How to write a scientific paper or thesis chapter or report

1
How to write a scientific paper(or thesis
chapter or report)

• Peter Billingsley
• School of Biological Sciences
• Generic Skills for Postgraduate Research Students
• April 2005

2
Aims of the session

• To review current methods of paper/report/
  chapter writing by attendees.
• To suggest and try an alternative method that
  works!!!
• To consider additional factors associated with
  paper writing including
• Authorship
• Journal selection
• Use of literature and literature databases
• Responding to referees

3
The perfect cup of tea

• Take 10 minutes
• Start writing a paper on how to make a cup of tea

• How did you do it?
• Review the approaches you have taken as a group

4
The Lewis Carrol Method
5
The Lewis Carrol Method why it doesnt work

• The structure of a Scientific Article
• Title
• Abstract
• Introduction
• Materials Methods
• Results
• Discussion
• Reference list

6
(No Transcript)
7
Your paper.. how?

• Do not dive in without a plan mind map to
  outline

Relevant background to the problem
A O
Title abstract
Hypothesis
Materials and Methods
Introduction
Figures
My paper
Reading
Analysis
References
Results
References
Tables
Discussion
statistics
Text
8
Your paper.. how?

• Before you begin writing (other than the
  materials and methods) complete your data
  analysis and preparation of figures and tables.
  Have all these as polished, finished products
  before starting to write the results.
• Remove any extraneous information things you
  are not going to use
• Lay the figures and tables out in front of you,
  and place them in the sequence in which you will
  use them. Storyboard.
• Is there anything missing? Do you need to do
  more work or more analysis?
• Write about each one in turn. Do not worry at
  this stage about the number of words you are
  using, just write. You can edit afterwards.

9
Try it
10
(No Transcript)
11
(No Transcript)
12
Methods
Results
13
Methods
Results
The main result a pot of tea made in standard
way
The testable variables

• Which tea tastes best?
• Does a tea cosy make the tea better or worse?
• Does it taste different in a mug or cup?
• Milk? Sugar? Sweetener? Lemon?

14
Methods
Results
The main result a pot of tea made in standard
way
The testable variables

• Which tea tastes best?
• Does a tea cosy make the tea better or worse?
• Does it taste different in a mug or cup?
• Milk? Sugar? Sweetener? Lemon?

15
But what do I do with these?
Only needed for leaf tea
Part of the standard cuppa?
16
Methods
Results
The standard technique for reference, tea is
made this way. Control
The main result a pot of tea made in standard
way
The testable variables

• Which tea tastes best?
• Does a tea cosy make the tea better or worse?
• Does it taste different in a mug or cup?
• Milk? Sugar? Sweetener? Lemon?

The variables which tea tastes best (note
change in technique)?
The variables milk or lemon? Sugar or
sweetener?
17
Methods
Results
18
The story so far..

• You have results and methods laid out and easy to
  write.
• Gone from disorganised mix of results, methods
  to an organised story
• Gone from solo effort to working with others.
  co-authors to come later!

19
Now write the hypothesis aims and objectives for
your study
20
Your paper.. How is it going?
Relevant background to the problem
A O
Title abstract
Hypothesis
Materials and Methods
Introduction
Figures
My paper
Reading
Analysis
References
Results
References
Tables
Discussion
statistics
Text
21
Your report.. what next?

• Discussion
• Major results as temporary headings
• What does each result mean? Discuss with support
  from the literature.
• Do your results support/contradict other studies?
  
• Are there other analyses you could have done.
• Be critical and terse. Do not waffle.
• Introduction.
• Make sure that all major subject areas are
  introduced.
• Use references different from but complementary
  to those used for the discussion.
• Abstract the last job.
• Cover the major points of your work (not of
  others) in the abstract. See Malaria Journal
• The abstract should tell the reader your results,
  not just techniques.

22
But before you start all this

• Where are you going to submit your article?
• Generic journal? Nature/Science?
• Subject specific journal?
• Technique journal?
• Impact Factors do you and your supervisor have
  a strategy?
• Instructions to authors
• Read them, stick to them
• Must get agreement on this from all co-authors
  before you start.. Or at least when the results
  storyboard is run through.
• (Storyboard great practice for a talk etc very
  efficient way of working)

23
Co-authorswho should you include?

• You
• Supervisor
• Collaborators
• Did you pay them to do the work??
• All by agreement (you can afford to be generous)
• Anyone who has had significant academic and
  practical input into the work

24
Effective Scientific Writing

• Title
• Dont get too long and wordy
• Use scientific style
• Must tell the reader what sort of content to
  expect
• e.g. The effects of soil perturbations on plant
  and bacterial diversity
• NOT A study to show how bacteria and plants are
  affected by changes in.

25
Effective Scientific Writing

• Abstract
• Should give the aims and/or rationale for the
  study
• Minimal methods e.g. PCR was used to no
  detail!
• Focus mainly on results
• e.g. Twelve bacterial 16S rDNA sequences were
  analysed. this implies that the work has a
  PCR element and so you dont need to spend time
  on methods.
• What are the major conclusions?
• The main, most important and interesting pieces
  of data may be presented, but not everything.
• This is the shop window of your piece of work.
  It should tell the reader what s/he will find.

26
Effective Scientific Writing

• Introduction
• Explain what the work was about not methods but
  context
• Refer to other studies for background
• Use references
• Give a reference when you write words you did not
  compose yourself
• Present your aims (based on hypothesis) usually
  the last paragraph.
• Do not describe results

27
Effective Scientific Writing

• Materials Methods
• Describe what you did
• The description should enable someone else to
  repeat what you did
• Do not list materials or equipment used
• Do not use minute details what is important?

28
Effective Scientific Writing

• Results I
• Presents the data you obtained and analysed.
• Do not reiterate the methods
• Do not discuss these data
• Give results in words supported by drawings,
  diagrams, graphs and/or tables
• e.g. "The growth rate of the organism was
  exponential (Fig.1)" not "Fig. 1 shows that the
  growth rate of the organism was exponential."

29
Effective Scientific Writing

• Results II
• Tables and Figures must have a legend and be
  numbered (Table 1, Figure 1, etc). Do not use
  Graph 1 or Chart 1
• Refer to the Figures sequentially i.e. Figure 1
  must be referred to before Figure 2.
• Drawings and photographs must have a scale e.g. 1
  cm or 10 ?m
• Do not present the same data more than once
• Describe statistical analysis

30
Effective Scientific Writing

• Discussion
• Describe what your results show
• Are your results confirming or contradicting
  others?
• Explain your results in the wider context
• Refer to relevant published work
• Do not repeat results
• Show how your aims have been met have you
  effectively tested your hypothesis?
• Point to weaknesses, future work (brief)

31
Effective Scientific Writing

• References I
• List all the sources you used and cited in your
  text
• Use Reference list not Bibliography
• List in sequence required by the journal
• Avoid reference to websites.
• Go back to original articles do not rely solely
  on on-line searches

32
Effective Scientific Writing

• General Advice
• Avoid 1 sentence paragraphs
• Use binomial system for names
• In vitro, in vivo et al. are italicised
• Check spelling and grammar
• Some abbreviations need a stop, e.g., i.e. others
  do not Dr, Mr
• gramme, g or centimetre, cm have no stop
• Data is a plural noun

33
Effective Scientific Writing

• Correct use of units
• The correct term for weight is mass
• Units such as cm/h, mg/mL, mL/kg/min and ?l/g are
  written as cm h-1, mg mL-1, mL kg-1min-1 and ?L
  g-1 respectively
• Centrifugation units given in g
• Greek symbols ? ? ? ?
• Use proper symbols for /- i.e. ?, and for
  degrees i.e.?C (Celsius)
• Space between number and unit (2 cm NOT 2cm)

34
Your paper what to do with the first draft..

• Edit the work at every step of the way then edit
  it as a whole entity.
• Step back think like a referee for a while!!
• Send it to co-authors and to friends/colleagues
  who you trust to give good feedback (red penners)
• Act on comments get agreement
• Check again against Instructions to Authors
  submit.

35
Keeping a reference database

• What is a reference database?
• Filing system for papers/publications
• Integrated with on-line databases (e.g. BIDS)
• Allows retrieval of references in a collection
• Allows formatting of references for publication
• Integration with word processing software
• Procite offered free by University (learn how
  to use it)

36
Keeping a reference database

• Why bother?
• Now probably an essential aid to accessing and
  keeping up with contemporary literature
• Primary literature is an essential resource for
  scientists a good database manager will also
  allow searches etc. of commercial databases (e.g.
  WOS)
• Can keep details and personal notes of references
  in one place
• Huge time and effort saver when writing reports,
  thesis and manuscripts

37
Keeping a reference database

• What are the advantages?
• Work as you go along
• Quality control - once checked, no more errors
• Only type your references once at most
• Flexibility - same references for different
  journals, reports etc.
• Integration with on-line databases, current
  contents and other information sources
• Can be made a group effort

38
Keeping a reference database

• What are the disadvantages?
• Work as you go along - requires self discipline
• Front-loaded - results/advantages may not be seen
  for some time
• Group databases rely on group responsibility
• NONE REALLY

39
Responding to Referees Comments

• Dont get mad or discouraged
• Sometimes the referees are trying to be helpful
• Respond to every comment, positive and negative
• Make changes only if you agree with them
• Address all comments - changes or otherwise - in
  a covering letter
• The reviewer is not always right!!
• Get help with the letter argue your points
  carefully. Not everyone reads the same things!!
• Respond quickly often a deadline which if
  missed means full resubmission.
• If aiming high, approach the journal first e.g.
  Nature can save some heartache!