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Ultimate guide to planning well-organised manuscripts for life scientists: an English scientific editor's top tips

 
Planning is essential for well-organised manuscripts

It’s no secret that experienced authors  — whether they write technical documents, children’s books or romance novels — make solid plans and outlines before they write a single word.

In the same way, I recommend you should plan your whole manuscript as a simple list of bullet points before you start to actually write. That's because it is virtually impossible to write well if you haven’t decided what you need to write about.

 

Why should I plan my manuscript?

If you don't have a plan, when you begin to write your brain will jump around thinking of all the things you need to include or read about, and this will distract you.

It is so much easier to make a good plan before you start writing - before you need to start to think about writing sentences, looking for references and worrying about grammar.

Refining your ideas will also allow you to check you’ve thought of everything you need to include. 

 

How do I start to make a plan?

It is important to think of planning as a distinct, separate task to writing. You should schedule some quiet time to just brainstorm and write down all of your ideas.

When I plan, I don’t worry about writing perfect sentences or being grammatically correct. I just want to write down all of my ideas — it can be messy and I might use a lot of paper — and then I start to arrange everything into a series of short bullet points.

At this stage, you can also start to assess the flow of information in your plan. For example, does the information in your Introduction flow from simple to complex?

 

When should I plan my manuscript?

You can start to plan as soon as the first idea for a new manuscript emerges. Your plan should be a living, changing document, even if it only starts as some scribbles on a scrap of paper or notepad.

Collect all of your ideas, list the data and facts you need to mention and note the relevant references. Store these notes carefully. They’ll be invaluable when you start to refine your plan by creating a series of bullet points before you start to write.

Even better, if you find a gap in your knowledge as you make your plan, then you can do a bit more reading and find the information you need - before you start writing.

If you're a little less organised, you should still start to plan at least one day before starting to write. This will let your ideas develop and mature. Looking at your plan with fresh eyes will help you see what you’ve missed or forgotten, and help you critically assess the flow of information.

 

Get some feedback on your plan before you start writing your manuscript

If you’re working with other collaborators or writing a chapter of your PhD thesis, then discuss your plan or bullet points with your colleagues or supervisors before you start to write. It’s much easier and quicker to get feedback and spot problems in a simple series of bullet points than having to drastically rearrange or rewrite the whole draft of your manuscript.

Try to be open and receptive to what your supervisor and colleagues say. I used to think any sort of advice and feedback was criticism – I’d feel like I’d failed because I did not create the perfect plan the first time. However, I didn’t realise that other people can often spot the gaps in your plan more easily than you.

If you’re a PhD student, your supervisors will know what is required for a publishable journal paper – your supervisors are likely to be experts in your field and will have suffered through the many rounds of submission, rejection, modification and changes required to get papers published in peer-reviewed journals.

Your supervisor might also be able to predict the questions that pesky “reviewer 3” is going to ask, so accept your supervisors’ ideas with an open mind, and learn as much as you can from their advice.

 

Remember you are an expert in your subject, but your readers may know nothing about your area of research

Most researchers are often so closely involved in their area of research that they find it hard to ‘step back’ and tell a simple story. I often find life scientists leave out the basic details that are necessary to help the reader understand.

It's easy to assume the future readers of your paper will be experts in your area of research. However, you must remember many of your readers will work in a different area. These readers won't be familiar with the other studies you mention or even the molecules/processes you studied.

When planning, think about including the details these readers will need. For example, you could plan to say "Jones et al. found gene X was not associated with the progression of squamous cell carcinoma" instead of "Jones et al. investigated the role of gene X in the progression of squamous cell carcinoma".

Telling the reader the actual result is more informative and helpful than assuming your readers already know that Jones et al. did not observe an association. If you wrote "Jones et al. investigated the role of gene X in the progression of squamous cell carcinoma", then the reader could think there is a relationship between gene X and squamous cell carcinoma. Even worse, the reader would need to find and read the Jones et al. study to fully understand your text. 

 

Creating a solid plan will give you confidence, save time and makes writing easier

Getting feedback and another perspective on your plan will give you confidence, so you know you are writing the correct information when you actually start to write. This might also save you time later, as there’s like to be less of the dreaded ‘red ink’ and fewer changes to deal with if you’re writing to the agreed plan.

Once you are satisfied with the general outline and plan in the bullet points, then you can start to write and expand each bullet point to some sentences, and then to an entire paragraph.

Your plan will also allow you mentally to break the large job of writing the whole draft into smaller manageable pieces. It is much easier to take 30 min to write a few sentences for one bullet point than trying to write a whole manuscript in one day.

 

Review the plan once the manuscript is written, and allow your plan to evolve

Of course, the best plans will always change. After writing the first draft of your manuscript, you might realise that you need to add in some extra information or that the flow of information is not quite right.

Sometimes you only realise the plan is in the wrong order when you actually write the first or second draft of your manuscript. For example, if you find yourself writing about an unusual protein or complex pathway that hasn’t been explained or briefly described yet in your text, then perhaps it’s a good idea to add in one or two introductory sentences - before you continue to describe how this protein or pathway interacts with other factors.

Apart from reading the text carefully and doing a spell and grammar check, it’s also important to quickly review the paragraph structure on every draft. You can check if the text in each paragraph is related to the same topic or point, or whether some paragraphs could be combined or even split into two.

You can also assess whether the flow of information in (and between) each paragraph is appropriate. Focus on telling the story of your research - are you guiding your reader from simple concepts to more complex information?

 

How long should paragraphs be? Do they all need to be the same length?

Well-placed paragraph breaks help to divide the text into manageable sections for the reader, almost like taking a deep breath when talking. Paragraph breaks also let your reader know you are going to describe a different point/concept.

There is no hard rule on paragraph length – paragraphs can be as short as two sentences or almost a whole page long (here, I'm thinking of double-spaced text in Microsoft Word®). The actual length of a paragraph is less important than the need for each paragraph to focus on a single topic or point.

If you’re in doubt and can’t decide between one long paragraph or two shorter paragraphs, I would suggest two shorter paragraphs are probably better. Of course, there is no right or wrong answer; use your judgment, and these decisions will get easier with practice.

 

Learn how to make good plans from reading the literature

If you’re new to scientific writing, simply telling you to make a plan isn’t very helpful if you have no idea where to start.

It can be useful to examine published journal papers as examples. So, I’ll walk you through this process. I selected a paper published on PLoS and will reverse engineer the Introduction section back to a bullet-point plan. This should help you imagine and understand how other authors could plan and organise the information in the Introduction section.

Please note I did not edit this manuscript and do not know the authors – I simply picked this paper from the PLoS homepage. PLoS is published under the Creative Commons Attribution (CC BY) licence, which grants permission to download, reuse, reprint, modify, distribute and/or copy the content as long as the original authors and source are cited. I have also informed the corresponding author of the manuscript about this blog post.

 

First, take a look at this Introduction

You can read the introduction section of the paper I selected by clicking the link below: 

Cham HJ, MacKellar D, Maruyama H, Rwabiyago OE, Msumi O, Steiner C, et al. (2019) Methods, outcomes, and costs of a 2.5 year comprehensive facility-and community-based HIV testing intervention in Bukoba Municipal Council, Tanzania, 2014-2017. PLoS ONE 14(5): e0215654. https://doi.org/10.1371/journal.pone.0215654

 

Let's reverse engineer the Introduction back to a series of bullet points

The introduction in this manuscript tells a simple, clear story. The authors guide the reader from basic knowledge (we all know what HIV is) to a distinct problem, and why it’s important to solve this problem. They also identify a distinct knowledge gap and clearly state the aims and purpose of the manuscript.

We could imagine the authors thought of the following ideas/bullet points when planning this well-written introduction: 

 

  • Timely diagnosis and initiation of antiretroviral therapy are necessary to control the spread of HIV and reduce mortality
  • Diagnosis and initiation of antiretroviral therapy are especially important in Tanzania; goals and guidelines have been defined
  • Problems that limit diagnosis and antiretroviral therapy in Tanzania; what is required to solve these issues
  • Lack of studies and knowledge on the efficiency/costs of HIV diagnoses in provider-based care in out-patient clinics
  • Description of the previously conducted community-wide intervention to diagnose HIV
  • Manuscript aims (describe outcome measures of community-wide intervention) and purpose (inform resource allocation for future programs)

 

Let's expand the first three bullet points with further information to create a detailed plan

You can see each of these bullet points represent the overall concept/purpose of each paragraph. Now, let’s imagine that the authors expanded each of these bullet points by creating a longer list of the items and details they needed to include in each paragraph.

Below, I've expanded the first three bullet points by listing the details included in the corresponding first three paragraphs of the Introduction. 

 

  • Timely diagnosis and initiation of antiretroviral therapy are necessary to control the spread of HIV and reduce mortality
    • UN 90-90-90 targets
    • Relationship between diagnosis and ART
  • Achieving diagnosis and initiation of antiretroviral therapy are especially important in Tanzania; goals and guidelines have been defined
    • Prevalence of HIV in Tanzania
    • Describe the Ministry of Health guidelines
  • Problems that limit diagnosis and antiretroviral therapy in Tanzania; what is required to solve these issues
    • National guidelines not implemented
    • Some progress in diagnosis and ART
    • Many HIV+ patients not aware of their HIV status
    • Low cost/rapid strategies for diagnosis essential in Tanzania
    • Comparison of cost/effectiveness of different strategies necessary

 

I hope you can see from this exercise that making a solid plan makes it so much easier to actually write. We could imagine that once the authors thought of everything they needed to include, they simply gathered the required data, information and references.

Then, all they had to do was write one or two sentences for each of the items in the expanded bullet point list. This is much easier than the massive task of thinking, arranging, referencing and collecting information at the same time as you try to write.

 

Applying this exercise to published papers you are familiar with

If you want to take this exercise further, look at a few journal papers you’ve already read a few times. Pick something related to your area of research or even a paper published by your supervisor or laboratory.

When you read those papers before, you probably focused on the methods or results, especially if you’re a PhD student trying to repeat similar experiments. Now, I’m going to ask you to switch your brain into a different type of mode – let’s call it ‘paragraph overview mode’.

Look at the overall structure of the paper, especially the paragraphs (rather than the finer details and content).

Can you identify the main point in each paragraph? What does each paragraph describe or talk about? Could you summarise each paragraph into one or two bullet points?

Once you’ve made a list of bullet points, can you see a relationship between the paragraphs? Does the information flow from simple/common knowledge to more complex concepts throughout each section of the paper? Does the overall structure of the paper tell a story that helps you (or maybe even someone who knows nothing about this topic) understand?

You might also like to compare different papers. Do some authors do a better job of telling a story? Can you spot any gaps where some information is missing? Can you find any paragraphs that seem out of order or that would be better if they were split into two paragraphs?

Finally, can you identify a general paragraph structure (or pattern) within the published papers in your field of research? Being aware of the typical paragraph structure and content, and thinking about this when you read other manuscripts, will really help you to develop the correct style for your area of research and write with more authority and confidence.

 

Conclusion

Making a plan before you start to write is essential if you want to write a well-organised manuscript. Your plan can be a simple series of bullet points that include everything you need to talk about in your manuscript.

You can start to plan as soon as you think of writing a new manuscript. If you're less organised, you should try to make a plan at least one day before you actually start to write.  

A clear plan will give you confidence that you are writing the correct information, save time, and make it much easier to write the actual manuscript - you can break the huge task of writing a whole manuscript into simply writing once or two sentences for each bullet point.  

Asking your supervisor or a colleague for feedback will help you to refine your plan, and hopefully reduce the changes you will need to make to your draft. Also, always think of including the basic details other "non-expert" readers will need to understand your area of research.

Finally, you can learn to plan by looking at other published papers - identifying the general pattern of the paragraphs within manuscripts in your field of research will help you develop confidence and write more professional manuscripts. 

 

I remember trying to write my first manuscript. Why was it so difficult? Why did I feel like a failure?

Now I’m a scientific editor, I know every single scientist struggles (or at least used to struggle) with writing manuscripts.

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