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Master's Thesis

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.


What is a thesis? For whom is it written? How should it bewritten?

Your thesis is a research report. The report concerns aproblem or series of problems in your area of research and it shoulddescribe what was known about it previously, what you did towards solvingit, what you think your results mean, and where or how further progress inthe field can be made. Do not carry over your ideas from undergraduateassessment: a thesis is not an answer to an assignment question. Oneimportant difference is this: the reader of an assignment is usually theone 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 theoriesand the strengths and weaknesses of them. The readers of a thesis do notknow what the "answer" is. If the thesis is for a PhD, theuniversity requires that it make an original contribution to humanknowledge: your research must discover something hitherto unknown.

Obviously your examiners will read the thesis. They will be experts inthe 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 thetopic clear to a reader who has not spent most of the last three yearsthinking about it.

Your thesis will also be used as a scientific report and consulted byfuture workers in your laboratory who will want to know, in detail, whatyou did. Theses are occasionally consulted by people from otherinstitutions, and the library sends microfilm versions if requested (yes,still). More commonly theses are now stored in an entirely digital form.These may be stored as .pdf files on a server at your university. Theadvantage is that your thesis can be consulted much more easily byresearchers around the world. (See e.g. Australiandigital thesis project for the digital availability of researchtheses.) Write with these possibilities in mind.

It is often helpful to have someone other than your adviser(s) read somesections of the thesis, particularly the introduction and conclusionchapters. It may also be appropriate to ask other members of staff to readsome sections of the thesis which they may find relevant or of interest, asthey may be able to make valuable contributions. In either case, only givethem revised versions, so that they do not waste time correcting yourgrammar, spelling, poor construction or presentation.

How much detail?

The short answer is: rather more than for a scientificpaper. Once your thesis has been assessed and your friends have read thefirst three pages, the only further readers are likely to be people who areseriously doing research in just that area. For example, a future researchstudent might be pursuing the same research and be interested to find outexactly what you did. ("Why doesn't the widget that Bloggs built forher project work any more? Where's the circuit diagram? I'll look up herthesis." "Blow's subroutine doesn't converge in my parameterspace! I'll have to look up his thesis." "How did that group in Sydney manage to getthat technique to work? I'll order a microfilm of that thesis they cited intheir paper.") For important parts of apparatus, you should includeworkshop drawings, circuit diagrams and computer programs, usually asappendices. (By the way, the intelligible annotation of programs is aboutas frequent as porcine aviation, but it is far more desirable. You wrotethat line of code for a reason: at the end of the line explain what thereason is.) You have probably read the theses of previous students in thelab where you are now working, so you probably know the advantages of aclearly 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 thatis not your own, you must usually state where in the scientific literaturethat result is reported. The only exceptions are cases where everyresearcher in the field already knows it: dynamics equations need not befollowed by a citation of Newton,circuit analysis does not need a reference to Kirchoff. The importance ofthis practice in science is that it allows the reader to verify yourstarting 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 tothe structure of knowledge in the discipline, or at least to trace themback to a level which we judge to be reliable. Good referencing also tellsthe reader which parts of the thesis are descriptions of previous knowledgeand which parts are your additions to that knowledge. In a thesis, writtenfor the general reader who has little familiarity with the literature ofthe field, this should be especially clear. It may seem tempting to leaveout a reference in the hope that a reader will think that a nice idea or annice bit of analysis is yours. I advise against this gamble. The readerwill probably think: "What a nice idea---I wonder if it'soriginal?". The reader can probably find out via the net or thelibrary.

If you are writing in the passive voice, you must be more careful aboutattribution than if you are writing in the active voice. "The samplewas prepared by heating yttrium..." does not make it clear whether youdid this or whether Acme Yttrium did it. "I prepared thesample..." is clear.

Style

The text must be clear. Good grammar and thoughtful writingwill make the thesis easier to read. Scientific writing has to be a littleformal---more formal than this text. Native English speakers shouldremember that scientific English is an international language. Slang andinformal writing will be harder for a non-native speaker to understand.

Short, simple phrases and words are often better than long ones. Somepoliticians use "at this point in time" instead of"now" precisely because it takes longer to convey the samemeaning. They do not care about elegance or efficient communication. Youshould. On the other hand, there will be times when you need a complicatedsentence because the idea is complicated. If your primary statementrequires 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 inmany theses, particularly in fields like biochemistry. Do not sacrificeaccuracy for the sake of brevity. "Black is white" is simple andcatchy. An advertising copy writer would love it. "Objects of verydifferent albedo may be illuminated differently so as to produce similarreflected spectra" is longer and uses less common words, but, comparedto the former example, it has the advantage of being true. The longerexample would be fine in a physics thesis because English speakingphysicists will not have trouble with the words. (A physicist who did notknow all of those words would probably be glad to remedy the lacuna eitherfrom the context or by consulting a dictionary.)

Sometimes it is easier to present information and arguments as a seriesof 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 touse this presentation too much: your thesis must be a connected, convincingargument, not just a list of facts and observations.

One important stylistic choice is between the active voice and passivevoice. The active voice ("I measured the frequency...") issimpler, and it makes clear what you did and what was done by others. Thepassive voice ("The frequency was measured...") makes it easierto 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 wasselected" implicitly attributes consciousness to plutonium. Thischoice is a question of taste: I prefer the active because it is clearer,more logical and makes attribution simple. The only arguments I have everheard for avoiding the active voice in a thesis are (i) many theses arewritten in the passive voice, and (ii) some very polite people find the useof "I" immodest. Use the first person singular, not plural, whenreporting work that you did yourself: the editorial 'we' may suggest thatyou had help beyond that listed in your acknowledgments, or it may suggestthat you are trying to share any blame. On the other hand, retain plural verbsfor "data": "data" is the plural of "datum",and lots of scientists like to preserve the distinction. Just say toyourself "one datum is ..", "these data are.." severaltimes. An excellent and widely used reference for English grammar and styleis A Dictionary of Modern English Usage by H.W. Fowler.

Presentation

There is no need for a thesis to be a masterpiece ofdesk-top publishing. Your time can be more productively spent improving thecontent than the appearance.

In many cases, a reasonably neat diagram can be drawn by hand fasterthan with a graphics package, and you can scan it if you want an electronicversion. Either is usually satisfactory. A one bit (i.e. black and white),moderate resolution scan of a hand-drawn sketch will be bigger than a linedrawing generated on a graphics package, but not huge. While talking aboutthe size of files, we should mention that photographs look pretty but takeup a lot of memory. There's another important difference, too. Thephotographer thought about the camera angle and the focus etc. The personwho drew the schematic diagram thought about what components ought to bedepicted and the way in which the components of the system interacted witheach other. So the numerically small information content of the linedrawing may be much more useful information than that in a photograph.

Another note about figures and photographs. In the digital version ofyour thesis, do not save ordinary photographs or other illustrations asbitmaps, because these take up a lot of memory and are therefore very slowto transfer. Nearly all graphics packages allow you to save in compressedformat as .jpg (for photos) or .gif (for diagrams) files. Further, you cansave space/speed things up by reducing the number of colours. In vector graphics(as used for drawings), compression is usually unnecessary.

In general, students spend too much time on diagrams---time that couldhave been spent on examining the arguments, making the explanationsclearer, thinking more about the significance and checking for errors inthe algebra. The reason, of course, is that drawing is easier thanthinking.

I do not think that there is a strong correlation (either way) betweenlength and quality. There is no need to leave big gaps to make the thesisthicker. Readers will not appreciate large amounts of vague or unnecessarytext.

Approaching the end

A deadline is very useful in some ways. You must hand inthe 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. Ifyou 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 bemade perfect in a finite time. There will inevitably be things in it thatyou 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 flipopen the bound copy. No matter how much you reflect and how many times youproof read it, there will be some things that could be improved. There isno point hoping that the examiners will not notice: many examiners feelobliged to find some examples of improvements (if not outright errors) justto show how thoroughly they have read it. So set yourself a deadline andstick 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 daysbefore word processors, spelling checkers and typing programs. Studentsoften paid a typist to produce the final draft and could only afford to dothat once.)

How many copies?

Talk to your adviser about this. As well as those for the examiners, the university libraries and yourself, you should make some distribution copies. These copies should be sent to other researchers who are working in your field so that:

  • they can discover what marvellous work you have been doing before it appears in journals;
  • they can look up the fine details of methods and results that will or have been published more briefly elsewhere;
  • they can realise what an excellent researcher you are. This realisation could be useful if a post- doctoral position were available in their labs. soon after your submission, or if they were reviewers of your research/post-doctoral proposal. Even having your name in their book cases might be an advantage.

Whatever the University's policy on single or double-sided copies, thedistribution copies could be double-sided paper, or digital, so thatforests and postage accounts are not excessively depleted by the exercise.Your adviser could help you to make up a list of interested and/orpotentially useful people for such a mailing list. Your adviser might alsohelp by funding the copies and postage if they are not covered by yourscholarship. A CD with your thesis will be cheaper than a paper copy. Youdon't have to burn them all yourself: companies make multiple copies forseveral dollars a copy.

The following comment comes from Marilyn Ball of the Australian National University in Canberra: "When I finished writingmy thesis, a postdoc wisely told me to give a copy to my parents. I wouldnever have thought of doing that as I just couldn't imagine what they woulddo with it. I'm very glad to have taken that advice as my parents reallyappreciated receiving a copy and proudly displayed it for years. (My mothernever finished high school and my father worked with trucks - he fixed 'em,built 'em, drove 'em, sold 'em and junked 'em. Nevertheless, they enjoyedhaving a copy of my thesis.)"

Personal

In the ideal situation, you will be able to spend alarge part---perhaps a majority---of your time writing your thesis. Thismay be bad for your physical and mental health.

Typing

Set up your chair and computerproperly. The Health Service, professional keyboard users or perhaps eventhe school safety officer will be able to supply charts showing recommendedrelative heights, healthy postures and also exercises that you should do ifyou spend a lot of time at the keyboard. These last are worthwhileinsurance: you do not want the extra hassle of back or neck pain. Try tointersperse long sessions of typing with other tasks, such as reading,drawing, calculating, thinking or doing research.

If you do not touch type, you should learn todo so for the sake of your neck as well as for productivity. There areseveral good software packages that teach touch typing interactively. Ifyou use one for say 30 minutes a day for a couple of weeks, you will beable to touch type. By the time you finish the thesis, you will be able totouch type quickly and accurately and your six hour investment will havepaid for itself. Be careful not to use the typing exercises as adisplacement activity.

Exercise

Do not give up exercise for theinterim. Lack of exercise makes you feel bad, and you do not need anythingelse making you feel bad while writing a thesis. 30-60 minutes of exerciseper day is probably not time lost from your thesis: I find that if I do notget regular exercise, I sleep less soundly and longer. How about walking towork and home again? (Walk part of the way if your home is distant.) Manypeople opine that a walk helps them think, or clears the head. You may findthat an occasional stroll improves your productivity.

Food

Do not forget to eat, and makean effort to eat healthy food. You should not lose fitness or risk illnessat this critical time. Exercise is good for keeping you appetite at ahealthy level. I know that you have little time for cooking, but keep asupply of fresh fruit, vegetables and bread. It takes less time to make asandwich than to go to the local fast food outlet, and you will feel betterafterwards.

Drugs

Thesis writers have a longtradition of using coffee as a stimulant and alcohol or marijuana asrelaxants. (Use of alcohol and coffee is legal, use of marijuana is not.)Used in moderation, they do not seem to have ill effects on the quality ofthesis produced. Excesses, however, are obviously counter-productive:several espressi and you will be buzzing too much to sit down and work;several drinks at night will slow you down next day.

Others

Other people will besympathetic, but do not take them for granted. Spouses, lovers, family andfriends should not be undervalued. Spend some time with them and, when youdo, have a good time. Do not spend your time together complaining aboutyour thesis: they already resent the thesis because it is keeping you awayfrom them. If you can find another student writing a thesis, then you mayfind it therapeutic to complain to each other about advisers and difficulties.S/he need not be in the same discipline as you are.

Coda

Keep going---you're nearly there! Most PhDs will admitthat there were times when we thought about reasons for not finishing. Butit would be crazy to give up at the writing stage, after years of work onthe research, and it would be something to regret for a long time.

Writing a thesis is tough work. One anonymous post doctoral researchertold 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 theirfriends and their social lives for a while. It's a tough period for almostevery student." She's right: it is certainly hard work, it willprobably be stressful and you will have to adapt your rhythm to it. It isalso an important rite of passage and the satisfaction you will feelafterwards is wonderful. On behalf of scholars everywhere, I wish you goodluck!


A suggested thesis structure

The list of contents and chapter headings below isappropriate for some theses. In some cases, one or two of them may beirrelevant. Results and Discussion are usually combined in several chaptersof a thesis. Think about the plan of chapters and decide what is best toreport your work. Then make a list, in point form, of what will go in eachchapter. Try to make this rather detailed, so that you end up with a listof points that corresponds to subsections or even to the paragraphs of yourthesis. At this stage, think hard about the logic of the presentation:within chapters, it is often possible to present the ideas in differentorder, and not all arrangements will be equally easy to follow. If you makea plan of each chapter and section before you sit down to write, the resultwill probably be clearer and easier to read. It will also be easier towrite.

Copyright waiver

Your institution may have aform for this (UNSW does). In any case, this standard page gives theuniversity library the right to publish the work, possibly by microfilm orother medium. (At UNSW, the Postgraduate Student Office will give you athesis pack with various guide-lines and rules about thesis format. Makesure that you consult that for its formal requirements, as well as thisrather informal guide.)

Declaration

Check the wording required byyour institution, and whether there is a standard form. Many universitiesrequire something like: "I hereby declare that this submission is myown work and that, to the best of my knowledge and belief, it contains nomaterial previously published or written by another person nor materialwhich to a substantial extent has been accepted for the award of any otherdegree or diploma of the university or other institute of higher learning,except where due acknowledgment has been made in the text.(signature/name/date)"

Title page

This may vary amonginstitutions, but as an example: Title/author/"A thesis submitted forthe degree of Doctor of Philosophy in the Faculty of Science/The Universityof New South Wales"/date.

Abstract

Of all your thesis, this partwill be the most widely published and most read because it will bepublished in Dissertation Abstracts International. It is best writtentowards the end, but not at the very last minute because you will probablyneed several drafts. It should be a distillation of the thesis: a concisedescription of the problem(s) addressed, your method of solving it/them,your results and conclusions. An abstract must be self-contained. Usuallythey do not contain references. When a reference is necessary, its detailsshould be included in the text of the abstract. Check the word limit.Remember: even though it appears at the beginning, an abstract is notan introduction. It is a résumé of your thesis.

Acknowledgments

Most thesis authors put in apage of thanks to those who have helped them in matters scientific, andalso indirectly by providing such essentials as food, education, genes,money, help, advice, friendship etc. If any of your work iscollaborative, you should make it quite clear who did which sections.

Table of contents

The introduction starts on page1, the earlier pages should have roman numerals. It helps to have thesubheadings of each chapter, as well as the chapter titles. Remember thatthe thesis may be used as a reference in the lab, so it helps to be able tofind things easily.

Introduction

What is the topic and why is itimportant? State the problem(s) as simply as you can. Remember that youhave been working on this project for a few years, so you will be veryclose to it. Try to step back mentally and take a broader view of theproblem. How does it fit into the broader world of your discipline?

Especially in the introduction, do notoverestimate the reader's familiarity with your topic. You are writing forresearchers in the general area, but not all of them need be specialists inyour particular topic. It may help to imagine such a person---think of someresearcher whom you might have met at a conference for your subject, butwho was working in a different area. S/he is intelligent, has the samegeneral background, but knows little of the literature or tricks that applyto your particular topic.

The introduction should be interesting. If youbore the reader here, then you are unlikely to revive his/her interest inthe materials and methods section. For the first paragraph or two,tradition permits prose that is less dry than the scientific norm. If wantto wax lyrical about your topic, here is the place to do it. Try to makethe reader want to read the heavy bundle that has arrived uninvited onhis/her desk. Go to the library and read several thesis introductions. Didany make you want to read on? Which ones were boring?

This section might go through several drafts tomake 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 toread it and to comment. Is it an adequate introduction? Is it easy tofollow? There is an argument for writing this section---or least making amajor revision of it---towards the end of the thesis writing. Yourintroduction should tell where the thesis is going, and this may becomeclearer during the writing.

Literature review

Where did the problem comefrom? What is already known about this problem? What other methods havebeen tried to solve it?

Ideally, you will already have much of the hardwork done, if you have been keeping up with the literature as you vowed todo three years ago, and if you have made notes about important papers overthe years. If you have summarised those papers, then you have some goodstarting points for the review.

If you didn'tkeep your literature notes up to date, you can still do something useful:pass on the following advice to any beginning PhD students in your lab andtell them how useful this would have been to you. When you start readingabout a topic, you should open a spread sheet file, or at least a wordprocessor file, for your literature review. Of course you write down thetitle, authors, year, volume and pages. But you also write a summary(anything from a couple of sentences to a couple of pages, depending on therelevance). In other columns of the spread sheet, you can add key words(your own and theirs) and comments about its importance, relevance to youand its quality.

How many papers? How relevant do they have tobe before you include them? Well, that is a matter of judgement. On theorder of a hundred is reasonable, but it will depend on the field. You arethe world expert on the (narrow) topic of your thesis: you must demonstratethis.

A political point: make sure that you do notomit relevant papers by researchers who are like to be your examiners, orby potential employers to whom you might be sending the thesis in the nextyear or two.

Middle chapters

In some theses, the middlechapters are the journal articles of which the student was major author.There are several disadvantages to this format.

One is that a thesis is both allowed andexpected 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 theinteresting and relevant data can go in the thesis, and not just thosewhich appeared in the journal. The degree of experimental detail is usuallygreater in a thesis. Relatively often a researcher requests a thesis inorder to obtain more detail about how a study was performed.

Another disadvantage is that your journalarticles may have some common material in the introduction and the"Materials and Methods" sections.

The exact structure in the middle chapters willvary among theses. In some theses, it is necessary to establish sometheory, to describe the experimental techniques, then to report what wasdone on several different problems or different stages of the problem, andthen finally to present a model or a new theory based on the new work. Forsuch a thesis, the chapter headings might be: Theory, Materials andMethods, , , , and then the conclusion chapter. For other theses, it mightbe appropriate to discuss different techniques in different chapters,rather than to have a single Materials and Methods chapter.

Here follow some comments on the elementsMaterials and Methods, Theory, Results and discussion which may or may notcorrespond to thesis chapters.

Materials and Methods

This varies enormously fromthesis to thesis, and may be absent in theoretical theses. It should bepossible for a competent researcher to reproduce exactly what you have doneby following your description. There is a good chance that this test willbe applied: sometime after you have left, another researcher will want todo a similar experiment either with your gear, or on a new set-up in aforeign country. Please write for the benefit of that researcher.

In some theses, particularly multi-disciplinaryor developmental ones, there may be more than one such chapter. In thiscase, the different disciplines should be indicated in the chapter titles.

Theory

When you are reportingtheoretical work that is not original, you will usually need to includesufficient material to allow the reader to understand the arguments usedand their physical bases. Sometimes you will be able to present the theory abinitio, but you should not reproduce two pages of algebra that thereader could find in a standard text. Do not include theory that you arenot going to relate to the work you have done.

When writing this section, concentrate at leastas much on the physical arguments as on the equations. What do theequations mean? What are the important cases?

When you are reporting your own theoreticalwork, you must include rather more detail, but you should consider movinglengthy derivations to appendices. Think too about the order and style ofpresentation: the order in which you did the work may not be the clearestpresentation.

Suspense is not necessary in reporting science:you should tell the reader where you are going before you start.

Results and discussion

The results and discussion arevery often combined in theses. This is sensible because of the length of athesis: you may have several chapters of results and, if you wait till theyare all presented before you begin discussion, the reader may havedifficulty remembering what you are talking about. The division of Resultsand Discussion material into chapters is usually best done according tosubject matter.

Make sure that you have described theconditions which obtained for each set of results. What was held constant?What were the other relevant parameters? Make sure too that you have usedappropriate statistical analyses. Where applicable, show measurement errorsand standard errors on the graphs. Use appropriate statistical tests.

Take care plotting graphs. The origin andintercepts are often important so, unless the ranges of your data make itimpractical, the zeros of one or both scales should usually appear on thegraph. You should show error bars on the data, unless the errors are verysmall. For single measurements, the bars should be your best estimate ofthe experimental errors in each coordinate. For multiple measurements theseshould include the standard error in the data. The errors in different dataare often different, so, where this is the case, regressions and fitsshould be weighted (i.e. they should minimize the sum of squares of thedifferences weighted inversely as the size of the errors.) (A commonfailing in many simple software packages that draw graphs and doregressions is that they do not treat errors adequately. UNSW student MikeJohnston has written a plottingroutine that plots data with error bars and performs weighted leastsquare regressions. It is athttp://www.phys.unsw.edu.au/3rdyearlab/graphing/graph.html). You can just'paste' your data into the input and it generates a .ps file of the graph.

In most cases, your results need discussion.What do they mean? How do they fit into the existing body of knowledge? Arethey consistent with current theories? Do they give new insights? Do theysuggest new theories or mechanisms?

Try to distance yourself from your usualperspective and look at your work. Do not just ask yourself what it meansin terms of the orthodoxy of your own research group, but also how otherpeople in the field might see it. Does it have any implications that do notrelate to the questions that you set out to answer?

Final chapter, references and appendices

Conclusions and suggestions for further work

Your abstract should includeyour conclusions in very brief form, because it must also include someother material. A summary of conclusions is usually longer than the finalsection of the abstract, and you have the space to be more explicit andmore careful with qualifications. You might find it helpful to put yourconclusions in point form.

It is often the case with scientificinvestigations that more questions than answers are produced. Does yourwork suggest any interesting further avenues? Are there ways in which yourwork could be improved by future workers? What are the practicalimplications of your work?

This chapter should usually be reasonablyshort---a few pages perhaps. As with the introduction, I think that it is agood idea to ask someone who is not a specialist to read this section andto comment.

References (See also under literature review)

It is tempting to omit thetitles of the articles cited, and the university allows this, but think ofall the times when you have seen a reference in a paper and gone to look itup only to find that it was not helpful after all.

Should you reference web sites and, if so, how?If you cite a journal article or book, the reader can go to a library andcheck that the cited document and check whether or not it says what you sayit did. A web site may disappear, and it may have been updated or changedcompletely. So references to the web are usually less satisfactory.Nevertheless, there are some very useful and authoritative sources. So, ifthe rules of your institution permit it, it may be appropriate to citeweb sites. (Be cautious, and don't overuse such citations. In particular,don't use a web citation where you could reasonably use a "hard"citation. Remember that your examiners are likely to be older and moreconservative.) You should give the URL and also the date you downloaded it.If there is a date on the site itself (last updated on .....) you shouldincluded that, too.

Appendices

If there is material thatshould be in the thesis but which would break up the flow or bore thereader unbearably, include it as an appendix. Some things which aretypically included in appendices are: important and original computerprograms, data files that are too large to be represented simply in theresults chapters, pictures or diagrams of results which are not importantenough to keep in the main text.


Some sites with related material

Writing and publishinga scientific paper
How to survive athesis defence
Researchresources and links supplied by Deakin University
"Final year projects":a guide from Mike Hart at King Alfred's College, Winchester, UK
PostgraduateStudent Resources supplied by University of Canberra
A useful aid to surviving meetings with management
The National Association of Graduate- Professional Students (USA)

Some relevant texts

Stevens, K. and Asmar, C (1999)'Doing postgraduate research in Australia'. MelbourneUniversity Press, Melbourne ISBN 0 522 84880 X.
Phillips, E.M and Pugh, D.S. (1994) 'How to get a PhD : a handbook forstudents and their supervisors'. Open University Press, Buckingham, England
Tufte, E.R. (1983) 'The visual display of quantitative information'.Graphics Press, Cheshire, Conn. 
Tufte, E.R. (1990) 'Envisioning information' Graphics Press, Cheshire,Conn.