Spanish
version: CÛmo escribir una tesis de doctorado French
version: Comment rediger une thèse 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
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
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 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.
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 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.
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.
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 descriptions
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.
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 "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.
Whatever the University's policy on single or double-sided copies, the distribution copies could be double-sided so that forests and postage accounts are not excessively depleted by the exercise. Your adviser could help you to make up a list of interested and/or potentially useful people for such a mailing list. Your adviser might also help by funding the copies and postage if they are not covered by your scholarship.
The following comment comes from Marilyn Ball of the Australian National University in Canberra: "When I finished writing my thesis, a postdoc wisely told me to give a copy to my parents. I would never have thought of doing that as I just couldn't imagine what they would do with it. I'm very glad to have taken that advice as my parents really appreciated receiving a copy and proudly displayed it for years. (My mother never finished high school and my father worked with trucks - he fixed 'em, built 'em, drove 'em, sold 'em and junked 'em. Nevertheless, they enjoyed having a copy of my thesis.)"
Personal
In the ideal situation, you will be able to spend a large
part---perhaps a majority---of your time writing your thesis. This may be bad
for your physical and mental health.
If you do not touch type, you should learn to do so for the sake of your neck as well as for productivity. There are several good software packages that teach touch typing interactively. If you use one for say 30 minutes a day for a couple of weeks, you will be able to touch type. By the time you finish the thesis, you will be able to touch type quickly and accurately and your six hour investment will have paid for itself. Be careful not to use the typing exercises as a displacement activity.
Coda
Keep going---you're nearly there! Most PhDs will admit that
there were times when we thought about reasons for not finishing. But it would
be crazy to give up at the writing stage, after years of work on the research,
and it would be something to regret for a long time.
Writing a thesis is tough work. One anonymous post doctoral researcher told me: "You should tell everyone that it's going to be unpleasant, that it will mess up their lives, that they will have to give up their friends and their social lives for a while. It's a tough period for almost every student." She's right: it is certainly hard work, it will be probably be stressful and you will have to adapt your rhythm to it. It is also an important rite of passage and the satisfaction you will feel afterwards is wonderful. On behalf of scholars everywhere, I wish you good luck!
A suggested thesis structure
The list of contents and chapter
headings below is appropriate for some theses. In some cases, one or two of
them may be irrelevant. Results and Discussion are usually combined in several
chapters of a thesis. Think about the plan of chapters and decide what is best
to report your work. Then make a list, in point form, of what will go in each
chapter. Try to make this rather detailed, so that you end up with a list of
points that corresponds to subsections or even to the paragraphs of your
thesis. At this stage, think hard about the logic of the presentation: within
chapters, it is often possible to present the ideas in different order, and
not all arrangements will be equally easy to follow. If you make a plan of
each chapter and section before you sit down to write, the result will
probably be clearer and easier to read. It will also be easier to write.
Especially in the introduction, do not overestimate the reader's familiarity with your topic. You are writing for researchers in the general area, but not all of them need be specialists in your particular topic. It may help to imagine such a person---think of some researcher whom you might have met at a conference for your subject, but who was working in a different area. S/he is intelligent, has the same general background, but knows little of the literature or tricks that apply to your particular topic.
The introduction should be interesting. If you bore the reader here, then you are unlikely to revive his/her interest in the materials and methods section. For the first paragraph or two, tradition permits prose that is less dry than the scientific norm. If want to wax lyrical about your topic, here is the place to do it. Try to make the reader want to read the kilogram of A4 that has arrived uninvited on his/her desk. Go to the library and read several thesis introductions. Did any make you want to read on? Which ones were boring?
This section might go through several drafts to make it read well and logically, while keeping it short. For this section, I think that it is a good idea to ask someone who is not a specialist to read it and to comment. Is it an adequate introduction? Is it easy to follow? There is an argument for writing this section---or least making a major revision of it---towards the end of the thesis writing. Your introduction should tell where the thesis is going, and this may become clearer during the writing.
Ideally, you will already have much of the hard work done, if you have been keeping up with the literature as you vowed to do three years ago, and if you have made notes about important papers over the years. If you have summarised those papers, then you have some good starting points for the review.
How many papers? How relevant do they have to be before you include them? Well, that is a matter of judgement. On the order of a hundred is reasonable, but it will depend on the field. You are the world expert on the (narrow) topic of your thesis: you must demonstrate this.
A political point: make sure that you do not omit relevant papers by researchers who are like to be your examiners, or by potential employers to whom you might be sending the thesis in the next year or two.
One is that a thesis is both allowed and expected to have more detail than a journal article. For journal articles, one usually has to reduce the number of figures. In many cases, all of the interesting and relevant data can go in the thesis, and not just those which appeared in the journal. The degree of experimental detail is usually greater in a thesis. Relatively often a researcher requests a thesis in order to obtain more detail about how a study was performed.
Another disadvantage is that your journal articles may have some common material in the introduction and the "Materials and Methods" sections.
The exact structure in the middle chapters will vary among theses. In some theses, it is necessary to establish some theory, to describe the experimental techniques, then to report what was done on several different problems or different stages of the problem, and then finally to present a model or a new theory based on the new work. For such a thesis, the chapter headings might be: Theory, Materials and Methods, {first problem}, {second problem}, {third problem}, {proposed theory/model} and then the conclusion chapter. For other theses, it might be appropriate to discuss different techniques in different chapters, rather than to have a single Materials and Methods chapter.
Here follow some comments on the elements Materials and Methods, Theory, Results and discussion which may or may not correspond to thesis chapters.
In some theses, particularly multi-disciplinary or developmental ones, there may be more than one such chapter. In this case, the different disciplines should be indicated in the chapter titles.
When writing this section, concentrate at least as much on the physical arguments as on the equations. What do the equations mean? What are the important cases?
When you are reporting your own theoretical work, you must include rather more detail, but you should consider moving lengthy derivations to appendices. Think too about the order and style of presentation: the order in which you did the work may not be the clearest presentation.
Suspense is not necessary in reporting science: you should tell the reader where you are going before you start.
Make sure that you have described the conditions which obtained for each set of results. What was held constant? What were the other relevant parameters? Make sure too that you have used appropriate statistical analyses. Where applicable, show measurement errors and standard errors on the graphs. Use appropriate statistical tests.
Take care plotting graphs. The origin and intercepts are often important so, unless the ranges of your data make it impractical, the zeros of one or both scales should usually appear on the graph. You should show error bars on the data, unless the errors are very small. For single measurements, the bars should be your best estimate of the experimental errors in each coordinate. For multiple measurements these should include the standard error in the data. The errors in different data are often different, so, where this is the case, regressions and fits should be weighted (i.e. they should minimize the sum of squares of the differences weighted inversely as the size of the errors.) (A common failing in many simple software packages that draw graphs and do regressions is that they do not treat errors adequately. UNSW student Mike Johnston has written a plotting routine that plots data with error bars and performs weighted least square regressions. It is at http://www.phys.unsw.edu.au/3rdyearlab/graphing/graph.html)
In most cases, your results need discussion. What do they mean? How do they fit into the existing body of knowledge? Are they consistent with current theories? Do they give new insights? Do they suggest new theories or mechanisms?
Try to distance yourself from your usual perspective and look at your work. Do not just ask yourself what it means in terms of the orthodoxy of your own research group, but also how other people in the field might see it. Does it have any implications that do not relate to the questions that you set out to answer?
It is often the case with scientific investigations that more questions than answers are produced. Does your work suggest any interesting further avenues? Are there ways in which your work could be improved by future workers? What are the practical implications of your work?
This chapter should usually be reasonably short---a few pages perhaps. As with the introduction, I think that it is a good idea to ask someone who is not a specialist to read this section and to comment.
Suggestions, thanks and caveats
This document will be updated
occasionally. If you have suggestions for inclusions, amendments or other
improvements, please send them. Do so after you have submitted the
thesis---do not use this invitation as a displacement activity. I thank
Marilyn Ball, Gary Bryant and Bill Whiten, whose suggestions have been
incorporated in this version. Substantial contributions will be acknowledged
in future versions. I also take this opportunity to thank my own thesis
advisers, Stjepan Marcelja and Jacob Israelachvili, for their help and
friendship, and to thank the graduate students to whom I have had the pleasure
to be an adviser, a colleague and a friend. Opinions expressed in these notes
are mine and do not necessarily reflect the policy of the University of New
South Wales or of the School of Physics.
