each
regression as a single column in your results table. Columns should be used for 4-6
alternative specifications and samples. Thus the standard error (or t-statistic or p-
value if you insist) should appear below the related coefficient in parentheses.
7. Insert tables inside the body of the paper. Journals insist upon tables at the end for
the final submitted version of the paper. This does not mean you should do it for
working papers or first submissions. There is a reason why the printed version of
your article puts the tables back into the text: it is easier to read a paper that way
without having to constantly flip to the end to find results and then flip back to the
text for interpretation. By putting the tables in the text you will also be more aware
of whether your paper has the right mix of text and tabular information.
8. Display standard errors, not t-statistics or p-values Unless the test that the
coefficient is not equal to zero is the only conceivable test of interest, display
standard errors. These give readers a direct view of the precision with which you are
estimating the coefficient. They are useful information for a variety of possible tests
and are still valuable even if the reader prefers not to engage in classical hypothesis
testing at all.
9. Use "a" (1%), "b" (5%), and "c" (10%) superscripts to show statistical significance.
if you show it at all. Using multiple asterisks (***) to display statistical significance
wastes space and gives the impression that you are rating hotels or restaurants. If
you really like asterisks, and there is something to be said for following common
practice (see below), then just pick a level of significance (1, 5, or 10) that seems
appropriate for your study (use 5% as the default) and then use a single asterisk for
that level.
10. Report significance for two-tailed tests only. You may think it is OK to use one-
tailed tests if your theory tells you the sign of the coefficient. However, this
potential justification is overwhelmed by the common practice of using two-tailed
test criteria. Many readers, will view the use of one-tailed tests as a cynical ploy to
exaggerate the significance of your results. Thus, with infinite degrees of freedom,
variables are significant at the 5% level for t-stats over 1.96, NOT 1.645, which is
the critical value of 10% significance in two-tailed tests.

The 10 Commandments for Figures

If you need to satisfy me because I'm your prof or you think I might be a referee, then just
follow the rules. If you want more information about the rationale behind the rules, they are
mainly based on the books by Edward Tufte which are really worth reading for the
examples and interesting discussion.

1. Avoid pie diagrams. Strongly avoid multiple pies. They have a very high ink-to-
information ratio and the eye finds it difficult to rank similar sized areas. People
find it difficult to perceive relative angles which is a key task involved in reading a
pie chart.
2. Use scatterplots. The show relationships in the data. Ideally you will find a way to
illustrate the key relationship in your paper in the form of a scatterplot. Then all the
 rest of your regression tables can show the relationship is robust to more
sophisticated technique.
3. Embed lots of useful information in your scatterplot For instance use different
symbols for points drawn from different samples (e.g. males with squares and
females with circles). Include 45 degree lines or regression lines where it assists in
interpretation. Label outliers.
4. In multiple line figures, label the lines rather than providing a legend . The labels
should be placed where the different curves are furthest from each other to avoid
confusion. It is very annoying to the reader to have to look back and forth, trying to
match patterns with remote legends.
5. Avoid 3d surfaces. Some people think these are cool but most viewers find them
very hard to understand. Paper is two-dimensional. Try to find two-dimensional
ways to illustrate the third dimension in data. Examples include contour lines (like a
topographic map) and multiple small side-by-side figures that are drawn for
different values of a third variable. NEVER use three-dimensional bar diagrams.
The information is uni-dimensional. Standard (2d) bars are OK but the 3d bar
distorts perception, particularly at low levels.
6. Use tables or just the text of the paper for reporting small bits of information . Not
all pictures are worth a thousand words. Some can be replaced entirely with two or
three words. Do so.
7. Think hard about whether it is important to include zero in your axes.
8. Use log scales for strictly positive variables with no natural units, especially when
you care about multiplicative relationships. For example stock prices over long
periods should probably be shown in a log scale so you can interpret the slope as the
rate of change. Almost never show time or shares in log scale since these variables
have natural units.
9. Do your figures in a command language like R (very powerful and free!) or Stata.
These programs take some time to master but it is worthwhile. Most figures done in
Excel are deficient in one way or another.
10. Insert figures inside the body of the paper. Journals insist upon figures at the end for
the final submitted version of the paper. This does not mean you should do it for
working papers or first submissions. There is a reason why the printed version of
your article puts the figures back into the text: it is easier to read a paper that way
without having to constantly flip to the end to find a figure and then flip back to the
text for interpretation. By putting the figures in the text you will also be more aware
of whether your paper has the right mix of text and visual information