Scientific Writing: Common Pitfalls & How to Avoid Them

Dr. Dhananjay Shukla
Published Online: April 2nd, 2021 | Read Time: 16 minutes, 49 seconds

The preceding chapters have given us a fair idea of how to go about writing an original manuscript for publication: the why, the what, and the how of manuscript writing. We have been primed with inspiration, research tools, and the nitty-gritty of techniques to carve out an original contribution to science from the banalities of repetitious clinical routines. But before we jump headlong into the unforgiving cauldron of publishing research, let us trim our intellectual exuberance with the reality check of the roadblocks, ruts, and pitfalls on the way to the crowning glory of our maiden publication. This wisdom is necessary so that we may avoid some common booby traps in manuscript writing, and learn to both avoid and handle the inevitable and repetitive failures, which should not snuff out our spark at the first setback.

BEFORE WE WRITE: the first hiccups

The writer’s block hits the prospective authors right at the starting block: how to generate a new idea for research? A few starting points are an unusual clinical observation, a complication of disease or treatment, or innovative use of a diagnostic or therapeutic tool. This is generally the most exciting phase of clinical research, and it is easy to get carried away in this Eureka mindset, ignoring the hard facts in the available literature on the subject. A rigorous review of literature is essential to ascertain the real value of the new finding or ideas. It is sobering but sane to remember that the first ideas born in an unprimed mind are generally mediocre, and need to be discarded; their value lies only in paving the way for better ideas to come. Another trap awaits us during the review of literature, what the psychologists call the confirmation bias:1 the tendency to selectively seek the literature favoring the author’s preset views, conniving at the uncomfortable evidence to the contrary. This ostrich-like approach generally dooms the project for a quick rejection; one must take the bull by the horns: rigorously test the validity and novelty of one’s idea against the literature, and dump the idea unsentimentally if it fails to pass the muster.

A major stumbling block - after the data has been collected on a suitable research idea- is what to start writing with: Abstract, Introduction, Material & Methods, Results or Discussion? The most logical starting point appears to be the Material & Methods, followed by the Results: 2,3 creative thinking is the most difficult part for the beginners, and the simplest way out is, to begin with how we did the study and what we found. Some new authors, however, bypass the starting troubles altogether: by choosing to write comments on a published original article. It is always easier to take a dig at others’ work than breaking new ground. Comments or Correspondence to Journal are typically are not peer-reviewed, and are more readily accepted by most journals. The desire to see one’s name in print is thus easily satisfied, deluding us into presuming the glory of authorship. However, only the original work carries any lasting value, and the earlier we brace ourselves for the real deal, the faster we shall learn the ropes. Yet another temptation for the beginners to avoid is submitting to non-indexed, regional, in-house journals, where acceptance is guaranteed. We should target the highest impact indexed and peer-reviewed journal that is compatible with our research theme, publish similar articles and caters to the intended readership.2-4

STRUCTURING THE MANUSCRIPT: tightening loose ends

Title and Abstract

The title should serve an invitation to the reader to look in: tiles that are either too short (and cryptic) or too long (and exhausting) are a put-off. 2,5 Similarly, Abstract is a window to the manuscript: most manuscripts are rejected here before peer review. The most common weaknesses include lack of a clear focus: the methods not relevant to the objectives, findings not derived from the methodology, and failure to arrive at logical conclusions from the findings. It is imperative to keep track of the main objectives of the study throughout the write-up and to finalize the title and the abstract only after drafting the manuscript. 3,4,6


As mentioned earlier, starting to write a paper with Introduction is a bad idea: 6 we cannot introduce what we do not know about. Introduction and Discussion are the weakest parts of the novice manuscripts: the main weakness of the Introduction being the absence of rationale of the paper in the last paragraph.7 Another common mistake is an expansive introduction with an extensive review of literature: authors are sometimes unable to differentiate Introduction from Discussion.8,9 The former should provide only enough background to explain what new question the study addresses, and what the importance of the proposed study question is, in about a tenth of the manuscript’s word count.5,9

Material and methods

Once a new idea or research question is validated, the methodological questions crop up: how to collect (the technique of intervention, investigation) and organize data (tables), how much data is needed (choosing a sample size) and the duration of follow-up.10,11 The rigor of methodology determines the destination of a manuscript, from a top-rung journal to a garbage bin.11 This becomes immediately evident by checking the extremely detailed instructions for authors of a top journal, say, Ophthalmology. In fact, if one is able to religiously abide by the methodological guidelines for such a journal, the manuscript is very likely to be accepted by one or the other journal.3 Common shortcomings in methodology include lack of clarity on study design, selection criteria for subjects, outcome measures (for ophthalmologists: visual and anatomical outcomes), redundant or ill-suited investigations or statistical design, ethical issues and follow-up data. For example, a common fallacy is to compare outcomes obtained at widely varying follow-up periods instead of a common point of time.3,12


Results are the heart of the matter. New authors often go overboard with this section, cluttering the essential outcomes and analyses with trivial data. The results should correspond exactly to the methods (tests, interventions) and detail only the findings relevant to the aim of the study. Reduplicating, rather than highlighting, the findings in the tables and graphics in the text is another common error.8,11 An important art to learn for the beginner is how to condense multiple tables created during analyses into 1-3 key tables (e.g., for a clinical ophthalmic study, 2 key tables would be on baseline demographics, and on intervention outcomes). Finally, some eager beavers start interpreting the data in this section, in continuation with statistical analysis.3,811,13 And remember that statistical analysis does not begin and end with P values; details of the tests used should be mentioned.3,13 Similarly, glossing over negative findings or complications invites rejection; addressing and explaining those impresses reviewers.


For beginners, this is the most challenging part of the paper, and also the weakest link. 7 Discussion includes a recap of the study outcomes, comparison with literature, strengths, and limitations of the study, and the conclusions. Summarizing the outcomes is a no-brainer; treacherous terrain begins with a comparison of outcomes with the previous studies, where claims of originality and relevance are tested. The exercise of pointing lacunae in existing literature without sounding too critical, and highlighting one’s findings without looking over-emphatic is a tightrope walk. Authors are sometimes guilty of overselling the study's strengths while pushing the limitations under the carpet.3,811,14 The final paragraph of the Discussion (and the manuscript) is for concluding remarks. While it is creditable to discuss the broader applications and future implications of the study, the temptation for wild speculations and extrapolations is a recipe for rejection and must be curbed.11


Though the International Committee of Medical Journal Editors (ICMJE) has outlined uniform requirements for biomedical journals, most journals are finicky about the small tweaks in their specific requirements, particularly in reference formatting.15 Loose formatting reveals a callous or careless attitude to the reviewer and nudges borderline manuscripts over the edge. A simple solution is to follow author instructions of the journal verbatim. We must also remember that more is not merrier: excessive references reveal not erudition but a lack of discretion.


There is no excuse for not paying attention to author instructions, which include following the language (British or American English), style, figure requirements, and ethics clearances, to mention a few. The use of passive voice (“A change in intraocular pressure was noted”) is considered escapist; we must commit ourselves in the active voice (“we noted a change in intraocular pressure”).7 Writing a manuscript is actually like writing a story against the backdrop of published work in the field: what we have found, and why it is important.5 When there are additional universal selling points of the story that we are unable to accommodate in the text due to space constraints, we can and should include them in the cover letter, to the editor.16 Finally, the manuscript should be tested for general readability of the manuscript by impartial feedback from colleagues before submission.4,5


A commitment to publish is a commitment to persist; most journals with repute and impact accept only 10-20% of the submissions. All the ruthless critique, reappraisal, revamping and redrafting BEFORE submission are intended to make the author certain of the quality of the submission. Once submitted, a paper should be backed to the hilt, not be surrendered to the dictate of a hardnosed reviewer. The reviewer’s criticism should be used constructively to improve the manuscript, to be resubmitted to a more welcoming journal. And do not forget to reformat the paper for the new journal’s specifications. How long should one persist with resubmissions? Some authors recommend giving up after the 3rd rejection;8 personally, I persist till 6th rejection…at least. Remember: the higher we aim, the more the number of rejections.

TO ERR IS HUMAN: summary and conclusions

Most journals don’t choose the divine option of forgiveness when dealing with human errors in the manuscripts; the more critically we judge our work before submission, the more kindly it shall be rated by the reviewers. We can avoid deviations from the theme by deciding early on the key message of the paper (what is known, what we add to the knowledge, and why it is important) and staying focused on it. After the first draft is ready, revisit the paper several times, preferably after a few days, and relentlessly trim redundant data: less is more. Once a genuine research question is addressed by suitable methodology, clarity, brevity and focus shall win the day for the aspiring researchers…eventually. Bon, voyage!


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Dr. Dhananjay Shukla
Senior Consultant and Director, Retina-Vitreous Service, Ratan Jyoti Netralaya
Dhananjay Shukla completed his post-graduation in Ophthalmology at G.R. Medical College, Gwalior in 1994. He joined Aravind Eye Hospital and Postgraduate Institute, Madurai for a Fellowship in IOL and Anterior Segment Microsurgery in 1995; he subsequently completed another Fellowship in Retina-Vitreous Service at the same centre, and joined rank as Assistant Professor of Ophthalmology in 1998. He continued there, and served as a Professor of Ophthalmology & Consultant, Retina-Vitreous Service (2007- 2012). After a brief stint as Medical Director and Vitreoretinal consultant at Centre for Sight, Ludhiana (Sept 2012- April 2014), he is currently working at Ratan Jyoti Netralaya, Gwalior, as Consultant, Retina-Vitreous Service (May 2014 onwards). He has been the Section Editor, Retina at the Editorial Board of Indian Journal of Ophthalmology since June 2011. He has contributed more than 70 free papers, posters and video presentations, and more than 100 faculty lectures at national & international conferences. He has 88 publications (71 as 1st or corresponding author) in indexed, peer-reviewed journals, including N Engl J Med, Ophthalmology, Arch Ophthalmol, Am J Ophthalmol, Surv Ophthalmol, Br J Ophthalmol, RETINA, Indian J Ophthalmol, etc. He is a reviewer for 18 international journals including Ophthalmology, RETINA, Br J Ophthal, etc. He has authored 18 chapters in various textbooks, including one on Eales disease in RETINA (Ryan SJ, editor-in-chief), 5th ed., 2013, and the same for Ryans RETINA (Schachat AP, editor-in-chief), 6th ed. 2018 as well as 7th edition (Sadda S, editor-in-chief; in press). He was co-investigator in two multicenter randomized clinical trials of drugs Ozurdex and Macugen. He has featured in Marquis Whos Who in Medicine & Healthcare (2007), Whos Who in Asia (2007, 2012), Whos Who in the World (2009), and Whos Who in Medicine & Health Care (2009, 2011). His current areas of interest include surgical management of macular disorders, pediatric retinal diseases and retinal vasculitis. In sports, he won the Athletic Championship (1987-1989) & Tennis championship (1998-91) as a student at G.R. Medical College, Gwalior. As a distance runner now, he has completed 3 certified marathon (42.2km) races (Dec 11, 2016, Feb 25, 2018 and April 15, 2019), with finish times of 4:01:29, 3:24:04 & 3:49:04 hours respectively, the last being the famous Boston Marathon 2019, for which he qualified the previous year.
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