How to Write a PhD Thesis

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. In an experimental thesis, the Materials and Methods chapter is often 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 (Stjepan Marcelja): 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 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 close to the computer in case the hypothetical thief who fancies your computer decides that s/he could use some disks or membory 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 also send it to yourself. 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.

If you haven't already done so, you should archive your electronic data, in an appropriate format. Spreadsheet and word processor files are not suitable for long term storage. Archiving data by Joseph Slater is a good guide.

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

One of the big FAQs for scientists: is there a word processor, ideally one compatible with MS Word, but which allows you to type mathematical symbols and equations conveniently? One solution is LaTeX, which is powerful, elegant, reliable, fast and free from http://www.latex-project.org/ or http://www.miktex.org/. As far as I know, the only current equation editor for MS Word is slow and awkward. (If anyone knows a way of writing equations in this software without using the mouse, many people including this author would like to hear from you!) Another solution is to use old versions of commercial software. Word 5.1 allows equations to be typed comfortably: it is faster in this respect than LaTeX, with the added advantage of 'what you see is what you get' (WYSIWYG). (If anyone knows how to run Word 5.1 on OSX, please let me know!) A search will find sites that provide discontinued software, but, not knowing whether this is legal or not, I shan't link to them. (I am told that LyX, available free at http://www.lyx.org/, is a convenient front-end to LaTeX that has WYSIWYG. )

Commercial word processors have gradually become bigger, slower, less reliable and more awkward to use as they acquire more features. This is a general feature of commercial software and an important input to the computing industry. If software and operating system 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. In our 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, although they are slow and cumbersome when typing, look easy to use in the shop.

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 (or its electronic equivalent). 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.

© 1996. Modified 2/11/06 Joe Wolfe / J.Wolfe@unsw.edu.au, phone 61- 2-9385 4954 (UT + 10, +11 Oct-Mar).

School of Physics, University of New South Wales, Sydney, Australia.