How to Write a PhD Thesis

Thesis writing: this guide gives simple and practical advice on the problems of getting started,getting organised, 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 widely used and appreciated by graduate students in diverse fields inthe sciences and humanities.

Getting Started

When you are about to begin, writing a thesis seems along, difficult task. That is because it is a long, difficult task.Fortunately, it will seem less daunting once you have a couple of chaptersdone. Towards the end, you will even find yourself enjoying it---anenjoyment based on satisfaction in the achievement, pleasure in theimprovement in your technical writing, and of course the approaching end.Like many tasks, thesis writing usually seems worst before you begin, solet us look at how you should make a start.

An outline

First make up a thesis outline: several pages containingchapter headings, sub-headings, some figure titles (to indicate whichresults go where) and perhaps some other notes and comments. There is asection on chapter order and thesis structure at the end of this text. Onceyou have a list of chapters and, under each chapter heading, a reasonablycomplete list of things to be reported or explained, you have struck agreat blow against writer's block. When you sit down to type, your aim isno longer a thesis---a daunting goal---but something simpler. Your new aimis just to write a paragraph or section about one of your subheadings. Ithelps to start with an easy one: this gets you into the habit of writingand gives you self-confidence. In an experimental thesis, the Materials andMethods chapter is often the easiest to write ? just write down what youdid; carefully, formally and in a logical order.

How do you make an outline of a chapter? For most of them, you might trythe method that I use for writing papers, and which I learned from mythesis adviser (Stjepan Marcelja): Assemble all the figures that you willuse in it and put them in the order that you would use if you were going toexplain to someone what they all meant. You might as well rehearseexplaining it to someone else---after all you will probably give severaltalks based on your thesis work. Once you have found the most logicalorder, note down the key words of your explanation. These key words providea skeleton for much of your chapter outline.

Once you have an outline, discuss it with your adviser. This step isimportant: s/he will have useful suggestions, but it also serves noticethat s/he can expect a steady flow of chapter drafts that will make highpriority demands on his/her time. Once you and your adviser have agreed ona logical structure, s/he will need a copy of this outline for referencewhen reading the chapters which you will probably present out of order. Ifyou have a co-adviser, discuss the outline with him/her as well, andpresent 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 somethingfor Chapter n, you will think "Oh I must refer back to/discuss this inChapter 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 haveaccumulated, 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 diskdrive). Do not keep back-up close to the computer in case the hypotheticalthief who fancies your computer decides that s/he could use some disks ormembory as well.

A simple way of making a remote back-up is to send it as an emailattachment to a consenting email correspondent, preferably one in adifferent location. You could also send it to yourself. In either case, becareful to dispose of superseded versions so that you don't waste diskspace, especially if you have bitmap images or other large files. You should also have a physical filing system: a collection of folderswith chapter numbers on them. This will make you feel good about gettingstarted and also help clean up your desk. Your files will contain not justthe 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 toone chapter or other. Stick them in that folder. Then put all the foldersin a box or a filing cabinet. As you write bits and pieces of text, placethe hard copy, the figures etc in these folders as well. Touch them andfeel 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 ina different location. Consider making a copy of your lab book. This hasanother purpose beyond security: usually the lab book stays in the lab, butyou may want a copy for your own future use. Further, scientific ethicsrequire you to keep lab books and original data for at least ten years, anda 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 notsuitable for long term storage. Archiving databy Joseph Slater is a good guide.

While you are getting organised, you should deal with any universitypaperwork. Examiners have to be nominated and they have to agree to serve.Various forms are required by your department and by the universityadministration. Make sure that the rate limiting step is your production ofthe thesis, and not some minor bureaucratic problem.

A note about word processors

One of the big FAQs for scientists: is there a wordprocessor, ideally one compatible with MS Word, but which allows you totype mathematical symbols and equations conveniently? One solution isLaTeX, 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. (Ifanyone knows a way of writing equations in this software without using themouse, many people including this author would like to hear from you!)Another solution is to use old versions of commercial software. Word 5.1allows equations to be typed comfortably: it is faster in this respect thanLaTeX, 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 meknow!) 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 toldthat LyX, available free at http://www.lyx.org/, is a convenient front-endto LaTeX that has WYSIWYG. )


Commercial word processors have gradually become bigger, slower, lessreliable and more awkward to use as they acquire more features. This is ageneral feature of commercial software and an important input to thecomputing industry. If software and operating system performance did notdeteriorate, people would not need to buy new computers and profits wouldfall for makers of both hard- and soft-ware. Software vendors want it tolook fancy and obvious in the demo, and they don't really care about itsease, speed and reliability to an expert user because the expert user hasalready bought it. In our example, it is much faster to type equations andto do formatting with embedded commands because you use your fingersindependently rather than your hand and because your fingers don't leavethe keyboard. However, click-on menus, although they are slow andcumbersome when typing, look easy to use in the shop.

A time table

I strongly recommend sitting down with the adviser andmaking up a timetable for writing it: a list of dates for when you willgive the first and second drafts of each chapter to your adviser(s). Thisstructures your time and provides intermediate targets. If you merely aim"to have the whole thing done by [some distant date]", you candeceive yourself and procrastinate more easily. If you have told youradviser that you will deliver a first draft of chapter 3 on Wednesday, itfocuses your attention.

You may want to make your timetable into a chart with items that you cancheck off as you have finished them. This is particularly useful towardsthe end of the thesis when you find there will be quite a few loose endshere and there.

Iterative solution

Whenever you sit down to write, it is very important towrite something. So write something, even if it is just a set ofnotes 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 improvesomething that is already written than to produce text from nothing. So putdown a draft (as rough as you like) for your own purposes, then clean it upfor your adviser to read. Word-processors are wonderful in this regard: inthe first draft you do not have to start at the beginning, you can leavegaps, you can put in little notes to yourself, and then you can clean itall up later.

Your adviser will expect to read each chapter in draft form. S/he willthen return it to you with suggestions and comments. Do not be upset ifa chapter---especially the first one you write--- returns covered in redink (or its electronic equivalent). Your adviser will want your thesisto be as good as possible, because his/her reputation as well as yours isaffected. Scientific writing is a difficult art, and it takes a while tolearn. As a consequence, there will be many ways in which your first draftcan be improved. So take a positive attitude to all the scribbles withwhich your adviser decorates your text: each comment tells you a way inwhich you can make your thesis better.

As you write your thesis, your scientific writing is almost certain toimprove. Even for native speakers of English who write very well in otherstyles, one notices an enormous improvement in the first drafts from thefirst to the last chapter written. The process of writing the thesis islike a course in scientific writing, and in that sense each chapter is likean assignment in which you are taught, but not assessed. Remember, only thefinal draft is assessed: the more comments your adviser adds to first orsecond draft, the better. Before you submit a draft to your adviser, run a spell check so thats/he does not waste time on those. If you have any characteristicgrammatical failings, check for them.
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