How to Write a Scientific Paper Content from the guide to life, the universe and everything

How to Write a Scientific Paper

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A scientist looks at a petri dish.
Writing is easy: it's just a matter of staring at a blank piece of paper until your forehead bleeds.
- Gene Fowler1

So, you've carried out some ground-breaking scientific research. Perhaps you've found a cure for all known diseases. Or reconciled quantum theory and general relativity. Or learned how to crochet with superstring. Or uncovered the meaning of life. Or alternatively, perhaps you've been slaving away in a lab for the last five years, working on some obscure project of little interest and even less practical use, and, unless you can expand your CV, your funding will run out in days. Either way, the answer is the same: you need to publish your work.

Now, assumptions are dangerous things. For example, one might assume that anyone who has carried out a piece of scientific research might be familiar with what a paper should look like. As anyone who has tried to guide a graduate student through the writing of their thesis will know, this is sadly untrue. Let us therefore take a tour of a typical paper. For the purposes of this Entry, the examples given are those that might be seen in a report of a clinical trial; the sort of thing that you might see mangled, misunderstood and misrepresented in your daily newspaper2. Scientific papers in other fields are, however, similar in spirit, if not in detail.


The Introduction introduces the paper; nothing to tax our woefully under-literate scientist so far. It does exactly what it says on the tin. And that hackneyed use of a phrase that has travelled from marketing slogan to tiresome cliché makes the first important point about our paper:

A scientific paper is an advertisement in a white coat

Oh yes it is. Even if you're not writing about a product you're actually selling (a new drug or high-tech piece of equipment, perhaps), you are still advertising what a wonderful piece of science you've done, how very clever you are, and why people who happen to have money to spend on research should send the blank cheque to your department3.

The Introduction provides a wonderful way to start selling yourself immediately. Perhaps more importantly, it also gives you a forum to start sticking the boot into your competitors. Any worthwhile Introduction has three main aims:

  1. To cite as many of your own previous papers as you possibly can. This will give the reader the impression that you are at the forefront of your field and are someone worthy of their precious reading time. Useful phrases here might include, 'in their seminal work, Bloggs et al. showed that...', 'as has been elegantly demonstrated by Bloggs et al...', 'much of the key work in this field has been carried out by Bloggs et al., who found...' and so forth.

  2. To explain that it is largely the sheer incompetence of your rivals that has left you to single-handedly advance the frontiers of knowledge. Phrases such as 'studies to date have failed to show...', 'a series of small, under-powered trials...' and '...although these findings are disputed' can work wonders.

  3. To provide some justification, however feeble, for the research you have been doing. If you've done parts 1 and 2 correctly, this should be a walk in the park...

Previous research by Boggins et al. (2002) has tenuously suggested a causal relationship between park-walking and writing fluency, although the small number of subjects has meant that no statistically significant correlation could be established. Previous work from our own group (Bloggs et al., 2007; Bloggs et al., 2008; Bloggs et al., 2009) has clearly demonstrated the potential for park-walking to revolutionise the generation of high-quality writing. To further assess4 the benefits of park-walking, we took a series of walks in the park with the aim of evaluating the niceness of the trees and ducks.


The dull bit. Like the instruction manual for a new digital camera or a set of health and safety regulations, no one actually reads this stuff, but it has to be there5. Unfortunately, you'll need to produce a bit more than the pencil drawing of a Bunsen burner and beaker of water that passed for a Methods section in secondary school, but let's see if we can get it out of the way as quickly as possible.

This section goes by several different names. Materials and Methods is common, but Patients and Methods may be found in clinical journals. Alternatively, journals of physics or chemistry may have a section called Theoretical Background or somesuch, but the end result is much the same6. In theory, the aim of the Methods section is to allow someone else to repeat your work. This must be avoided at all costs. Someone repeating your work will almost certainly either a) find that your results are impossible to replicate because you clearly forgot to plug the machine in; or b) use them to discover the profound, Nobel-prize winning 'duck-tree quantum niceness paradigm' that you somehow overlooked.

So, how might we prevent our no doubt unscrupulous rivals from stealing our thunder? Here are some suggestions:

  • Be tiresomely specific. The longer the list of the precise conditions under which your work was carried out, the less likely anyone will be willing or able to replicate them. Specify a time, a date, an ambient temperature, an air pressure, a longitude, a latitude, a compass direction, an altitude above sea level, some obscure brand of laboratory equipment, the view from the window, and the colour underwear you had on at the time, and no-one will bother to read the list, let alone try to replicate it.

  • Be hopelessly vague. If you can't be specific, go as far in the other direction as you can. This is a tricky one to pull off, as pesky peer reviewers are likely to ask you for details before they'll publish your paper. The ideal, if you can manage it, is to refer to methods published some months previously in the most esoteric journal you can dig up. Anyone wanting to read them will have to wait so long for their departmental library to track down a copy that by the time it arrives they'll have forgotten why they wanted it in the first place.

  • Take refuge in statistics. As a wise man once said, there are lies, damn lies, and statistics. Include a long and impenetrable sub-section called 'Statistical Methods' in your paper and the chances of anyone replicating your work, or even wanting to, will be slashed. Of course, they could go and ask a statistician about it, but who wants to talk to one of those?

Ducks and trees were compared by use of the Wilcoxon two-sample test for ordinal and continuous data, with differences interpreted at the 5% statistical significance level. Time spent in the park was assessed by the Kaplan-Meier method, and the log-rank test was used to evaluate the thickness of trees. Potential predicting factors were entered into analysis of variance and covariance models one at a time together with duck species and interaction term. Primary duck analysis was carried out by intention to feed, with the last slice of bread carried forward7.


In god we trust; all others must have data
- CR Reynolds

The important bit. Here is where you show, in a veritable flurry of charts, graphs, photos and tables, exactly what the hell you've been doing with yourself for the past three years8. So, what goes into the Results?

  • Your Main Objective

Sadly, there's really no way out of this. If the stated objective of your study was to 'evaluate the niceness of the trees and ducks', your readers are going to be a little suspicious if the entire Results section is devoted to the prettiness of the flowers. If you're very cunning, you might be able to get away with retrospectively determining your main objective based on the strength of your various data sets. This is, however, generally frowned upon.

  • The Experiments that Worked

Right, you've disposed of that annoying primary endpoint in two sentences at the start of the Results. Now you can go to town. Everything you did that was even remotely relevant to the study and that actually succeeded can go in here. The flowers were pretty? In they go. The sun shone? In it goes. Songbirds fluttered about your head as you strolled lazily around the edge of the lake? Take a photograph of it (see the next section). You tripped over a loose stone near the playground and got tangled in the swings? A minor secondary endpoint, not worthy of publication. If you can prove that any of your findings are actually statistically significant, say so repeatedly and include as many 'p values' as possible.

  • Pretty Pictures

Lots of 'em. Unless, that is, you're morally obliged to include any results you'd rather not. That dratted primary objective, perhaps. In that case, simply bury it in the text. Anyone reading the paper will assume that all the data of any worth will have been tabulated, plotted, scanned, photographed or coloured in with a crayon. Anything that appears only in words isn't worth the paper it's printed on. Words are what poets use, for heaven's sake. We are scientists.

At this point, it's worth being reminded of the single most important fact in 21st Century scientific publishing:

Photoshop is your friend

Use it wisely. And often.

  • Other Stuff You Have No Choice About

This one is a bit difficult to give general advice on, as it will vary widely from subject to subject. In our clinical trial example, this section can be summed up in two words: side effects. We don't want to talk about them. They're nasty and embarrassing, and sometimes smelly. Sadly, people seem to want to read about them, so in they must go. But do it quickly, somewhere near the bottom of a page where they might be overlooked. You could, of course, try to prove they would have happened anyway, but it's hardly worth the effort.


We've done the advertising bit. We've done the dull bit. We've done the important bit. Now we have to do the bit that is a little of all three.

  • Discursive Advertising

The first thing you might want to do in a Discussion is summarise your findings. Let's put that another way. The first thing you should do in a Discussion is summarise your findings in a way that leaves their Earth-shattering profundity and monumental contribution to the sum of human knowledge in no doubt whatsoever. Throughout the Results section you've been bound by the convention that says 'thou shalt not interpret'. In the Discussion, there are no such restrictions. Speculate to your heart's content. Draw together disparate strands of research in a dazzling display of scientific erudition and literary flair. Quote your own papers. Trash your rivals' research. Go crazy.

  • Discursive Dullness

In in the maelstrom of brilliance that is your Discussion, there are a couple of nagging things that you're obliged to do. Best to just close your eyes and get on with it.

  1. Compare your findings with previous work. Well, we're already halfway there, having covered our (thoroughly consistent and beautifully written) previous papers, and those (clearly flawed and probably badly spelled) of our rivals. A quick trawl through PubMed or the equivalent in your own field, a copy and paste of choice phrases from the abstracts (see below) of one or two, and you're sorted.

  2. Note the weaknesses of your study. What?! There are none. What are they talking about? The only weakness of the study was that it was so bloody fantastic that there's no research left for anyone else to do... Look, just take a deep breath, swallow your pride and make something up. You could have counted more ducks. Climbed more trees. Not fallen in the lake. There's always something.

  • Discursive Importance

We've done it. We've made it to the last page. There's just one more thing to do. We need a Conclusion. A single, pithy statement that encapsulates your genius, the robustness of your methodology, the significance of your results and the insight of your discussion. Unfortunately, you only have 11 words left before you go over the journal's word limit.

In conclusion, this study shows that ducks are nicer than trees.

And the Rest

Did that last paragraph say, 'there's just one more thing to do'? Oh dear me, no...

  • The Title

Yes, you have to decide what to call your paper. Remembering that the credibility of a paper depends on how many people read it, the title should contain as many important 'keywords' as possible, plus at least one colon and, preferably, a question mark. If at all possible, there should also be some nebulous and ineffective pun or play on words. In recent years, journals have got wise to all this, and many now impose strict word limits.

Can't See the Ducks for the Trees? A Random Walk Analysis of Park Loveliness and Correlations With Individual Component Nicety Scores With Reference to the Lake Viscosity-Paddling Coefficient and Leaf Distribution Wind Spread Hypothesis: Practical and Theoretical Considerations for Optimal Enhancement
  • The Abstract

The Abstract is a short summary of the most important bits of your paper and will, in all probability, be the only part of it that anyone ever reads. Every journal insists on its own Abstract style and specified length. The only thing that is certain is that, to say everything you want to say, you will need about 58 more words than are actually permitted.

  • The Reference List

Destroyer of sanity. Ruiner of evenings. This, again, is something that varies from journal to journal. Do they want all the authors listing, or just the first three? Or six? Do they want journal names in italics? Should I put volume numbers in bold? Should I put the year of publication in parentheses? Should I promise a PhD student their name on the paper if they'll sort all this out for me? Oh yes9.

  • Co-authors and Acknowledgements

Lab politics. Who goes first? Who goes last? What order does everyone else come in? Should they be full authors, or just acknowledged at the end of the paper? Who else should be acknowledged? The lab technicians? The tea lady? The cleaners?

Just remember that everyone named as an author will have to sign a piece of paper saying that they've read it at least once. The clarity and brevity of a paper are significantly inversely correlated10 with the number of people trying to write it.


Well, here we go. We've written our masterpiece – now to send it on its way to peer review and glory. But first we need to know the head of department's middle name. And we need a form signed by our boss, who is the senior author despite having been on sabbatical in the Bahamas for the past two years. And we have to agree to hand over all intellectual and financial rights in our work to a multinational publishing company. And we know we'll have to deal with at least one rejection. And a whole string of sarky comments from our rivals (because even though peer review is a blinded process we know who they are).

You flick idly through a copy of New Scientist when a job advertisement catches your eye. 'Medical Writer'? There are people who have to do this for a living all the time? Suddenly your life doesn't seem so bad. With a shrug, you press the 'Submit' button on the journal's website and head back to your bench. There is science to be done. Now, where did those ducks get to?

1Though often attributed to Douglas Adams.2No, not fish and chips.3Preferably directly to you rather than to your boss or some departmental committee, who will probably not spend it all on a lab technician to do your research for you so that you can sit in the canteen drinking coffee all day.4Yes, it's a split infinitive. It's almost compulsory.5All right, all right... some people will read the Methods. After all, your techniques are so brilliant, it's only to be expected that people will want to follow in your footsteps. You are the Good King Wenceslas of science.6Though possibly with more Greek letters.7This is, of course, all gibberish. Or is it..?8For better or worse, the fact that you played the back end of a cow two years in a row in the departmental pantomime won't get you very far here.9Or you could invest in one of the bibliography management packages that are available. Just hope that, when it's mangled your references beyond all redemption, the PhD student hasn't gone home for the evening.10r<-0.99; p<0.0001.

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