How to Write a Scientific Paper

Most people not working in science have no idea of what it means to write, review, and publish a scientific paper. Why should they? Scientists learn the basic rules and customs from our mentors and advisors in grad school, and then continue learning by trial and rejection.

The overall style of a scientific paper is quite different from other written forms of communication and can be off-putting for casual readers. The generally forbidden passive voice is encouraged, so sentences like “In order to test this hypothesis, an experiment was designed….”. are perfectly common and acceptable. The great majority of papers are divided into well-defined sections: Introduction, Methods (sometimes called Materials and Methods), Results, Discussion, and References. Figures and Tables are distributed mostly in the Results section, each with legends that can be quite long and detailed.

Introductions are short summaries (a few paragraphs long) of what the paper is about, including some mention of work that came before, with lots of references. This means something like “Previous workers (Smith 2012, Jones et al. 2014) have found that standard evolutionary models do not fit the kinetic data…” There is no explanation of basic knowledge (like what is evolution or enzyme kinetics) since the reader is assumed to be a trained scientist in the field or a related field to the subject of the paper.

It is unheard of to make a new claim without any reference to previous work—even breakthrough revolutionary works of genius must refer to previous work in the area. There is also a practical reason to include lots of references. The odds are high that some of the people being referenced will be reviewers, and nothing makes a reviewer more cranky than not seeing his/her own work referenced. (Yes, I speak from experience.)

The Introduction is generally followed by a Methods section, which goes into varying amounts of depth and detail, depending on the field. When PCR was a new technique, I used to present all the PCR conditions and primer sequences. Now, people just say “by PCR”.

The Results section is required to be crisp, to the point, and limited to basics. No flowery language is allowed. A typical sentence might read “We found no evidence for homeostasis (Figure 1).” The heart of the Results section is the data, presented in figures and tables. Some Results sections can be incredibly dense, with a huge amount of information crammed into one sentence. Here is an example from a paper I recently read:

Figure 5 shows that a genotype’s vertex degree and its number of latent phenotypes are weakly, but significantly positively correlated (Spearman’s r = 0.13, p < 1.2 × 10−41), indicating that mutationally robust circuits have an increased capacity for exaptation.

Then comes the fun part, the Discussion. Here the authors are allowed a bit more leeway in terms of eloquence, and even some degree of deeper thought. Here, and not in the Results section, the meaning of the results can be discussed, almost always in the context of what everyone else has found, both in agreement and in contrast with the work presented. Thoroughness is key. Leaving out some key work by other groups is often fatal. All Discussions must include at least one paragraph of self-criticism, wherein the authors point out weaknesses of the paper, whether in methodology (“Our sample size was considerably smaller than that of Wheatly et al.,…”), or in the consistency of the data. All instances of disparity between the presented work and that of others should be brought out, and explanations for these disparities must at least be attempted. 

The entire approach is decidedly low key. A paper that purports to have “made a significant and groundbreaking discovery that will change the nature of how we think about…” would not even get sent out for review. It ain’t the internet. The use of qualifiers like “could” or “might explain” or “is consistent with” or “lends support to the idea that” are very common. Phrases like “we have proven that” simply do not appear (with the exception of mathematics, and some rare physics papers).

Books aren’t scientific papers, of course, so none of this applies to them. I felt a huge sense of freedom while writing my first trade book, since I realized I could say almost whatever I wanted to. (I still included lots of graphs, which turned out to be a mistake for sales, but that’s another discussion.)

Is this the best way for scientists to communicate? I don’t know. The style of 19th-century papers was completely different. They were long, and long-winded, with philosophical musings and off-topic tangents, all now forbidden. Some people have said we need to reform the way we write papers. Maybe, but I will bet it won’t happen, at least not any time soon.

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1 Response to How to Write a Scientific Paper

  1. dgilmanjm says:

    Carl Woese made a significant and groundbreaking discovery that should have caused the scientific community to abandon LUCA, but he dared not put that in his paper. 😀

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