for the preparation of a Ph.D. thesis
PREPARATION OF A Ph.D.
CHAPTER 1 - INTRODUCTION
DECLARATION OF AUTHENTICITY
This thesis contains no material which has been accepted for the award of any other degree or diploma in any University, and is less than 100,000 words in length. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person, except where due reference has been made.
Remember to sign the declaration prior to thesis submission.Monash
University guidelines states that where "work in the thesis
is based on joint research or publications, [the declaration] discloses
the relative contributions of the respective authors. Where practicable,
the statement should be countersigned by the other contributors".
All students are advised to read the conditions for the Degree of Doctor of Philosophy from the university in which they are enrolled prior to writing their thesis. These brochures contain information which is relevant to many facets of undertaking a Ph.D. including: rules, procedures, guidelines and advice. This booklet for both The University of Melbourne and Monash University was last updated in 1994.
1.1 WORDS OF ADVICE
I intend this handout to offer "words of advice" on the preparation of Ph.D. theses. Only too often have supervisors received first drafts of theses, manuscripts and other works where the submitting author has paid no (or very little) attention to the requirement for style or presentation of their work. This is particularly pertinent at the stage of thesis writing. Nothing is more frustrating to a supervisor, or anybody, who is proof-reading/criticising a thesis than to find that the work lacks fundamental "polish and presentation". On the other side of the coin is to advise the student of this, and their initial reaction is "Oh you're just being picky, there's nothing really wrong". Time initially spent on thesis layout and an eye to detail will be of great benefit both for the submission process and your long term involvement in manuscript and grant submissions. To offer a correctly laid out thesis to an individual to criticise means that an individual will focus on scientific relevance, logic and data and not punctuation and sentence construction.
I would like to draw your attention to some all too common pitfalls that can be found at some stage during the writing of every thesis.
1.2 THE UNIVERSITY OF MELBOURNE'S REQUIREMENTS
Format of the thesis (taken from the Degree of Doctor of Philosophy)
The following are obligatory:
(i) When the thesis is submitted, the candidate shall also submit a declaration from the supervisor and head of department that the thesis is ready to go forward to examination (form available from the Office of Graduate Studies).
(ii) Three copies of the thesis must be submitted. Monash University requires four copies of the thesis to be submitted. Check with your enrolled institution.
(iii) All three copies must contain (Prescription 18):
(a) an abstract of 300-500 words in English; and
(vi) A candidate may not use reprints or journal articles in their published form as part of the body of the thesis. While a thesis may be published in whole or in part prior to submission, it should both in form and content be presented as a unified whole, prepared specifically for submission for examination for the degree. Any parts of the thesis which have been previously published should be indicated in the preface.
(vii) A title page must show the title of the thesis, the name of the department or faculty in which the research was carried out and the full name of the author. Candidates who have pursued a course of study by research alone shall state on the title page: "Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy". Candidates who have pursued a course of study with coursework component shall state: "Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy (with coursework component)". Candidates who have pursued a course of study by thesis and musical composition shall state: "Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy (by thesis and musical composition).
(viii) The name of the author, the title (abbreviated if necessary) and the year of submission must be on the spine.
(ix) All these should normally be presented in English. Should a candidate wish to present a thesis in a language other than English, application must be made at an early stage in the candidature. The Ph.D. Sub-Committee will consider such an application only if full justification is provided by the department and may then recommend to the Academic Board that the candidate be permitted to present the thesis in the relevant language. Where permission is granted, a substantial summary of the thesis in English should be bound in with the thesis.
(x) At the conclusion of the examination two copies of the thesis shall be made available to the Office of Graduate Studies in permanent binding so that they can stand on a shelf as books. One of these shall be printed on acid-free paper (suitable paper is available from the Bookroom). The words "Produced on acid-free paper" should be printed or typed on the title page of this copy. The remaining copy will be at the disposal of the candidate.
You will note that these guidelines are "fairly loose",
and because not all aspects of thesis preparation are defined, omissions
or inaccurate presentation of data, references, appendices, footnotes
etc. frequently occur.
When stating a chemical you should provide the suppliers name in full eg., Tris (hydroxymethyl) aminomethane (Sigma Chemical Co. Ltd., St Louis, MO, USA). Any references to Sigma thereafter should be (Sigma Chemical Co. Ltd.).
Remember that we obtain chemicals from a number of local distributors eg., Amersham International Sydney, however it is manufactured and marketed from Amersham International, Buckinghamshire, UK.
The Materials and Methods section should be of sufficient detail to enable the examiner to determine what was actually undertaken.
Be consistent in use of spacing when typing 15 min, 1 ul, 1 M and
do not run them together as 15min, 1mg, 1ul, 1M.
Diagrams and figures should be photocopied on A4 paper and bound in the appropriate place in the text. The figures are to appear as a right-hand page and the legend should appear at the bottom of the figure or on the page facing the figure. Alternatively, figures may be interspersed throughout the text, however if computer graphics are used the quality and resolution must be equal to that obtained by photographic reproduction.
Each figure legend should stand alone from the body of the text
i.e., by reading the figure legend the figure should be self explanatory.
The easiest (and most consistent) way to lay out figure legends is
to have them all as a lefthand page i.e., opposing a figure bound
on the righthand side. Do not number figure pages. In the text use
the abbreviation Fig. 4.1. to denote the first figure for chapter
4 and provide in the front of the thesis a page listing the location
of figures. For the layout of the figure legend use the same formula.
The figure number, title (which may be presented in bold), then description.
Fig 4.1 Schematic representation of the PTHrP gene.
The coding regions and untranslated sequences are indicated by the
closed and open boxes, respectively. Indicated above the map are
the positions of the....
4.1 In Text
There are a number of ways to lay out references in the text, some of which are clearly wrong and others that become cumbersome to deal with. Most students should be able to use Reference Manager and this program should reduce the amount of time required.
I would recommend the following layouts since they are fairly uniform and easy to work with.
At the end of a sentence ...................as previously reported (Smith and Jones, 1970; Smith et al., 1972). Note, that following the authors name a comma should appear then year of publication, a semicolon should be between references. For more than two authors use the abbreviation et al., this should be in italics and a full stop should follow "al." since this is an abbreviation. When quoting more than one reference, references should be ordered in priority of chronology then the alphabetical listing of the authors. If one author has more than one publication in a given year the following can be adopted "Smith et al., 1981a, b, c; .........". When using this referencing system Smith et al., 1981a denotes the first cited reference of this series by the author and should be consistent throughout the thesis.
References in the text. "Smith and Jones (1970) or Smith et al. (1972) should be used. When using "et al." in the text do not include a comma after the authors name prior to the open bracket.
4.2 In the Bibliography
Book articles should be laid out according to the following recommendations. Name(s) of authors (surname and initials); title of book; edition (if relevant); place of publication; publication and year of publication. Where necessary, the relevant pages should be cited.
Sambrook, J., Fritsch, E.F. and Maniatis, T. Molecular Cloning. A laboratory Manual (2nd ed.) Cold Spring Harbor Laboratory Press, New York, 1989.
Journal articles should be laid out as follows: Name(s) of authors (surname and initials); title of article; journal name; volume number; page numbers; year of publication.
Smith, T.K. and Jones, J.M. Methods for PCR amplification of genomic material. Journal of Biological Chemistry. 20: 357-361, 1991.
Both The University of Melbourne and Monash University request references to be laid out according to the abovementioned format, although Monash University allows citations to follow the rules of citation adopted by one or other of the leading journals in the relevant field or discipline.
List authors alphabetically, then chronology and list the reference in full.
I am aware of two students that have not completed the references in full and have been requested to amend their thesis by including a full author list, title of publication and first and last page numbers. The best procedure that you can adopt is to provide all information in the first instance!
Your final check should be to ensure that all references cited in
the text are included in the bibliography, that the names and dates
of the citations are consistent.
The first rule is that you must be consistent with the abbreviations you use. Only too frequently are abbreviations altered between chapters due solely to the time difference in writing. I would recommend that at the stage of writing you have on a separate sheet of paper the abbreviations that you are using in the thesis and adhere to them so you are consistent throughout the body of the text.
Remember when you first use an abbreviation you should supply the
unabbreviated name in full eg., sodium dodecyl sulphate (SDS). You
should also provide a table as an appendix, listing abbreviations
in alphabetical order.
5.1 Common mistakes in abbreviations
i.e., and eg., should be used and not ie, eg, or ie., e.g.,
Mr for relative molecular weight, the "r" should be subscript
HIV+, CD4+ both are superscript "+" signs.
Decide on whether to use aa or a.a. throughout the thesis and do not alter. Other abbreviations frequently altered throughout theses include:
kb to Kb, Kbp
eg., EcoRI not EcoRI or EcoR1
5.2 Common mistakes in the text
The thesis is to be written in the "past tense" as all scientific writing is conducted. You should not include statements to you, such as "I undertook an analysis of", since the thesis is of your work. At the other extreme, avoid the use of "we".
Cross referencing in the thesis should be extensive as should referencing. Do not make unsupported claims - it is better to "over reference" than to "under reference".
Southern blotting is named after Ed Southern and therefore should have a capital "S". As a result of this, it is accepted that Northern and Western blotting also have upper case first letters.
Hyphenation A hyphen should be used in adjectival descriptions
"naturally-occurring plasmids" not
hybridisation or hybridization
1,25 (OH)2 D3 or 1,25 (OH)2 vit D3 1,25 dihydroxyvitamin D3
-4 to -3 years Enrolment and commencement of candidature. Begin literature review, material and methods and reference section of thesis.
-3 to - 2 years Confirmation of candidature. The University of Melbourne candidates are required to submit a research outline including literature review of approximately 2000 words one year after commencement of their candidature.
-12 months Final plan of thesis chapters and experiments to be completed. Post doctoral fellowships and positions will be pursued. Potential extensions of candidature and scholarships may be considered - consult with your supervisor.
-6 to -4 months The writing process will commence in earnest. During this period you will finalize all figures for your thesis.
Public presentation of research findings by seminar. The format of this is to be set by the Department, but optimally it would occur in the final six month period of the candidature.
At this stage you will be engaged in application for post-doctoral positions. You may be required to submit fellowship applications during this period and this should be taken into consideration.
-4 to -1 month Writing and re-writing work corrected by other colleagues and your supervisor.
-2 months Along with your supervisor decide on appropriate examiners. At The University of Melbourne, the candidate must provide an 80 word summary to be forwarded along with the list of potential examiners to the Office for Research. After lodgement of the 80 word summary, you will receive the "submission of PhD thesis: statement by supervisor and head of department (GS6B)" which must be signed by your principal supervisor (co-supervisor if the principal is absent) and presented to the School of Graduate Studies on submission of the three copies of the thesis. Your supervisor will receive an authorized copy of the 80 word summary from the School of Graduate Studies together with the "PhD examination nomination form (GS6A)." The GS6A form is required to be returned to the School of Graduate Studies within three weeks. The GS6A and GS6B forms are attatched in the appendix.
Day -10 to -14 You will be aware that you are nearly completed. Final corrections to be completed and the last outstanding items are to be dealt with. Check that printers and binders will be open in the next two weeks. Printers and binders frequently close during January and around Easter.
Day -6 Insertion of final amendments. Start to adjust pagination and check the table of contents.
Day -5 Final print of thesis. Print off top copy and proofread the entire thesis paying particular attention to pagination, typographicals, and inconsistencies in layout. Make sure that the table of contents is correct to the final page numbers.
Day -4 Collate all typed pages to be taken to the printer. Organize the thesis as it would be bound, but keep figure legends and tables at the back of the top copy. Ensure that the printer will print your copies on acid-free paper.
Day -3 Thesis is collated. Ensure that each copy of the thesis is in the same order. If inserting figures or tables make sure that they are inserted in the correct place according to the table of contents. Include published papers as addition evidence at the back of the thesis to the binders. The thesis must be sewn and bound with stiff covers covered with cloth. Some cover colours are not acceptable by the Librarian/University, but black, blue, maroon and green, which are the usual thesis colours are accepted by all Universities.
During binding the edges should be trimmed. On the spine of the thesis in gold lettering reading from top to bottom, the surname of the candidate, the title of the thesis (abbreviated if necessary) and the year of submission. An abbreviated title should be determined prior to lodgement of the thesis at a binder. Type out the details to be listed on the spine of thesis so there is no confusion at binding.
Books may be bound by different procedures. The most durable method is where holes are punched in the paper then pages are sewn, in the other method commonly employed, a wedge is cut on the edge of the paper, the space is sewn and glued. The latter method is somewhat inferior and may lead to a "broken spine" and subsequent dislodgement of pages. This does not occur in the first method of binding.
Most binders will take two working days to bind a thesis since they like to keep the thesis in the press overnight to ensure a satisfactory result.
If you have glued photographs smaller than A4 size onto A4 paper, the binder will introduce spacer segments in the spine so the thesis will not fan after binding.
Day -1 Thesis collected from binder. Check all copies ensuring all pages are present and bound in correct orientation. If you have not indicated which copy is produced on "acid-free paper" do so at this stage.
Day 0 Submission
Candidate: sign declaration on all copies
Supervisor/Department Head: Sign "statement by supervisor upon submission of thesis"
At Monash University the supervisor is to provide 40-50 work summary
of the thesis (this appears in the graduation program). The University
of Melbourne requests the graduation summary after examination of
7.1 Number of copies
You are requested to submit three copies of your thesis for examination if enrolled at The University of Melbourne and four copies if enrolled at Monash University. One copy remains with the University library and two copies are sent for review. After review, the first returned copy is lodged in the Department of Medicine Library, the second is forwarded to the candidate. From time to time an examiner may request to keep a copy of the thesis rather than return it. You should take this into consideration and produce more than three copies of your thesis.
Ideally you should produce five copies:
1) The University Library copy
At the time of submissions of the relevant copy numbers of the thesis, a consent form signed by the supervisor must accompany the thesis. This form certifies that the work embodied in the thesis is that of the candidate, except where otherwise acknowledged in the thesis, that the thesis is properly presented and prima facie worthy of examination. At The University of Melbourne submission, the Head of Department is also required to sign this form. At both The University of Melbourne and Monash University the candidate is also asked to sign a certificate which entails:
1. I agree/do not agree that this thesis may be made available for
consultation with the University.
At least one month (approximately two months) prior to submission, the student and supervisor(s) should meet to discuss potential examiners and a list of examiners should be constructed. The student has the right of refusal of potential examiners. At this stage an 80 word summary of the thesis should be finalized and this, along with potential referees, are forwarded to the University for examiner selection. It is assumed that the student will not know their final examiner and that no correspondence should occur between student and members on the list of potential examiners. Monash University however, formally discloses the names of the two examiners and instructs the student not to enter into any correspondence with them.
8.1 Time spent under examination
The Office of Graduate Studies asks examiners to complete their work within 2 months, though examinations sometimes take considerable longer than this.
8.2 Recommendations of examiners
Six recommendations are available to examiners when submitting a first report on a thesis:
(a) Pass without amendment
Special procedures may be adopted for oral examinations if neither examiner is able to attend. The University does allow a telephone link-up to occur (and I am aware of one such instance) whilst Monash University will appoint at least two academic members of staff to act as oral examiners. The examiner who wishes the oral to be held will supply a list of questions to be addressed to the candidate and the answer to these will be transmitted to the examiner. Under these circumstances the supervisor wil not normally be one of the academic members of staff involved in the oral examination except at the request of the examiner or examinee.
8.3 Corrections and amendments to the thesis
Theses requiring corrections must be submitted within the time specified in the letter of advice to the candidate from the Office of Graduate Studies. For a thesis requiring only minor amendments, approximately four weeks would be normally allowed. Usually, corrections and minor amendments will be incorporated into the thesis as an addenda which is inserted into the front of the thesis. Corrections and amendments to theses in the light of examiners reports are reviewed by the Chairman of Examiners.
Major amendments which are too extensive for inclusion as an addenda
require revisions to be incorporated into the text.
9.1 FINAL THOUGHTS
The writing process cannot start too early. Formulate your materials and methods sections, pencil out ideas for diagrams, make a list of abbreviations. All these "little" things will save time in the final crucial months.
Get a draft chapter to your supervisor as early as possible (that is, after you have put it through a rigorous examination) for comments. Do not hand your supervisor a complete draft of your entire thesis which you consider final - you might be in for a surprise.
Be a support network for each other. Offer to critically read someones thesis. You will benefit by identifying ways to layout a thesis (or ways not to layout) and you will polish up your punctuation and grammar skills. At the same time you will assist the person writing.
Matthew Gillespie June 1995