How To Write A PhD In Biological Sciences: A Guide For The Uninitiated

Cover
Half Title
Title Page
Copyright Page
Dedication
Contents
List of Tables
List of Figures
Welcome
About the Author
I. Right from the Very Start
1. Introduction
1.1. So you are doing a PhD?
1.1.1. What is a PhD?
1.1.2. Is a PhD more than a thesis?
1.1.3. Criteria used to judge PhD studies
1.1.4. Who are the examiners?
1.1.5. What will you do after your PhD?
1.1.6. Think about your career before you start your PhD
1.1.7. Don’t rely on becoming an academic
1.1.8. Doing a PhD is really hard work
1.1.9. Your mental health will likely suffer
1.1.10. Any PhD has to be yours
1.1.11. Does it matter where you do your PhD?
1.1.12. What to look for in an advisor
1.1.13. What to avoid in an advisor
1.1.14. What makes a good project?
1.1.15. Funding your PhD studies
2. Reconciling Yourself to Doing Things You’ve Been Avoiding
2.1. And learning lots of other stuff…
3. The Scientific Project and Scientific Living
3.1. Example: Invasive species
3.2. Should society lead the sciences or sciences lead society?
3.3. Carl Sagan’s “Baloney detection kit”
3.4. Live your life scientifically
3.5. Citizen science
4. Keeping Track of Your Mental Health
4.1. Being physically active improves mental wellbeing
4.2. Time to think
4.3. Balancing work with life
II. The Nuts and Bolts of Writing for the Biological Sciences
5. How to Get Started with Writing
5.1. How to write a hypothesis
5.1.1. What is a hypothesis?
5.1.2. What a hypothesis isn’t
5.1.3. A formulaic way to start writing your hypothesis
5.1.4. Teleological versus causal hypotheses
5.1.5. How to evaluate your hypothesis
6. Being Aware That You Can Get It Wrong
6.1. Changing the likelihood of a hypothesis
6.2. Increasing the statistical power
7. What Happens If You Don’t Have a Hypothesis?
7.1. Central problem
7.2. Does it matter that you don’t have a hypothesis?
7.3. Avoid HARKing
8. What’s the Big Idea?
8.1. So where would we find these big ideas?
9. Writing a Paragraph
9.1. Topic sentence
9.2. Supporting sentences
9.3. The magic of threes
9.4. Use an example
9.5. Avoid lists
9.6. The last sentence of the paragraph: The clincher
9.7. Above all – read it!
9.8. How does the paragraph fit into the flow?
9.9. Seeding ideas
9.10. Breaking the rules
9.11. Some common paragraph mistakes
10. Construct a Logical Argument in Your Writing
10.1. Arguments in Latin
10.2. Other arguments in English
11. Storytelling in Science?
11.1. The danger of a teleological argument
11.2. Science is the very opposite of storytelling. Or is it?
11.3. Can storytelling help memory of science?
12. Why Do You Need to Cite?
12.1. Research is built on existing work and ideas
12.2. Your citations say a lot about you
12.3. Cite while you write (not afterwards)
12.4. Citation styles
12.4.1. Vancouver style
12.4.2. Harvard style
12.5. Moving from Harvard to Vancouver
12.6. Where within a sentence should the citation come?
12.7. What about the order of the citations in a string?
12.8. What about citations as taxonomic authorities?
12.9. Is it possible to mis-cite?
12.10. Should I cite without reading the paper?
12.11. What should I not cite?
12.12. Do I cite the review or the primary literature?
12.13. What is primacy and why does it matter?
12.14. How many citations are enough?
12.15. Should I cite myself?
12.16. Should I cite my friends?
12.17. Does the impact factor of the cited article matter?
13. Literature Databases
13.1. Searching the literature using a database
13.2. Keywords
13.2.1. Boolean terms or operators
13.2.2. Proximity operators and parentheses
13.2.3. Wildcards
13.2.4. Combining searches
13.3. Moving items into your reference manager
13.4. Citation searches
13.4.1. What else are literature databases used for?
13.5. Administrators want metrics
13.6. Searching by scientist’s name
13.6.1. Overcoming the difficulties of common names
13.7. Google Scholar, Web of Science or Scopus?
13.8. What’s the difference between indices?
14. Reference Managers
14.1. Other points to consider
15. What Software Should I Use to Write My PhD?
15.1. Alternatives to conventional word processors
15.2. Naming versions of files
15.3. How many versions of each file should you keep?
16. What to Do When Faced With a Paywall?
16.1. Go to your library
16.2. Look for links from Google Scholar
16.3. Google the title in quotes
16.4. Go to the author websites and look for links
16.5. Go to the institutional repository of the author
16.6. Try an Open Source OA tool
16.7. Write to the author and request a pdf
16.8. Go to an academic social media site
16.9. Black open access
16.10. Use your contacts at other universities
16.11. Go back to your librarian and ask them for help
16.12. Get an interlibrary loan
17. Scientific Names and Taxonomic Authorities
17.1. Scientific names
17.1.1. Consider this example
17.2. Different codes for the nomenclature of different taxa
17.2.1. Peculiarities of plant taxonomy
17.2.2. Other times to use italics
17.3. Common names
17.4. Should common names have capitals?
17.4.1. View 1 - Yes
17.4.2. View 2 - No
18. Writing Style
18.1. Develop your writing style
18.2. Don’t bamboozle
19. Retaining Your Own Voice When Writing
19.1. Does writing ‘I’ or ‘we’ help people to understand who you are?
19.2. The Vonnegut advice
20. Writing Concisely
20.1. Rule 1. Take writing seriously
20.2. Rule 2: Identify and stick to your message
20.3. Rule 3: Get to the point
20.4. Rule 4: Keep your methods and results contained
20.5. Rule 5: Do not repeat yourself (too often)
20.6. Rule 6: Avoid unnecessary or inefficient ‘lead‐ins’
20.7. Rule 7: Use first‐person, active voice
20.8. Rule 8: Remove unnecessary words
20.9. Rule 9: Simplify your language
20.10. Rule 10: Seek and embrace feedback
20.11. Rule 11: Read it yourself
21. Writing a PhD If English Is Not Your First Language
21.1. Message from an editor
21.2. Must a ‘native English speaker’ check your work?
21.3. So if not a native English speaker, who should do it?
21.4. But surely my native tongue can be used for something?
22. Making Sure That You Don’t Plagiarise
22.1. How to know if you have plagiarised
22.2. What to do if plagiarism is detected in your work
22.3. How can you make sure that you never plagiarise?
22.4. What is autoplagiarism?
23. Academic Phrasebank
23.1. How to find the phrase that you need
23.2. Getting started
24. Why Critical Reading Is Crucial for Improving Your Writing
24.1. Making notes on good and bad styles
24.2. Some examples
24.3. Make handwritten notes
24.4. Recognising good or bad in what you read
25. What Is Needed for Your Research Proposal?
25.1. Structure
25.2. Proposal introduction
25.3. Methods and materials
25.4. Hypothetical results
25.5. Your proposal – what is it good for?
25.5.1. Copy and paste directly into your thesis
25.5.2. Use it to raise money to do your studies.
25.5.3. Deposit the proposal to conform to Design and Analysis Transparency
26. Making a Presentation from Your Chapter, Paper or Proposal
26.1. So where do you start?
26.1.1. Here are some simple rules to help guide you to build your presentation
26.1.2. A formula for presenting a proposal
26.2. Know your story first and then make your presentation
26.3. Slide layout
26.4. Practice, practice, practice
27. Starting Out Transparent
27.1. Preregistration
27.1.1. Does this mean that you can’t perform any data exploration?
27.1.2. Will preregistration of research eliminate the bias from science?
27.1.3. What platform should you use?
27.2. Transparency as you move forwards
28. Generating Funding for Your PhD Research
28.1. Funding databases
28.2. Reasons you might want to apply for funding
28.2.1. Mendeley: //www.mendeley.com/
28.2.2. Open 4 Research: https://www.open4research.eu
28.2.3. Research Professional: https://www.researchprofessional.com/
28.2.4. Opportunities in your department or societies
29. Fear of Submitting Written Work
29.1. What is impostor syndrome?
29.2. Think of it this way
29.3. What can you do to help yourself overcome the fear of submitting written work?
29.4. When is it good enough to submit to my advisor?
30. Why Use a Formula to Structure Each Chapter or Paper?
30.1. So what is the formula?
30.1.1. My take on how to write a formula paper
30.1.2. Start with an outline
30.1.3. Next flesh out the outline with citations
30.1.4. Lastly it’s time to write the text
31. Data Management
31.1. Should the cloud be the only copy of your data?
31.2. Backing up in the field
31.3. Make a data management plan, and stick to it
III. The Sections of Your Chapter
32. Writing the Sections That Make up Your Data Chapter
32.1. Title page
32.1.1. Names and addresses are important
32.2. The title
32.2.1. Some title ideas to start you off
32.2.2. Things to avoid in your title
32.3. Keywords
33. The Abstract
33.1. So what would a good abstract contain?
33.2. Where do you start?
33.3. When do you write your abstract?
33.4. Do abstracts for conferences differ?
33.5. Where do people go wrong in writing the abstract?
34. The Introduction
34.1. Why do we need an introduction?
34.2. So what do we put into the introduction?
34.3. And the construction…?
35. The Materials and Methods
35.1. Sections or subheadings
35.2. Study organism or study system
35.3. Animal husbandry / growing conditions / culturing techniques
35.4. Repetitive methodology
35.5. Do you need to include formulae?
35.6. Experimental manipulations and data collection
35.6.1. Equipment
35.7. Data analysis
35.8. Did you leave anything out?
36. The Results
36.1. The correct approach – responding to your hypotheses
36.2. When to have a table or graph?
36.3. Descriptive results
36.4. Responding to hypotheses
36.5. Common mistakes
37. The Discussion
37.1. First paragraph of the discussion
37.2. To sub-section or not to sub-section the discussion?
37.3. Caveats and limitations
37.4. Should you speculate in the discussion?
37.5. Don’t beat up on others
37.6. Where next?
37.7. Last paragraph
37.7.1. Never repeat text
38. The Acknowledgements
38.1. Thank your funders
38.2. People and organisations to thank
38.3. Who not to thank (in your manuscript acknowledgements)
39. The References
39.1. Vancouver style
39.2. Harvard style
39.3. Digital Object Identifiers (DOIs)
39.3.1. DOI tools
40. Tables
41. Figures
41.1. Graphs
41.2. Maps
41.2.1. Maximising the content of your figure
41.3. Conceptual diagram
41.4. The composite figure
41.4.1. Ideas for composite figures
41.5. Sending your graphics file to the publisher
41.5.1. Vectors vs. bitmaps
41.5.2. Sizing your figure
41.6. The figure legend
42. Who Did What?
42.1. CRediT where it’s due
42.2. Ordering the author line up
43. Supplementary Material
43.1. What can go into supplementary material?
43.2. Towards transparency and repeatability of scientific studies
43.3. Why stop with just depositing your data and analyses online?
IV. After the Data Chapters
44. Now That You Have Finished Your Data Chapters
45. How to Introduce Your PhD Chapters
45.1. Citing your chapters
45.2. Formulate the objectives of your study?
45.3. Review consistent thesis themes
45.4. Removing the contents of chapters to place in the introduction
45.5. How long should the introductory chapter be?
46. How to Conclude Your PhD
46.1. Using the funnel structure
46.2. What to include in the concluding chapter?
46.3. Concluding section
47. Formatting Your Thesis
47.1. Must do check-list before submitting your thesis
47.2. Mistakes people make
The Obligation to Publish Your Work
Last Note
Bibliography
Index