Writing a Thesis Zosia Chrzanowska-Lightowlers >20 PhD students MRes – Curriculum Chair, Director for Admissions and Recruitment Faculty of Medical Sciences Newcastle University 9th February 2018

Where to start ? Find the relevant guidelines for your thesis

Examination procedures and forms http://www.ncl.ac.uk/students/progress/student-resources/PGR/keyactivities/ThesisSubmission.htm

Examination procedures and forms http://www.ncl.ac.uk/students/progress/student-resources/PGR/keyactivities/Examination.htm

Examination procedures and forms http://www.ncl.ac.uk/students/progress/student-resources/PGR/handbook.htm Examiner handbook pdf

Types of thesis Standard By publication Divided into chapters with results and interpretations By publication Only for staff candidates Need to make a prima facie case for the submission A series of ≥4 related papers in period of registration All authors must provide written confirmation you were the major contributor ≥10,000 word introduction Potentially publishable as a review Can be difficult to examine as papers have already satisfied external referees!

How to start ? Read the information

Read the information 1 page

do not ask your supervisor READ these documents do not ask your supervisor http://www.ncl.ac.uk/students/progress/assets/documents/GuidelinesfortheSubmissionandFormatofThesis-January2018.pdf http://www.ncl.ac.uk/students/progress/student-resources/PGR/keyactivities/Examination.htm http://www.ncl.ac.uk/students/progress/student-resources/PGR/keyactivities/ThesisSubmission.htm

How do I write a book ? Read the information Talk to your supervisor – make a plan, - structure your thesis - plot completion dates

Talk to your supervisor – make a plan, - structure your thesis Preparation is key Read the information Talk to your supervisor – make a plan, - structure your thesis - plot completion dates Daunting prospect Divide your thesis into many smaller sections short sections seems more achievable ! This requires good planning or you will produce lots of small pieces of text that do not link together

Preparation is key Read the information Talk to your supervisor Graduate School – long documents course

Formatting a huge document…

Attend the courses https://workshops.ncl.ac.uk/public/fms/ Book on-line Thursday 15th March

Attend the courses https://workshops.ncl.ac.uk/public/fms/ Book on-line Thursday 29th March

Talk to your supervisor Graduate School – long documents course Help is at hand Read the information Talk to your supervisor Graduate School – long documents course Writing development centre http://www.ncl.ac.uk/library/subject-support/wdc/ one to one sessions online resources distance tutorials

A word of caution Read the information Talk to your supervisor Graduate School – long documents course Be careful who you ask for advise Former students / postdocs Friends Parents

A word of caution Plagiarism You will submit an electronic form of your thesis in parallel with the paper copies http://www.ncl.ac.uk/right-cite/ http://mbbs-tutorials.ncl.ac.uk/plag/

Looking at other theses Another word of caution Looking at other theses Your supervisor’s shelf Often groups evolve a “house style” that may not suit you The library Will have a wide range of theses similar to your field BE CAUTIOUS ! - it is your thesis No one else has your project, your intro and discussions must be tailored to your research If you feel strongly about a particular format, discuss it with your supervisor first and agree on the strategy before starting work

A example of a typical thesis layout plans can vary by subject area Title page (what is your title!) Abstract (one page, 300 words) Table of contents List of Figures and Tables Abbreviations Acknowledgements Statement of originality

A example of a typical thesis layout Introduction Materials + Methods Results chapter(s) Typically have one aim per chapter Often have separate mini introductions and specific discussions Concluding discussion chapter Context with literature Strengths, weaknesses, How far through your original aims did you get ? Future work Bibliography

What is the point of a thesis ? Prove you have developed the skills to be an independent, competent scientist

What is the point of a thesis ? Prove you have developed the skills of an independent, competent scientist Criteria – all theses Authentic Scholarly Professional Well-structured, -written and -presented

What is the point of a thesis ? Prove you have developed the skills of an independent, competent scientist Criteria – all theses Authentic Scholarly Professional Well-structured, -written and -presented Knowing what the examiners are looking for helps !

MPhil candidates Should Demonstrate advanced level of knowledge Show broad reading of relevant literature Theses need not, but often do contain material worthy of publication

PhD/MD candidates Should Provide evidence of adequate industry Demonstrate training in the scientific process Demonstrate ability for originality Understand relationship with wider field Theses should contain material worthy of publication

Getting down to business Most importantly BEFRIEND YOUR READER

Getting down to business First impressions are important BEFRIEND YOUR READER

How to BEFRIEND your reader Plan, plan, plan What are your chapters ? What is the story ? Do you have the data ? Get the flow right

Plan, plan, plan Get your chapters in order – 3rd year report – but be flexible Follow the story NOT the calendar Make a time plan, what written by when

Table of contents 1 Introduction Page 1.1 History of problem 1 1.2 First issue 1 1.2.1 sub issue 1 2 1.2.2 sub issue 2 4 1.3 Second issue 1.3.1 sub issue 1 5 1.3.2 sub issue 2 7 1.3.3 sub issue 3 8 1.3.4 sub issue 4 12 1.4 Third issue 1.4.1 sub issue 1 14 1.4.1.a sub sub issue 1 15 1.4.1.b sub sub issue 2 16 1.4.2 sub issue 2 18 1.5 Fourth issue 20 1.6 Fifth issue 1.6.1 25 etc, etc…

Plan, plan, plan Get your chapters in order What are the easy bits ? Abbreviations Materials and methods product code, source, concentration manufacturer’s protocol ? or modified ?

Plan, plan, plan Get the easier sections done early Abbreviations Materials and methods can you reference, did you modify ? Does a diagram explain it more simply ?

Volumes are NOT useful without stock concentrations ! Plan, plan, plan Get the easier sections Abbreviations Materials and methods are they accurate ? Volumes are NOT useful without stock concentrations !

Abstract Concise Comprehensive Clear Context

Plan, plan, plan Introduction - What are you trying to do with this ? General area Questions remaining AIMS

Language Accurate Scientifically stringent Grammatically correct Avoid colloquial phrasing

Language Accurate Scientifically stringent Grammatically correct Avoid colloquial phrasing “In the technical sense, it was much easier to use cell extracts or isolated enzymes alone with RNA templates.” “We chose to use…….” “It was significantly different……” “Each and every primer…..” “About 3ug RNA…”

Results chapters Introduction – more defined Methods – does it need a section ? Results – are the data good enough ? Discussion – conclude points from this section of work

Results chapters Results – are the data good enough ?

Results chapters Results – are the data good enough ? What form to present it ?

Results chapters Results – are the data good enough ? What size to present it ?

Results chapters Results – are the data good enough ? What size to present it ? Avoid this !

Results chapters Results – are the data good enough ? What form/size to present it ? Keep it near the relevant text !!!!!!!!

Results chapters Results – are the data good enough ? What form to present it ? Keep it near the relevant text !!!!!!!!

Results chapters Results – are the data good enough ? What form to present it ? Keep it near the relevant text !!!!!!! Make figures clear

How easy is this to understand ?

0.5 what ?

0.5 what ? And where ? ng template

What are we to learn from this ? ng template

What did we expect to see ? ng template

Good figures should be a freestanding story ng template Expected PCR product size

Title and legend ng template Expected PCR product size Figure 3.5. Fluorescent MPAT RNA14 products separated on a 10% denaturing gel.

Title and legend ng template Expected PCR product size Figure 3.5. Assessing various PCR conditions for the fluorescent MPAT. Fluorescent MPAT RNA14 products were separated on a 10% denaturing polyacrylamide gel. Molecular weight markers (lane 7) and sizing controls of tRNAs (lane 1) and a PCR product of a defined size (mt-ND3, lane 2) were loaded alongside the PCR products generated using increasing amounts of template (lanes 3-6).

Results chapters Results – are the data good enough ? What form/size to present it ? Keep it near the relevant text !!! Have a discussion section

Final discussion chapter Aims – how far did your work get in answering the original questions ? Results – bring a general overview and connection between all the chapters Future work – IF the project were to continue what would be the key experiments Finale – make a strong concluding statement

References The university recommends the “Harvard” format (and supplies an appropriate Endnote format!) So, in the main text use: (Kirby et al., 2010) rather than [278] Ask your supervisors for advice as Institutes might suggest alternatives

Appendices Publications arising Publications in preparation Plasmid maps Antibody tables (Company/cat. no./dilution) Primer tables (name/seq/position/acc number)

Tips Make sure you cite references as you go, or else you might forget which goes where Use text boxes for graphics – keep them in place Appendices – use them as necessary Backup, Backup, Backup!

Finished ? Get friends and family to proofread If English is not your first language, it can be helpful to employ a proof-reader Lists are available in the Student Union The cost is quite reasonable The proof-reader will (must!) only alter English and not the concept you are trying to express. Remember – your supervisor will focus mainly on your science rather than your English.

Finished ? CHECK Are your Figures and Tables consecutively labelled ? Are they referred to correctly or AT ALL in the text ? Are your subsections in the right order ? Are they referred to correctly ? Understand what you have written If it is in there, the examiners can ask you Be sure you can defend the content

Do – make your life easier Make sure you do enough expt repeats at the time Make sure they are of a good enough standard Save high resolution JPEG/TIFFS (named !!) Try and make them into figures as you go along for your lab book Keep good records, cross reference electronic images & lab books Backup your data Backup your writing (save by date)

Do – make your life easier Make a bibliography as you go Add notes to the Endnote entries Good ref for assembly factors Contradicts Bloggs et al. Had primer sequences for PCR The university recommends the “Harvard” format (and supplies an appropriate Endnote format!) Remember, in the main text use: (Kirby et al., 2010) Make sure you know when to use which reference Seminal or most recent ?

Write the lot before showing it to your supervisor !! Do NOT Write the lot before showing it to your supervisor !! Say ‘we’ Repeat yourself ! Waffle Keep changing tense Use different abbreviations or spelling options (subunit, sub-unit, sub unit) Use 10 µl, 10µl, 10ul Have section 1.2.2.3.4.5 Have 8 panel figures

Do NOT Have figures you do not refer to Put in data that you do not believe Put in things you do not understand Over-extrapolate !!!!!!!! Say anything you cannot defend Use ‘significant’ if it is not statistically valid Tell them ‘because my supervisor said to’ Tell them ‘it was too hard’ Say ‘it was too expensive’ Say ‘I didn’t know how’

Before you are Finished Liaise with your supervisors nominate examiners well in advance of submission

Before you are Finished Liaise with your supervisors nominate examiners well in advance of submission FINAL Title – what is your title! Abstract – 1 page, 300 words

Finished ? Liaise with your supervisors nominate examiners well in advance of submission Final printing takes much longer than you think ! Colour toner ? Enough paper ? Correct quality paper ? Binding Soft binding first (Library)

So EVERY thesis is DIFFERENT REMEMBER This is a report of YOUR project Every PhD project is different So EVERY thesis is DIFFERENT

Prepare well for your viva Good Luck! Prepare well for your viva