How to Write a PhD Thesis 0

How to Write a PhD Thesis
some notes by
Joe Wolfe
School of Physics
The University of New South Wales
Sydney 2052 Australia
Spanish version: CÛmo escribir una tesis de doctorado
French version: Comment rediger une thèse
This guide to thesis writing gives some simple and practical advice on the problems of getting
started, getting organized, dividing the huge task into less formidable pieces and working on
those pieces. It also explains the practicalities of surviving the ordeal. It includes a suggested
structure and a guide to what should go in each section. It was originally written for graduate
students in physics, and most of the specific examples given are taken from that discipline.
Nevertheless, the feedback from users indicates that it has been consulted and appreciated by
graduate students in diverse fields in the sciences and humanities.
l Getting started
m An outline
m Organisation
m Word processors
m A timetable
m Iterative solution
l What is a thesis? For whom is it written? How should it be written?
m How much detail?
m Make it clear what is yours
m Style
m Presentation
m How many copies?
m Personal
m Coda
l Thesis Structure
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How to Write a PhD Thesis
l How to survive a thesis defence
Getting Started
When you are about to begin, writing a thesis seems a long, difficult task. That is because it is a
long, difficult task. Fortunately, it will seem less daunting once you have a couple of chapters
done. Towards the end, you will even find yourself enjoying it---an enjoyment based on
satisfaction in the achievement, pleasure in the improvement in your technical writing, and of
course the approaching end. Like many tasks, thesis writing usually seems worst before you
begin, so let us look at how you should make a start.
An outline
First make up a thesis outline: several pages containing chapter headings, sub-headings, some
figure titles (to indicate which results go where) and perhaps some other notes and comments.
There is a section on chapter order and thesis structure at the end of this text. Once you have a
list of chapters and, under each chapter heading, a reasonably complete list of things to be
reported or explained, you have struck a great blow against writer's block. When you sit down to
type, your aim is no longer a thesis---a daunting goal---but something simpler. Your new aim is
just to write a paragraph or section about one of your subheadings. It helps to start with an easy
one: this gets you into the habit of writing and gives you self-confidence. Often the Materials
and Methods chapter is the easiest to write---just write down what you did; carefully, formally
and in a logical order.
How do you make an outline of a chapter? For most of them, you might try the method that I use
for writing papers, and which I learned from my thesis adviser: assemble all the figures that you
will use in it and put them in the order that you would use if you were going to explain to
someone what they all meant. You might as well rehearse explaining it to someone else---after
all you will probably give several talks based on your thesis work. Once you have found the
most logical order, note down the the key words of your explanation. These key words provide a
skeleton for much of your chapter outline.
Once you have an outline, discuss it with your adviser. This step is important: s/he will have
useful suggestions, but it also serves notice that s/he can expect a steady flow of chapter drafts
that will make high priority demands on his/her time. Once you and your adviser have agreed on
a logical structure, s/he will need a copy of this outline for reference when reading the chapters
which you will probably present out of order. If you have a co-adviser, discuss the outline with
him/her as well, and present all chapters to both advisers for comments.
Organisation
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How to Write a PhD Thesis
It is encouraging and helpful to start a filing system. Open a word-processor file for each chapter
and one for the references. You can put notes in these files, as well as text. While doing
something for Chapter n, you will think "Oh I must refer back to/discuss this in Chapter m" and
so you put a note to do so in the file for Chapter m. Or you may think of something interesting or
relevant for that chapter. When you come to work on Chapter m, the more such notes you have
accumulated, the easier it will be to write.
Make a back-up of these files and do so every day at least (depending on the reliability of your
computer and the age of your disk drive). Do not keep back-up disks close to the computer in
case the hypothetical thief who fancies your computer decides that s/he could use some disks as
well.
A simple way of making a remote back-up is to send it as an email attachment to a consenting
email correspondent, preferably one in a different location. You could even send it to yourself if
your server saves your mail (in some email packages like Eudora this is an optional setting). In
either case, be careful to dispose of superseded versions so that you don't waste disk space,
especially if you have bitmap images or other large files.
You should also have a physical filing system: a collection of folders with chapter numbers on
them. This will make you feel good about getting started and also help clean up your desk. Your
files will contain not just the plots of results and pages of calculations, but all sorts of old notes,
references, calibration curves, suppliers' addresses, specifications, speculations, letters from
colleagues etc., which will suddenly strike you as relevant to one chapter or other. Stick them in
that folder. Then put all the folders in a box or a filing cabinet. As you write bits and pieces of
text, place the hard copy, the figures etc in these folders as well. Touch them and feel their
thickness from time to time---ah, the thesis is taking shape.
If any of your data exist only on paper, copy them and keep the copy in a different location.
Consider making a copy of your lab book. This has another purpose beyond security: usually the
lab book stays in the lab, but you may want a copy for your own future use. Further, scientific
ethics require you to keep lab books and original data for at least ten years, and a copy is more
likely to be found if two copies exist.
While you are getting organised, you should deal with any university paperwork. Examiners
have to be nominated and they have to agree to serve. Various forms are required by your
department and by the university administration. Make sure that the rate limiting step is your
production of the thesis, and not some minor bureaucratic problem.
A note about word processors
Commercial word processors have gradually become bigger, slower, less reliable and harder to
use as they acquire more features. This is a general feature of commerical software and an
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How to Write a PhD Thesis
important input to Moore's Law. If software and operating performance did not deteriorate,
people would not need to buy new computers and profits would fall for makers of both hard- and
soft-ware. Software vendors want it to look fancy and obvious in the demo, and they don't really
care about its ease, speed and reliability to an expert user because the expert user has already
bought it. For example, it is much faster to type equations and to do formatting with embedded
commands because you use your fingers independently rather than your hand and because your
fingers don't leave the keyboard. However, click-on menus, however slow and cumbersome,
look easy to use in the shop.
LaTeX is powerful, elegant, reliable, fast and free from http://www.latex-project.org/ or
http://www.miktex.org/. An alternative is to use old versions of commercial software. Word 5
allows equations to be typed without touching the mouse and is as fast in this respect as LaTeX.
Sites exist to provide discontinued software to people who are interested in speed and reliability,
but, not knowing the legality of what they do, I shaln't link to them.
A timetable
I strongly recommend sitting down with the adviser and making up a timetable for writing it: a
list of dates for when you will give the first and second drafts of each chapter to your adviser(s).
This structures your time and provides intermediate targets. If you merely aim "to have the
whole thing done by (some distant date)", you can deceive yourself and procrastinate more
easily. If you have told your adviser that you will deliver a first draft of chapter 3 on Wednesday,
it focuses your attention.
You may want to make your timetable into a chart with items that you can check off as you have
finished them. This is particularly useful towards the end of the thesis when you find there will
be quite a few loose ends here and there.
Iterative solution
Whenever you sit down to write, it is very important to write something. So write something,
even if it is just a set of notes or a few paragraphs of text that you would never show to anyone
else. It would be nice if clear, precise prose leapt easily from the keyboard, but it usually does
not. Most of us find it easier, however, to improve something that is already written than to
produce text from nothing. So put down a draft (as rough as you like) for your own purposes,
then clean it up for your adviser to read. Word-processors are wonderful in this regard: in the
first draft you do not have to start at the beginning, you can leave gaps, you can put in little notes
to yourself, and then you can clean it all up later.
Your adviser will expect to read each chapter in draft form. S/he will then return it to you with
suggestions and comments. Do not be upset if a chapter---especially the first one you write---
returns covered in red ink. Your adviser will want your thesis to be as good as possible, because
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How to Write a PhD Thesis
his/her reputation as well as yours is affected. Scientific writing is a difficult art, and it takes a
while to learn. As a consequence, there will be many ways in which your first draft can be
improved. So take a positive attitude to all the scribbles with which your adviser decorates your
text: each comment tells you a way in which you can make your thesis better.
As you write your thesis, your scientific writing is almost certain to improve. Even for native
speakers of English who write very well in other styles, one notices an enormous improvement
in the first drafts from the first to the last chapter written. The process of writing the thesis is like
a course in scientific writing, and in that sense each chapter is like an assignment in which you
are taught, but not assessed. Remember, only the final draft is assessed: the more comments your
adviser adds to first or second draft, the better.
Before you submit a draft to your adviser, run a spell check so that s/he does not waste time on
those. If you have any characteristic grammatical failings, check for them.
What is a thesis? For whom is it written? How
should it be written?
Your thesis is a research report. The report concerns a problem or series of problems in your area
of research and it should describe what was known about it previously, what you did towards
solving it, what you think your results mean, and where or how further progress in the field can
be made. Do not carry over your ideas from undergraduate assessment: a thesis is not an answer
to an assignment question. One important difference is this: the reader of an assignment is
usually the one who has set it. S/he already knows the answer (or one of the answers), not to
mention the background, the literature, the assumptions and theories and the strengths and
weaknesses of them. The readers of a thesis do not know what the "answer" is. If the thesis is for
a PhD, the university requires that it make an original contribution to human knowledge: your
research must discover something hitherto unknown.
Obviously your examiners will read the thesis. They will be experts in the general field of your
thesis but, on the exact topic of your thesis, you are the world expert. Keep this in mind: you
should write to make the topic clear to a reader who has not spent most of the last three years
thinking about it.
Your thesis will also be used as a scientific report and consulted by future workers in your
laboratory who will want to know, in detail, what you did. Theses are occasionally consulted by
people from other institutions, and the library sends microfilm versions if requested (yes, still).
More and more theses are now stored in an entirely digital form (i.e. the figures as well as the
text are on a disk). A consequence of this is that your thesis can be consulted much more easily
by researchers around the world. Write with these possibilities in mind.
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It is often helpful to have someone other than your adviser(s) read some sections of the thesis,
particularly the introduction and conclusion chapters. It may also be appropriate to ask other
members of staff to read some sections of the thesis which they may find relevant or of interest,
as they may be able to make valuable contributions. In either case, only give them revised
versions, so that they do not waste time correcting your grammar, spelling, poor construction or
presentation.
How much detail?
The short answer is: rather more than for a scientific paper. Once your thesis has been assessed
and your friends have read the first three pages, the only further readers are likely to be people
who are seriously doing research in just that area. For example, a future research student might
be pursuing the same research and be interested to find out exactly what you did. ("Why doesn't
the widget that Bloggs built for her project work any more? Where's the circuit diagram? I'll look
up her thesis." "Blow's subroutine doesn't converge in my parameter space! I'll have to look up
his thesis." "How did that group in Sydney manage to get that technique to work? I'll order a
microfilm of that thesis they cited in their paper.") For important parts of apparatus, you should
include workshop drawings, circuit diagrams and computer programs, usually as appendices.
(By the way, the intelligible annotation of programs is about as frequent as porcine aviation, but
it is far more desirable. You wrote that line of code for a reason: at the end of the line explain
what the reason is.) You have probably read the theses of previous students in the lab where you
are now working, so you probably know the advantages of a clearly explained, explicit thesis
and/or the disadvantages of a vague one.
Make it clear what is yours
If you use a result, observation or generalisation that is not your own, you must usually state
where in the scientific literature that result is reported. The only exceptions are cases where
every researcher in the field already knows it: dynamics equations need not be followed by a
citation of Newton, circuit analysis does not need a reference to Kirchoff. The importance of this
practice in science is that it allows the reader to verify your starting position. Physics in
particular is said to be a vertical science: results are built upon results which in turn are built
upon results etc. Good referencing allows us to check the foundations of your additions to the
structure of knowledge in the discipline, or at least to trace them back to a level which we judge
to be reliable. Good referencing also tells the reader which parts of the thesis are de***ions of
previous knowledge and which parts are your additions to that knowledge. In a thesis, written for
the general reader who has little familiarity with the literature of the field, this should be
especially clear. It may seem tempting to leave out a reference in the hope that a reader will
think that a nice idea or an nice bit of analysis is yours. I advise against this gamble. The reader
will probably think: "What a nice idea---I wonder if it's original?". The reader can probably find
out via the library, the net or even just from a phone call.
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If you are writing in the passive voice, you must be more careful about attribution than if you are
writing in the active voice. "The sample was prepared by heating yttrium..." does not make it
clear whether you did this or whether Acme Yttrium did it. "I prepared the sample..." is clear.
Style
The text must be clear. Good grammar and thoughtful writing will make the thesis easier to read.
Scientific writing has to be a little formal---more formal than this text. Native English speakers
should remember that scientific English is an international language. Slang and informal writing
will be harder for a non-native speaker to understand.
Short, simple phrases and words are often better than long ones. Some politicians use "at this
point in time" instead of "now" precisely because it takes longer to convey the same meaning.
They do not care about elegance or efficient communication. You should. On the other hand,
there will be times when you need a complicated sentence because the idea is complicated. If
your primary statement requires several qualifications, each of these may need a subordinate
clause: "When [qualification], and where [proviso], and if [condition] then [statement]". Some
lengthy technical words will also be necessary in many theses, particularly in fields like
biochemistry. Do not sacrifice accuracy for the sake of brevity. "Black is white" is simple and
catchy. An advertising copy writer would love it. "Objects of very different albedo may be
illuminated differently so as to produce similar reflected spectra" is longer and uses less common
words, but, compared to the former example, it has the advantage of being true. The longer
example would be fine in a physics thesis because English speaking physicists will not have
trouble with the words. (A physicist who did not know all of those words would probably be
glad to remedy the lacuna either from the context or by consulting a dictionary.)
Sometimes it is easier to present information and arguments as a series of numbered points,
rather than as one or more long and awkward paragraphs. A list of points is usually easier to
write. You should be careful not to use this presentation too much: your thesis must be a
connected, convincing argument, not just a list of facts and observations.
One important stylistic choice is between the active voice and passive voice. The active voice ("I
measured the frequency...") is simpler, and it makes clear what you did and what was done by
others. The passive voice ("The frequency was measured...") makes it easier to write
ungrammatical or awkward sentences. If you use the passive voice, be especially wary of
dangling participles. For example, the sentence "After considering all of these possible materials,
plutonium was selected" implicitly attributes consciousness to plutonium. This choice is a
question of taste: I prefer the active because it is clearer, more logical and makes attribution
simple. The only arguments I have ever heard for avoiding the active voice in a thesis are (i)
many theses are written in the passive voice, and (ii) some very polite people find the use of "I"
immodest. Use the first person singular, not plural, when reporting work that you did yourself:
the editorial 'we' may suggest that you had help beyond that listed in your aknowledgements, or
it may suggest that you are trying to share any blame. On the other hand, retain plural verbs for
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"data": "data" is the plural of "datum", and lots of scientists like to preserve the distinction. Just
say to yourself "one datum is ..", "these data are.." several times. An excellent and widely used
reference for English grammar and style is A Dictionary of Modern English Usage by H.W.
Fowler.
Presentation
There is no need for a thesis to be a masterpiece of desk-top publishing. Your time can be more
productively spent improving the content than the appearance.
In many cases, a reasonably neat diagram can be drawn by hand faster than with a graphics
package. Either is usually satisfactory. The computer-generated figure has the advantage that it
can be stored in the text and transmitted electronically, but this advantage disappears if you are
not going to store your thesis as a file for transmission. You can scan a hand drawn figure. As a
one bit, moderate resolution graphic, it will probably not be huge, but it will still be bigger than a
line drawing generated on a graphics package.
In general, students spend too much time on diagrams---time that could have been spent on
examining the arguments, making the explanations clearer, thinking more about the significance
and checking for errors in the algebra. The reason, of course, is that drawing is easier than
thinking.
I do not think that there is a strong correlation (either way) between length and quality. There is
no need to leave big gaps to make the thesis thicker. Readers will not appreciate large amounts
of vague or unnecessary text.
Approaching the end
A deadline is very useful in some ways. You must hand in the thesis, even if you think that you
need one more draft of that chapter, or someone else's comments on this section, or some other
refinement. If you do not have a deadline, or if you are thinking about postponing it, please take
note of this: A thesis is a very large work. It cannot be made perfect in a finite time. There will
inevitably be things in it that you could have done better. There will be inevitably be some typos.
Indeed, by some law related to Murphy's, you will discover one when you first flip open the
bound copy. No matter how much you reflect and how many times you proof read it, there will
be some things that could be improved. There is no point hoping that the examiners will not
notice: many examiners feel obliged to find some examples of improvements (if not outright
errors) just to show how thoroughly they have read it. So set yourself a deadline and stick to it.
Make it as good as you can in that time, and then hand it in! (In retrospect, there was an
advantage in writing a thesis in the days before word processors, spelling checkers and typing
programs. Students often paid a typist to produce the final draft and could only afford to do that
once.)
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