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At first impression it’s much harder to spot general formulas for the discussion part of your manuscript, paper, project report or dissertation compared with other sections as discussions vary so much between different projects. Because of this, discussions are often an area where new writers struggle. However, good news, there are some general concepts that you can put into practice and you will end up with a decent framework to build on.

This guide will  give some tips for what is worth including, what not to include, and how you can try to get the balance right. Near the end there is also a section on differences between PhD theses / dissertations and manuscript/project reports.

Before we get into the do’s and don’t, it’s probably worth thinking about why discussions exist…

What is the point of a discussion?

The primary purpose of the discussion is to give readers specific guidance about what was accomplished in the study, the scientific/biological/medical/engineering significance. It is your chance to shape the thinking of your readers and to protect yourself from criticism for any limitations your work might have.

Remember, you (should) know more about your subject than the majority of your readers. This includes knowing more of the relevant surrounding and preceding literature. Therefore, the discussion also serves another important role; putting your findings into context with what has gone before.

Important – the discussion is not another results section.

 Do’s and Don’ts


  • Keep it focused on the core message
  • Clearly state if your conclusions support your hypotheses
  • Explain unexpected results
  • Explain reasons for observed differences compared with previous findings
  • Consider other ways to interpret your data
  • Explain what is new (without exaggerating)
  • Try to take a holistic view as far as possible


  • Don’t just repeat your results!!!!
  • Don’t go on too long – keep it focused
  • Don’t make it too short – 🧐 address the things you need to
  • Don’t overreach.
  • Don’t introduce new terms or deep ideas.
  • Don’t focus too much on limitations
  • Don’t include future directions that you could have easily done!
  • Don’t ignore controversies!
  • Don’t discuss each experimental finding as an independent result
Remember it’s a discussion! Not another results section!

I’ll expand on some of these points below.


This discussion is the most flexible section of a manuscript / project report and as such will be driven by what your story is in terms of its length, structure and flow. There aren’t firm rules and some of the following sections might connect better if rearranged or combined in different ways. However, here is a guideline layout and examples of the different types of paragraph from published work.

 Synopsis (paragraph 1 in guide)

discussion structure Summarise the goal of the study and how your data addresses that goal. I know this sounds like I am saying to repeat your results but what I really mean is to combine your key findings into a simple message. Make this short. A two or three sentence paragraph should do it. Assemble the phrasing to emphasise the points that you will delve deeper into the following paragraphs.

If your study is quite simple you might not need this. However, if you are delivering 7 figures of 5+ panels each this first paragraph can help to bring it all together again, reminding the reader how the pieces of the story connect and setting up your big hitting paras.

If you hit 150 words for this you have likely gone too far. Stop and parse it back. Focus focus focus.

As usual, try to finish this paragraph (and the rest) with forward looking wrap sentences that leads you into the next step. Now, let’s move onto delivering the big stuff (see what I did there).

Example synopsis paragraph:

In the current study, we assayed the consequences of ACTN4 knockdown on skin cell motility and the organization of keratinocyte matrix adhesion structures. Knockdown of ACTN4 perturbs the directionality of keratinocyte motility, results in an increase in focal contact surface area, and leads to multifaceted changes in hemidesmosome-like protein complexes. Specifically, in ACTN4-knockdown cells, we demonstrate mislocalization of α6β4 integrin from the base to the main body of the lamellipodium, reduced β4 integrin dynamics, and reduced recruitment of the BP antigens to α6β4 integrin clusters.

Paper ref.

Bring out the big guns – what have you discovered and how does it fit? (paragraphs 2, 3, 4)

downloadFocus the next (3 or so) paragraphs on the major findings. Choose a logical order to deliver these; usually the most significant/impactful finding first followed by secondary findings. Usual rules; 1 key point per paragraph, fully supported.

This part of your discussion is where you will usually deal with whether or not your data supports or refutes your hypotheses and why. Take a holistic approach; try to consider the whole data set together, especially when a single piece of data doesn’t fit with the rest.

When you are planning what to write, focus your early energies on identifying what these paragraphs will deliver. Write down the key messages you want to deliver as an accessible and ideally relatively short sentence. Use that sentence as your lead in, your topic sentence, for that paragraph. Then stay on message. This’ll make sure that you focus your work on the things you want your reader to take away rather than rambling on.

Remember you will need to set up your discussion points in your introduction, you don’t want to be surprising the reader with something completely new here (intro guide).

Also remember you don’t need to refer to data figures or specific data numbersYou’ve already described them. Also don’t repeat what you have already written in the results . If you find that you are restating your findings just using different phrasing you should stop and ask yourself why you are doing this! If the reason is because you didn’t write your results clearly enough the first time then you should go back and fix that rather than trying to make up for poor delivery in the discussion (need some tips of results writing? comprehensive guide here, or short version here).

The discussion is for putting the data into a wider context. However, you might want to consider bringing in your updated model/diagram at this point. Make sure the diagram helps though, and isn’t too much of a stretch relative to your data.

Make sure you cover your competitors’ work. Even if you think you did it better!

If other people have published related work don’t ignore it! One thing for sure; your reviewer won’t appreciate it if you have ignored their seminal work in the field!

Wherever your data fits with or disagrees with others people’s findings cite that and think about why differences may have occurred: What have you added/changed? Why is your study better? Or even what other studies have been published in between that, combined with yours, leads you to a different interpretation. Also think about how do your findings compare with studies of related proteins/drugs or in other tissues/disease? These are all things that are worth explicitly stating.

These key finding paragraphs will inevitably have lots of primary data references. You might find that you need to them to be a little longer than the usual 200 word paragraph limit to be comprehensive but still stay on message (don’t go crazy though – I’m a little uncomfortable about the length of my example below!).

The biggest killer to a paper is that it isn’t novel, so you really need to emphasise here what aspects of your findings are new. But make sure you don’t overstate this; that 1980s paper that did the same sort of work with earlier technology may have already established the paradigm. Your study is still an improvement, it might add mechanism or important validation but don’t try and sell it as bigger step forward than it really is.

Example key finding paragraph:

A focus of the current study was to assess the role of Col XVII in migration and compare the motility phenotype of keratinocytes in which we have induced a knockdown in Col XVII expression with those of BPAG1e- and β4 integrin-deficient cells. Our data reveal that Col XVII-knockdown cells exhibit the same motility and lamellipodial defects as the latter cells, although the mechanism is subtly different. In this regard, the role of Col XVII in migration is somewhat controversial. For example, evidence has been presented that the extracellular domain of Col XVII that is proteolytically shed impairs keratinocytes ability to close scratch wounds (46). Conversely, the shed ectodomain of Col XVII has been demonstrated to promote squamous cell carcinoma cell transmigration (49, 53). Moreover, one group has shown that GABEB cells lacking apparent Col XVII expression demonstrate a migratory phenotype, whereas another has provided data indicating that Col XVII knockdown inhibits migration via reduced signaling to p38 MAPK (11, 22). Our data are consistent with the latter report because they indicate that Col XVII loss induces motility and signaling defects in keratinocytes. Intriguingly, our data also provide key insight into the mechanism via which Col XVII might regulate signaling to p38 MAPK. It likely does so by mediating both the localization and activation of Rac, a critical regulator of the p38 MAPK pathway (47).


Deal with the issues – limitations and caveats – (Paragraph 5)

Quick note on student papers; a problem I have frequently encountered when grading student papers is that the descriptions of the limitations section gets overly long and overly negative. Don’t go on and on here. Similarly don’t be too superficial,  your marker knows you had a time limit, they know you might have limited numbers of biological repeats, they certainly know that the data might be more reliable if gathered by experienced researchers (I’ve seen this included as a limitation way more often than you would expect!). Using more than one sentence to say any of these superficial and obvious problems won’t add any valuable insight – if you do feel it’s necessary to include something like this then do it in a way that is short and focused, “sample size limitations preclude robust statistical inferences” (better still, indicate what sample size you would actually need – calculator here).

To avoid these problems aim for a balanced approach that emphasizes the strengths of your study while still acknowledging where limitations mean that you can’t be as confident. To be more positive about your findings, try to phrase your sentences so that they focus on what you can interpret rather than what you can’t.

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The balance comment also extends to just how much space you devote to limitations. If your limitations extend to much more than your major findings then you will leave the reader with the impression that the major take away from the study is that your experiments weren’t very good. Not much chance of convincing an editor to publish if you even you aren’t convinced the findings are strong enough to be believable.

What I like to do here is describe the different ways you could interpret your data based on the data I have. Rather than present these alternate interpretations as a problem, I would instead detail how to differentiate between those interpretations in the future. Also presenting arguments as to why you are willing to accept your limitations can help reduce their negative impact: “To resolve this dilemma would require 100 extra human samples, which is unethical to request at this time.”

Careful though; if a limitation or alternate interpretation could have been addressed relatively easily then a reviewer can, will, and really should, get you to do the experiment! You might as well just do the experiment now!

Example paragraph discussing limitations:

The participants in our study were drawn from University students and staff members and therefore there is a selection bias toward well-educated participants. Moreover, our participants reflected the local University population and were skewed toward lighter skin types. This has two important implications for the generalizability of our findings. First; one would predict that our cohort would have higher baseline cancer-risk awareness levels and as such are likely to be vigilant when applying sun protection [43,46]. This may suggest that the disproportionately poor coverage of the eyelid region could be even more striking in the general population. It should be noted, that in our post questionnaire just under half of the respondents did not cite a specific reason for missing the eyelids so, despite a perceived general awareness, their application was still relatively poor. Second; our cohort may respond more to our information based intervention strategy than a broader cross-section of the public and therefore we may be over estimating the magnitude of the improvement. However, information based intervention is a standard and proven efficacious approach in wide variety of contexts in diverse groups of patients/participants and as such we do not believe this to be a major limitation here [47,48,49].


Describe wider biological implications (paragraph 6). 

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As you progress through your discussion you should get wider and wider with what your data means (i.e. the opposite order, or mirror image, to your introduction). Put your findings into real-world context.

This is also the place where you can talk about the next big question(s). A specific agenda for future research based on the questions generated by the current findings is much more helpful here than vague suggestions. I often integrate these type of phrases into my limitations eg stressing the value of making an animal models to counter a limitation of absence of immune cells in a culture model.

As with limitations, don’t go too far here. A long list of what needs to be done next could leave a reader thinking “what have they actually done!”

Reviewers also appreciate how specific research recommendations will advance the field. For biological research this can often include the wider implications for clinical needs eg can it open an avenue toward therapeutic development?

Often this paragraph is combined with the conclusions.

Example paragraph combining biological implications, next step and conclusions.

The critical interactions through which the N-terminus of laminin α3a might mediate mesenchymal cell signalling are as yet unknown. Possibilities include a direct interaction with a cell surface receptor expressed by mesenchymal cells or alternatively the domain might interact with other extracellular matrix molecules and the resultant macromolecular complex may influence cell behaviour. Granulation tissue is a major clinical problem, not only in LOC syndrome but in a range of much more common conditions such as rheumatoid arthritis, chronic venous leg ulcers, transplant surgery and others. A fuller understanding of the role of laminin α3a in this sometimes undesirable biological process might lead to the identification of novel targets for therapeutic intervention.



Round it out. Tie it up with a neat little bow.

In positive language, describe your core finding and what it means to the big picture. Refer to your equivalent section of the intro to make sure you are covering the correct points.

Likely this short paragraph will be quite similar to the last line of your abstract (or vice versa) and will pick up on one or more of the bigger reasons for your research you covered in the first paragraph of your intro. In some journals, the conclusion is viewed as being so important that gets its own separate section. So, nail it. It’s the last chance to influence your reviewer’s and reader’s opinions.

Differences between PhD thesis discussions and manuscripts

Length. Whereas a manuscript or project report thesis should only be the length required to deliver the points that you need, your thesis examiner will expect you to be comprehensive in your doctoral work.. That’s not to say it should be long for the sake of being long! Although the freedom to express yourself at length is fundamentally a good thing, each individual paragraph and each individual sentence should still be succinct and focused.

Despite the increased length, your discussion still shouldn’t discuss things that aren’t relevant! However, there is no real reason for you not to address anything that is relevant and to go deeper into concepts and raised and, especially, what else could be done. Indeed, as all good science generates questions I would expect to see a more developed next steps section (go bold; cost, time, sample availability are not an issue here, just the quality of the questions!).


Width. Can you go wider and still stay relevant? Well yes, you probably can. A common problem in thesis writing is that you have got so far into your niche that you struggle to get back out again. In your discussion you can go wider; talk about other model systems, talk about different tissues, talk about the Mongol invasion of the Punjab in the 1300s*. Well, maybe not the last one, but your discussion can be a chance to have fun and really explore all aspects of your work and not just the stuff that was directly related to the core hypotheses.

Depth. To be fair, I’ve just said depth for completeness! Your manuscript discussion will be  deep too so this isn’t really a difference. Make sure whatever you cover,  in whatever writing format, is deep enough to be useful; superficial coverage of a comment or assertion won’t add value to your work.

well of discussion

A note of figure references; above I said not to refer to figures in your discussion and that generally holds true for a thesis too, despite the longer format. In your thesis you might choose to have chapter discussions, essentially  the same as a manuscript style, and then perhaps a more complete discussion which discusses the combined findings. As a concession to the longer format, I would be relatively happy to see backward references to specific chapters or collections of subsections. If you do decide to include these, focus the sentence on the message rather than where the info is; you don’t want your reader to feel like they should flip back through ~100 pages to find something that you should have explained fully the first time!

As you progress through your doctoral studies everyone you have ever met will tell you that they wished they started writing earlier. Mostly, people think that it is only the results, methods and literature review that can be covered as you go, as the deeper intro and discussion parts will only come together once you have assembled the whole story. That’s not totally true. You can chip away at paragraphs within your discussion as you go.

Each time you read a key paper think about how it connects with what you are investigating. Your study might add or might challenge these findings. As you progress to later in your studies you will have a better idea of which way the work is going and so your notes should start containing relevant details about which ways your approaches differ and why this can explain what is going on.

*My PhD was on laminin alpha3; specifically on a rare genetic skin disease (LOCS) and a new family of laminin splice isoforms (LaNts). However, the Mongol invasion of the Punjab did end up in my discussion. It was relevant but somewhat random in the grand scheme of things! We had a fun time discussing it during my viva. It continues to amuse me that that bit made it in and I wish we published it somewhere.* EDIT; after posting this, I got asked about this part of my thesis, so have posted it here as a blog post.*

Final comments 

Or should that be “conclusion”?

listA discussion in a manuscript or project should be the length in needs to be! I’ve seen 3 paragraphs that worked really well and 11 paragraphs that really got after it and didn’t feel long, and those were both from papers from the same author. So a key point is, don’t force it; use the style that works for your story. If something needs discussed, discuss it. If things stand alone, are complete and clear in their own right, then let them lie.

My biggest tip for discussions, as with other sections, is to get a draft down without worrying too much about content and then edit edit edit. Make sure everything works for you. Don’t be afraid to play with order or to remove things that aren’t adding value.

Like the rest of science writing it gets easier with time so Don’t Panic.

This guide is part of a series that I am building. If you liked this, you might also enjoy the results one or intro one. Check back here in the future, more coming soon.

Comments on this guide or any of the others appreciated….

About the author

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Dr Kevin Hamill is a Senior Lecturer in Cell and Molecular Biology at the University of Liverpool, in the Department of Eye and Vision Science, Institute of Ageing and Chronic Disease. His lab focuses on cell-matrix interactions; you can read about ongoing work elsewhere on this blog, on the lab webpages, or in his published work. As well as supervising PhD, Masters in Research and Undergraduate research projects, Kevin is the academic lead for the Lab skills Module of MRes Clinical Sciences program where he teaches fundamental skills for life scientists.

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