Writing a scientific paper training

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This presentation was given to animal science students, and was adapted from a number of sources (in the reference list). It is intended to help students understand how to structure a scientific article and the basics of scientific writing.
  • 1. Library Training: Writing a Scientific Paper 1 3 A U G U S T 2 0 1 9 ElizabethMoll-Willard FacultyLibrarian:AgriSciences emw@sun.ac.za
  • 2. Outcomes •Getting started •IMRAD •Authorship •General guidelines for length of a manuscript Basics •Figures and tables •Methods •Results and Discussion •Conclusion and Introduction •Abstract, title, keywords •Acknowledgements and References Steps •Writing styles •Writing tips Scientific writing
  • 3. The Basics
  • 4. The basic principles of all research Objectivity • The question of bias Repeatability • Anyone should be able to repeat your experiment with another sample and get the same or similar results Reliability • Instruments need to produce the same results if used by a researcher in future Validity • Your research should represent the best possible version of the truth at the time (guard against errors)
  • 5. Am I ready to write an article? What I ask myself •Have I done something new and interesting? •Is there anything challenging in my work? •Is my work related directly to a current hot topic? •Have I provided solutions to some difficult problems? What reviewers ask when looking at my work •Does the paper contain sufficient new material? •Is the topic within the scope of the journal? •Is it presented concisely and well organized? •Are the methods and experiments presented in the way that they can be replicated again? •Are the results presented adequately? •Is the discussion relevant, concise and well documented? •Are the conclusions supported by the data presented? •Is the language acceptable? •Are figures and tables adequate and well designed?, are there information duplicated? Are they too many? •Are all references cited in the text included in the references list?
  • 6. Types of articles Full articles, or original articles, are the substantial completed pieces of research that are of significance as original research. Letters/rapid communications/short communications are quick and early communication of significant and original advances. They are much shorter than full articles (usually strictly limited in size, depending on each journal). Review papers or perspectives summarize recent developments on a specific hot topic, highlighting important points that have previously been reported and introduce no new information. 6
  • 7. Choosing my journal Steps to follow: (1 – the invisible step: often your supervisor will suggest one) 1. Check the DHET accredited list – make sure of a peer review process 2. Check the Journal’s impact factor 3. Have a look at the scope and policies of the journal 4. Consider the funding aspect – is there funding for open access? Who is paying page fees? 7 BEWARE THE PREDATORS
  • 8. Author Guidelines Always have a look at these to see what the journal wants! ◦ They set out structure, referencing style, caption style, etc 8
  • 9. IMRaD structure (most used) I • Introduction: what did you do? MR (central report section) • Methods: how did you do it? • Results: what did you find? aD • and Discussion / Conclusion: what does it mean? 9
  • 10. ARRIVE Use other guidelines to help – for example: ◦ Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines are intended to improve the reporting of research using animals – maximising information published and minimising unnecessary studies. 10
  • 11. 11
  • 12. The Authorship question Principles of the order of listing: General principle: it is in order of significant contribution to the paper First author is usually the “principal investigator” of that experiment: ◦ Conducts and / or supervisors the experiment, the data analysis and the results processes ◦ They will usually put the paper together and submit it to the journal Corresponding author – does not necessarily have to be first author ◦ Could be first author ◦ Or could be senior author from the institution Make sure to include all who should be included, but don’t fall into the trap of “gift authorship” – including authors who did not contribute significantly Names – make sure you follow the spelling / style that authors use!
  • 13. General guidelines for length of a manuscript NB look at the journal's Guide for Authors, but an ideal length for a manuscript is 25 to 40 pages, double spaced, including essential data only. Here are some general guidelines: Title: Short and informative Abstract: 1 paragraph (<250 words) Introduction: 1.5-2 pages Methods: 2-3 pages Results: 6-8 pages Discussion: 4-6 pages Conclusion: 1 paragraph Figures: 6-8 (one per page) Tables: 1-3 (one per page) References: 20-50 papers (2-4 pages) Taken from: https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take- seriously 13
  • 14. Steps to writing a paper
  • 15. Steps of writing a journal article Figures and tables Methods Results and Discussion Conclusion and Introduction Abstract, title, keywords Acknowledgements and References
  • 16. Step 1: Figures and tables
  • 17. Figures and tables Figures vs tables: general rules ◦ Tables give the actual experimental results ◦ Figures are used for comparisons of experimental results with either previous works or calculated/theoretical values The most important point: No illustration (figure, table, etc.) should duplicate any information found elsewhere in the article (legends should be self-explanatory) The colour question: ◦ Colour used to bring in a cost question when it came to print charges for print journals ◦ Now with online-only publication, you can use colour – but be tasteful ◦ Black and white is sometimes still the most striking to relate your data, while colour can cloud things
  • 18. Figures and tables – the don’ts Font size matters – keep things readable No indistinguishable data! Keep things clean and distinguishable Don’t put long tables in text – you can rather include it in supplementary tables (eg. Lists of species) Include scale where necessary (photographs etc) Be consistent – eg. Decimals comma vs full stop Graphs ◦ Only use line diagrams for a time series or consecutive samples. Otherwise use a histogram (bar graph) ◦ No crowded plots! Only use a three / four data sets max per graph ◦ Don’t forget to label your axis clearly
  • 19. Step 2: Methods Step 1: Figures and tables
  • 20. Headings or subheadings – very NB Describe how you studied the problem ◦Don’t describe procedures already published (only novel) ◦Identify equipment, materials etc. ◦Be detailed! Include variables etc. ◦Ethical issues should be covered – did you get ethics / how ◦Don’t add comments / discussion / results here Methods (2-3 pages)
  • 21. Protocols If the method you are using is already established then only a brief description / broad summary and a reference is necessary BUT If a new method, then you have to describe it in as much detail as possible in order to allow for *replicability* Remember to use standard numbers: ◦ Chemicals, taxa of species, units of measurements 21
  • 22. The order of your method Remember to mirror your order as written in results: Description of the site Description of the surveys or experiments done, giving information on dates, etc. Description of the laboratory methods, including separation or treatment of samples, analytical methods, following the order of waters, sediments and biomonitors. If you have worked with different biodiversity components start from the simplest (i.e. microbes) to the more complex (i.e. mammals) Description of the statistical methods used (including confidence levels, etc.) 22
  • 23. Step 3: Results and Discussion Step 2: Methods Step 1: Figures and tables
  • 24. ◦Tell a story about your results – use subheadings to structure nicely, keep the golden thread running ◦ Subheadings let you group similar results together ◦Include: ◦ Main findings (not all are needed – can add supplementary materials for data that is secondary importance) ◦ This would be findings from experiments in methods sections ◦ Highlight findings that ◦ Differ from previous publications ◦ Are unexpected ◦ Results of the statistical analysis Results
  • 25. ◦Importance of your figures and tables ◦ The most efficient way to present your results / findings ◦ Captions and legends must be detailed ◦ Your figures and tables must be self-explanatory – no need to read in text ◦ Don’t duplicate results that are described in the text or other illustrations – let them work together instead ◦ Don’t include references – you are not referring to other work, but to your work. You will refer to other work in the discussion. Results
  • 26. This is the most important section – as it speaks to YOUR work ◦Discussion and results should correspond ◦Can now start to bring in published results vs yours Discussion
  • 27. What to avoid: 1. Avoid statements that go beyond what the results can support. 2. Avoid unspecific expressions such as "higher temperature", "at a lower rate", "highly significant". Quantitative descriptions are always preferred (35ºC, 0.5%, p<0.001, respectively). 3. Avoid sudden introduction of new terms or ideas; you must present everything in the introduction, to be confronted with your results here. 4. Speculations on possible interpretations are allowed, but these should be rooted in fact, rather than imagination. To achieve good interpretations think about: ◦ How do these results relate to the original question or objectives outlined in the Introduction section? ◦ Do the data support your hypothesis? ◦ Are your results consistent with what other investigators have reported? ◦ Discuss weaknesses and discrepancies. If your results were unexpected, try to explain why ◦ Is there another way to interpret your results? ◦ What further research would be necessary to answer the questions raised by your results? ◦ Explain what is new without exaggerating 5. Revision of Results and Discussion is not just paper work. You may do further experiments, derivations, or simulations. Sometimes you cannot clarify your idea in words because some critical items have not been studied substantially. 27
  • 28. Step 4: Conclusion and Introduction Step 3: Results and Discussion Step 2: Methods Step 1: Figures and tables
  • 29. 1. Explains the problem 2. What kind of work has been done on the topic (mini literature review): ◦Potential solutions ◦Suggested solution ◦Limitations / differing opinions 3. Aim/ purpose or thesis statement (usually in the final paragraph) Introduction
  • 30. ◦ Explains how your work advances the field – answering the questions in your introduction, points brought up in discussion ◦ If you want to suggest future experiments, this is the place ◦ This section is sometimes the last paragraph in discussion, and sometimes it is standalone Conclusion
  • 31. Step 5: Abstract, title, keywords Step 4: Conclusion and Introduction Step 3: Results and Discussion Step 2: Methods Step 1: Figures and tables
  • 32. Abstract, title, keywords These are your marketing tools for your paper You want people to read your work, so make sure you have good marketing. Databases and search engines typically search through these, and use these to organize information.
  • 33. Your abstract Write to sell your article – it is the advertisement to make people read your article ◦ This means make it easy to read, make it interesting, make it understandable ◦ BUT still be accurate, still be specific and brief – showcase your work You get different styles of abstracts – have a look at the journal requirements!
  • 34. Your title Keep it short and simple ◦ BUT describe your paper adequetly Tips for effective titles: ◦ identify main issue of the paper ◦ Begin with the subject of the paper ◦ Are accurate, unambiguous, specific and complete ◦ Are as short as possible Your aim is that your title will get “noticed” – keep away from abbreviations or rarely used terms
  • 35. Keywords Think of your keywords like hashtags on Twitter – they are what drives search engines and databases to select YOUR paper to display in the results They are like labels Abbreviations – only established ones (eg. DNA) For example: “silo music and silo quake: granular flow-induced vibration” Keywords: silo music, silo quake, stick-sap flow, resonance, creep, granular discharge
  • 36. Step 6: Acknowledge ments and References Step 5: Abstract, title, keywords Step 4: Conclusion and Introduction Step 3: Results and Discussion Step 2: Methods Step 1: Figures and tables
  • 37. Acknowledgements and References Two things to keep in mind: ◦ It can be journal specific – have a look at the journal style guidelines for authors ◦ Reference managers can help but you need to do a quality check Reference management tools Programs that assist you in storing your citations, managing your citations and then inserting citations in a specific citation style while you write your assignment
  • 38. Acknowledgments You are recognizing those who helped in your research! They include: ◦ Supervisors / other advisors ◦ Financial support (eg. NRF) ◦ Proof readers / editors / typists ◦ Suppliers if they gave materials (eg. If you sampled from a specific farm, that farm) ◦ Data analysts / statisticians / graphic makers
  • 39. References Check the style! It is usually under “guidelines / instructions for authors” General principles: ◦ Don’t go overboard – only use references that you have actually used the article / material ◦ Make sure you aren’t referencing from an abstract or a secondary source – read the full article! ◦ DON’T ◦ Cite yourself excessively ◦ Cite one author excessively ◦ Cite only from one region – try to be as international as possible
  • 40. How to skim read First sentence of each paragraph Introduction + conclusion Table of contents Abstract Title, author, journal, date
  • 41. Scientific writing
  • 42. Writing tips Write early and write often • the more you write, the easier it becomes and it becomes a habit Don't get it right, get it written • drafting helps you to clarify your thoughts, start by writing the parts you are clear on, this identifies the bits that need more work
  • 43. Main points to remember when writing: A 'golden thread‘ ◦ an overall line of argument - running through the paper, holding it together 'Sign-posts‘ ◦ crisp titles, sub-titles and headings that identify the direction being followed 'Authority‘ ◦ good engagement with existing literature and a comprehensive bibliography - the bibliography is the window to the paper and its author
  • 44. Things to avoid Avoid long quotations ◦ rather paraphrase or break up the quote with your own commentary Avoid sloppy and inaccurate presentation and ensure that your references are correct ©https://www.jewellerymonthly.com/a-diamond-in-the-rough/
  • 45. Topic Sentence • Summarises argument • Indicates approach Elaboration • May provide additional information or restate the topic sentence in a more extended way. Evidence • Maybe be quantitative or qualitative data, or analysis of data. Link • This makes the connection to the next paragraph explicit. Paragraph structure
  • 46. The funnel approach Your topic Effect of cold storage on longevity of proteas General Proteas Cold storage methods for proteas Go from the general to the specific Cold storage positively impacts the Protea market through lengthening their shelf life
  • 47. Sources do not clearly relate to the research problem; Lack of defining and identifying the most relevant sources related to the research problem; Relying exclusively on secondary analytical sources; Uncritically accepting another researcher's findings and interpretations Reporting isolated statistical results rather than synthesizing them; and, Only including research that validates assumptions Common Mistakes to Avoid
  • 48. Peer review 48
  • 49. Arrive guidelines. Available: https://doi.org/10.1002/9781118951446.ch22 Becker, Lucinda & Denicolo, Pam. 2012. Publishing journal articles. London: SAGE. Available in library: RCOM 808.066 BEC Borja, Anjela. 2014. 11 steps to structuring a science paper editors will take seriously. Available: https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take-seriously Caterjian, A., 2013. Editorial special: writing a journal article. Australian Journal of Clinical Hypnotherapy & Hypnosis, 35(2), p.55. Available: https://link.gale.com/apps/doc/A379569226/AONE?u=27uos&sid=AONE&xid=d73f3ad8 Day, Robert A. & Gastel, Barbara. 2006. How to write and publish a scientific paper. 6th edition. Westport: Greenwood Press. Available in library: RCOM 808.0665 DAY Elsevier. 2012. Structuring an article. In Publishing connect: How to get published series. Available: https://www.elsevier.com/connect/how-to-get-published-3-structuring-an-article Gustavii, Bjorn. 2008. How to write and illustrate a scientific paper. 2nd edition. Cambridge: Cambridge University Press. Available in library: RCOM 808.0665 GUS Lourens, Amanda. 2007. Scientific writing skills: guidelines for writing theses and dissertations. Stellenbosch: SUN Press. Available in library: R 808.0665 LOU References & Tools
  • 50. Thank you!
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