How To Write A Thesis (and a
research paper)
Derek Eamus
Outline of today’s talk:
Run through the STRUCTURE of the thesis
Run through the CONTENT of each chapter
Provide some GUIDELINES about GOOD and BAD ways of
writing a thesis
If you only take ONE message home to-day, make sure it is
this one:
START WRITING NOW
YES – Start writing up your data and writing papers in
your 2nd
and 3rd years of enrolment
DO NOT WAIT UNTIL 30 months into the PhD
Please note:
Most of what I say to-day is directly relevant
to writing a research paper
Page 1 of thesis….
Contains:
thesis title
then statement containing:
—degree for which the thesis is submitted
—your name—date submitted and the name and address of
the University
Page 2 of thesis….
Statutory Declaration page
Certify that the work in the thesis is your own, except
where duly acknowledged
Certify that the work has not been submitted for another
degree
Pages 3-5 of thesis…..
Page 3 -Table of contents: page numbers for each section
Page 4 - List of figures and tables with page numbers
Page 5 - List of abbreviations - very important
Page 6
Abstract
Often a word limit - 250 - 500 words
First paragraph - states the aim and field of research
2-6 paragraphs of main results
2 paragraphs of main conclusions
Page 7
Acknowledgements -
you know, thank your mum for having you, your dad for
paying for you, your husband/wife/partner/
boyfriend/girlfriend/dog. Usually say one nice word about
your supervisor, if possible.
Page 8-156
The thesis…..
Two Models
Model A
There are several experimental/observational chapters
Each experimental chapter has its own introduction, M/M,
results, discussion and conclusion
Model A
Each chapter can be viewed as a paper for a journal
The introduction of each experimental chapter defines
the specific topic of inquiry for each chapter and gives the
literature review relevant to the topic in that chapter
Model A
The M/M, results and discussion/conclusion relate only to the work
described in that specific chapter
The first chapter is a general thesis introduction – defines the
broad area of study and introduces the key literature and theory
underpinning the work in the thesis. Defines the hypotheses to be
tested/questions to be asked.
Model A
The last chapter in the final discussion and conclusions and draws
together the different findings from each of the experimental
chapters. This chapter discusses what further work would be done
if time allowed.
Model B
There is one Introductory chapter, one M/M chapter, one Results
chapter, a Discussion and a Conclusion chapter. The whole thesis can
be viewed as a single paper.
The M/M chapter gives ALL the M/M details for ALL the work
described in the thesis. Similarly the results chapter gives all the
results presented in the thesis.
Which Model?
Both models are acceptable
For an experimental science such as physiology, ecology,
biochemistry, etc, I much prefer model A. It is easier to
think about ‗bite-size chunks‘ of work (ie each individual
chapter).
Chapter One - Three parts
Part One
Introduce the reader to the ENTIRE subject area of the thesis
Define the outer boundaries of the thesis
Define the major underlying theories of the field of study
Provide the underlying RATIONALE of the work described in the
thesis
Define the key terms that describe the field of study. For
example, a thesis on CHILLING INJURY of PLANTS will have
subsections in Chapter 1 that :
–define chilling injury
–describe symptoms of chilling injury
–provide a synopsis of each of the current PARADIGMS that have
credence in the field of chilling injury research.
Part Two
Put the work described in the thesis into context using
what others have done
Tell the reader what was done in the past 5 years that
resulted in you deciding that the work in the thesis was
worth doing
Part Three
Define the hypotheses you will test, or the questions you
will address
Note the overall structure here – start out with the big
picture stuff. Define the broad boundaries of the field of
study
Chapter Two: Experimental/observational chapter
Chapter Two is the first experimental/observational chapter
There will be an INTRODUCTION for this chapter
The introduction is SPECIFIC to the work described in this
chapter
Chapter Two – Introduction
There are two major pre-requisites to writing a good
introduction
First, a detailed knowledge of the literature
Second, a clear picture in your mind before you start
writing, of the story you want to tell
What is the BACKGROUND to the work described in this
chapter?
For example – in a chapter on ―Impacts of acid rain on
photosynthetic rates of trees‖ we would
(a) refer to classic papers that document the existence of acid rain
in 3 or 4 countries;
(b) refer to papers that show acid rain in those 3 or 4 countries is
damaging trees structurally, physiologically and in other ways.
What work has been done in the recent past that led you to do the
work in this chapter? For example:
(a) Show that acid rain reduces growth rate, reduces chlorophyll
content and influences stomatal aperture
(b) Therefore, since all three factors influence photosynthesis or
reflect a change in carbon economy, we would conclude that looking
at acid rain and photosynthesis is a logical extension of this
previous work
Lead the reader logically and concisely from a set of
previous observations to the hypothesis that you will test in
this chapter
For example……
―Stomata of leaves close in response to water stress (ref.) and also
in response to external applications of the plant hormone, abscisic
acid (ref.). We hypothesise that water stress results in stomatal
closure by causing an accumulation of abscisic acid in the leaf.
Therefore we shall measure changes in foliar abscisic acid levels
during a period of water stress in three species.‖
Note the structure –
X found A, and Y found B.
Putting result A and B together, we predict C, which we
test by method M
A chapter will often address three or four hypotheses, using a
common set of related methods
The hypothesis must be explicitly stated and each hypothesis will
have detailed rationale as to why this hypothesis is being tested- ie
what led you to think that this hypothesis was worth looking at
Hypotheses are sometimes replaced by ―questions
addressed‖. I prefer hypotheses tested. Either, though,
must be explicitly stated
Chapter Two - Materials and Methods
This is often the easiest part to write, so it is often
good to start with this section first
Use sub-sections - eg:site
climate
species studied (species names in italics AND taxonomic authorities
provided)
growth conditions
measurements made
statistical tests applied
For fieldwork:
give dates
give map/GPS references for sites
state number of replicates at each level (leaf, tree, plot,
site and treatments)
For equipment used, give:
manufacturer
country of origin
model number
For a commonly used method, cite two or three references
that describe the method - no need to describe old
methods that have been used for the past 5-50 years and
which are well accepted and understood
State the details required for someone to be able to
replicate the experiment –
Eg: pot size, growth medium used, voltage used on the
electrophoresis system, concentration of pollutant added to
the water (tap water? RO water? Triple distilled water?
Seawater? - synthetic or taken from which site, how
stored, for how long?)
How many replicates were used?
What age animals?
How often were measurements made - hourly, monthly?
Statistical Design - randomised plot? Linear
regression? ANOVAR? What software was used? What
version? What level of significance was accepted? Which
transforms were used to correct for homogeneity of
variance? What tests were done to check for homogeneity
of variance?
Chapter Two – Results
Results are obviously important
There are TWO, inter-weaving parts to a results
section
Chapter Two - Results - Part One
Set of TABLES and FIGURES
Tables and figures are numbered sequentially throughout
the thesis - a good way to do this is Fig 2.1, Fig 2.2, Fig 2.X,
Fig 3.1, Fig 3.2 etc. The first number refers to the chapter
number, the second refers to the figure number
Set of TABLES and FIGURES
Tables and figures must have a legend that is self
explanatory and which defines any abbreviations and
symbols used in the figure/table
Tables - all columns must have headings and units
Figures - axes labeled and units given
Chapter Two - Results - Part Two
Written description of the data
Tell the reader what you want him/her to get from the data
State which differences are significant
Highlight the important trends and differences/comparisons
Take the reader by the hand and lead them gently through the
data, starting at Figure 1! (Yes - some people start with Fig #3)
State three things about the results:
First -
what was the observed trend in y as a function of x?
State what the trend was (eg: linearly increased; declined
asymptotically; etc)
Second -
what was the difference between the control and the treatment-
was it the FORM of the relationship, or
the slope of the response, or the magnitude of the change in what
was measured.
DO NOT SAY that the control and treated fish differed in length
TELL the reader that the control fish were 23% longer than the
treated fish
Third -
state the statistical significance level of the difference,
eg P<0.05
Do NOT omit some valid and useful comparisons -
for example….
Table 1 – a comparison of the quantum yield of two species
measures in January and July. Data are means, standard error.
Means followed by the same letter are not significantly different
from each other.
Quantum yield
January July
Species 1 0.05 + 0.00001 a 0.04 + 0.000014 b
Species 2 0.03 + 0.000015 c 0.0225 + 0.00010 d
A typical description of these data (PLEASE NOTE - the word
DATA is PLURAL, so these data, NOT this data) might be:
―Both species 1 and 2 showed a significant decline in quantum yield
between January and July. In addition, species 1 maintained a larger
quantum yield at both times of the year than species 2.‖
Is this an adequate description of the results? NO.
Table 1 – a comparison of the quantum yield of two species
measures in January and July. Data are means, standard error.
Means followed by the same letter are not significantly different
from each other.
Quantum yield
January July
Species 1 0.05 + 0.00001 a 0.04 + 0.000014 b
Species 2 0.03 + 0.000015 c 0.0225 + 0.00010 d
Why not?
Because it misses an interesting point - that the
percentage decline in quantum yield between January and
July is much larger in species 2 than in species 1, even
though the absolute decline is larger in species 1
A better table would show this:
Quantum yield
January July Percentage decli
between Jan and J
Species 1 0.05 + 0.00001 a 0.04 + 0.000014 b 20
Species 2 0.03 + 0.000015 c 0.0225 + 0.00010 d 25
So - don‘t omit meaningful comparisons in your data. I
stress the word MEANINGFUL.
A common error is to include a figure or table and then
not to write about it in the results section. DO NOT do this!
Think about the sequence in which you present the data.
Think about the NARRATIVE TALE that you wish to tell.
Have the results in a logical, meaningful sequence. It might
be that you don‘t present the data in the order that you
obtained it.
Chapter Two - Discussion and Conclusion
This is where people have the most problem -
why?
BECAUSE THEY DON‘T DRAW UP A
SKELETON/FRAMEWORK BEFORE THEY START
WRITING THE DISCUSSION
A small effort now, in arranging the discussion in skeleton format,
will save much work later on
Chapter Two – Discussion
You need two things:
First - an intimate knowledge of the literature
Second - an intimate knowledge of your data
With regard to the literature - for each of the papers
that you will cite in this chapter, have the papers out with
you as you write. This will speed things up. You may have a
pile of 30-60 papers with you………. Or….
………. Even better, have your notes taken from the paper
with you - printed from your bibliography software.
For the framework -
here is how I do it…
First - deal with the trivia - for example:
where we grow plants
deal with the fact that CO2 enrichment chambers were identical to
each other - refer to the data that show the microclimate in each
chamber was the same.
This is trivial in the sense that it does not relate directly to the
AIMS, but it is a necessary consideration before discussing the
result.
Get this stuff out of the way first.
Second - decide, before you start writing, the story you believe
the data show. You must have a sense of narrative before you write
Third - construct a framework on paper. Do this by:
Writing 2 sentences for each key result. Order them into
the correct sequence for the story. Don‘t put unrelated
results next to each other.
If the results don‘t link with each other - it‘s a bad paper
you are trying to write. Stop now!
Highlight, in a few words for each, the LINKS between the
different sets of data you have presented
Look for mutually supportive data links and also internal
inconsistencies. Make a list of both - you will have to deal
with both in the discussion
Draw a flow diagram of results and links
Highlight internal consistencies and
inconsistencies in your data sets …………
Eg : you find that growth rate of treatment 1 was higher than
treatment 2, and that treatment 1 had a higher rate of
photosynthesis
but a lower leaf N content than treatment 2,
then the growth rate result is consistent with the photosynthesis
results BUT INCONSISTENT with the foliar N data. You will have
to refer to both of these facts
Start to develop the arguments for the story you
wish to tell…….
Eg:
in an experiment in which acid rain (which contains N) was
sprayed on trees and the growth, foliar N content and rate
of photosynthesis were measured, we might say:
“ The rate of light-saturated photosynthesis increased in response to acid rain input.
If this increase was maintained at all light levels, the increase in C supply would be
expected to increase the rate of growth of trees treated with acid rain, as was
observed (Table 1). Increased foliar N content is associated with an increased rate
of photosynthesis (ref), as was observed in the present study (Table 2). It is
concluded that the N present in the acid rain treatment increased foliar N content
and hence the rate of photosynthesis and subsequent growth rate.”
NOTE THE FOLLOWING POINTS:
If you use comparative statements (eg ‗larger than‘ or ‗smaller
than‘) then you must define both sides of the statement - ie say
that X is larger than Y. Don‘t just say X is larger - it begs the
question - larger than what?
Cite references to support statements
Keep sentences and paragraphs small and don‘t be verbose.
For example:
it has been previously shown that X increases with increased Y….
This is verbose.
replace with ―X increased with increased Y‖ (so delete the ―it has
previously been shown‖)
Keep sentences and paragraphs small and don‘t be verbose.
For example:
look at what you write and see how many words and phrases are
actually redundant or can be reduced
A common structure for a PARAGRAPH:
State the result (or set of 2 or 3 related results) that you wish to
discuss in this paragraph, at the start of the paragraph. No need for
stats, they are in the results section
Note: 1 paragraph = 1 major point to discuss
Now - has anyone found the same? If yes - cite 2 references that
support your finding. If no - great - something to discuss
If no one else has found that result - INTERPRET it:
What does this result mean, from the perspective of the plant,
ecosystem, management technique you are investigating?
What are the ramifications of this result? How does this result
relate to the stated hypotheses/ questions you are addressing?
If no one else has found that result - INTERPRET it:
Is it possible you have made a methodological/ analytical
mistake?
What do you conclude from your result?
Ask yourself - do(es) the result(s) you are discussing in
this paragraph support or refute what others have found?
If the results support others, cite a few references to
show this.
If the result is in contradiction to what others have found, discuss
this fact.
Why is there a contradiction? What does it mean if you are right
and the others are wrong? How might you explain that both your
results and those of others are both correct? Is it a different
species/ ecosystem/ climate/ chemical? Different temperature/
light/method of analyses?
Each paragraph contains a linked set of
interdependent one, two or three results, which,
when put into the correct sequence and structure
leads the reader through the following sequence of
thoughts:
W h a t w a s fo u n d ? H o w d o e s th is c o m p a re w ith
(T h is is a s u b -s e t o f w h a t o th e rs fo u n d ?
a ll th e re s u lts )
W h a t is n e w a b o u t th is
s e t o f re s u lts (w h y s h o u ld
W h a t re s u lts a re m u tu a lly
th e y b e p u b lis h e d ? )
s u p p o rtiv e a n d w h ic h a re
c o n tra d ic to ry ? H o w d o I
e x p la in in te rn a l
c o n tra d ic tio n s in m y d a ta ?
H o w d o I e x p la in
a n y c o n tra d ic tio n s
b e tw e e n m y w o rk
a n d th a t o f o th e rs ?
W h a t im p o rta n t
c o n c lu s io n d o I w a n t to
m a k e fro m th is p a ra g ra p h ?
Chapter Two – Conclusions
Address the following points in this section:
Have the results supported or refuted your hypotheses?
Have you answered ALL of your original questions?
Address the following points in this section:
What additional information would you need to collect to resolve
internal inconsistencies or overcome limitations in your data? Can
these be obtained relatively quickly?
Have you resolved the conflict between your data and the data of
others?
Last Chapter
This is the FINAL Discussion and Conclusion
It brings all the results together and makes the
final big story
It asks (and answers) the questions:
Did the thesis actually address the questions/ hypotheses
outlined in Chapter One?
What next? What work would be needed to bring this
story to a close
Now What?
Put the chapter you‘ve just written away for 10 days
Re-read every paragraph critically. Ask yourself
the following questions:
Does the writing lead the reader along a simple logical path
from an observation, by way of discussion, involving
comparing your data with others and discussing similarities
and differences, and INTERPRETING the results?
A common mistake with discussions is to make it
merely a re-statement of results. This is not good!
Are any sentences more than 25 words? Can they be
shortened?
Are there any paragraphs more than 200 words
long? Can they be shortened or turned into two
paragraphs?
What is the conclusion you want the reader to reach
in each paragraph? Is it explicitly stated?
NOW -
some style pointers
Reference Lists
There are many styles - decide on the journal of your
choice and FOLLOW their RULES COMPLETELY
A typical reference list structure is:
Name, initial., name, initial. (date). Title of paper.
Journal name volume No, pp.
Is the date in (brackets), or not? Is there a full stop after
the date?
Are the journal names in full or abbreviated? Are the
journal names italicised? Is there a comma after the journal
name?
Is the volume number in bold?
Note the dot comma after the initials in the authors
Books need publisher and place of publication
In the text, are references listed alphabetically or chronologically?
For example:
(Jones 1986, Williams 1980)
or
(Williams 1980, Jones 1986)
Are references separated by a comma, or semi-colon, in the text?
Is ‗et al‘ italicised, and does it have a full stop after?
Writing Guides
The word data is PLURAL so should be followed by the word ARE
not IS
Use the past tense in papers to refer to work described in the
paper
The word ‗however‘ is usually followed by a comma. The phrase ―
―However, it was removed…..‖
is not the same as
―However it was removed…..‖
The phrase:
―Figure 3 presents the relationship between stomatal aperture and
transpiration rate‖
is better written as
―Transpiration rate increased with increasing aperture (Fig 3)‖
because:
(a) it is shorter and more concise
(b) the first version tells us nothing about the relationship between
the two variables, but the second version is explicit about the
relationship
Remove excess verbage at all costs, eg:
It can be seen that…..
It is known that…..
The present study shows that…..
Reports on savannas worldwide indicate that…..
Comparative evaluation of the total leaf area of the two species
shown in Table 3 reveals that….
Avoid colloquialisms and slang
Make the subject and object agree and make the
tenses agree, within a sentence. For example:
―The seven books found on the shelf, stacked into a
neat pile, is unlikely to remain untouched in the
future‖
What is wrong with this sentence?
First - the ‗seven books‘ are plural, so it should be ‗….are
unlikely…‘
Second - the use of two negatives which causes confusion
- unlikely and untouched
Another example:
― This study is funded by the CRC for Tropical Savannas.
We were also ably supported by the technical assistance of
Fred.‖
First problem - the study WAS funded by the CRC
Second problem - the ‗is‘ (present tense) does not agree
with the ‗were‘ (past tense)
The word fewer is NOT the same as the word LESS.
Use fewer for comparing discontinuous variables, use
less for continuous variables
Most sentences with commas in should have two
commas present
How to Write a Paper – some
additional notes
Format
Type the MS in double space
Study and memorise the rules for authors for the journal,
especially:
page size, margins
section headings and subsection headings for bold, UPPER CASE, underlined
etc
the use of et al. - is it every time a paper is cited with more than two authors,
or do you cite the full author list the first time the citation appears in the
text?
Check figure and table structure - legend on the same page or
separate page?
Should the table have vertical and horizontal lines separating each
column and row?
Should figures have all 4 sides boxed in or only the x and y axes
drawn? Should ticks go in or out?
Should pages be numbered?
Structure
Title Page:
Title (check style)
Authors (check style)
Address - dept/school, faculty, university, PO Box etc
Key Words 2-6 words that describe the content
Running title - not all journals want these, limited to 4-6 words to appear at
the top of each page
Date of submission
Abstract - on its own page
Introduction
Materials and Methods - less detail than a thesis
Results - selective, not all results included
Discussion and Conclusions
Reference List
The End…………..