Writing Manual for Scientific Papers

An initiative of Alistair Anderson and Peter Large. Tips and help on how to write scientific papers, reports and theses.

This work is still not complete, only the three following sections are at present available.
© A.J. Anderson and P.J. Large 1995.

1. The Materials and Methods Section
2. The References Section
3. Preparation of Figures (Illustrations) for Publication

1. The Materials and Methods Section

The purpose of the Materials and Methods section is to allow a competent scientist to repeat your work. Since theses, reports and papers are likely to be used by your successors in the lab and by other scientists, as sourcebooks of methods, it is important that procedures are well documented and that details are correct. Once you've left the lab, it might be possible to fill in missing information by asking your supervisor or one of your former colleagues, but this is not such an easy option for someone across the Atlantic who is struggling to repeat your work.

In my opinion, one of the most common mistakes is for authors of theses and papers to quote irrelevant information, while missing out the essential details. The purpose of these notes is to help you decide what is, and what is not, important information.

Materials

A common practice is to state that an enzyme was purchased from Sigma, and to quote the town and/or country. Opening Sigma's catalogue will probably reveal that the offending enzyme is available in various specific activities and from various sources. It might not matter whether the hapless scientist trying to repeat your work uses chooses enzyme from rat liver instead of elephant's pancreas, but details of which the enzyme preparation you used might possibly be more useful than Sigma's address.

No-one, nowadays, needs to point out that distilled water was used for preparation of solutions and readers in the developed world will probably assume that you used analytical grade chemicals where these were available. It would, however, be useful to state where HPLC-grade materials, recrystallized chemicals and redistilled solvents are necessary. It would also be appropriate to mention the use of low quality chemicals were used (perhaps bags of sugar instead of Analar sucrose), if their use could conceivably affect the results.

It is particularly important to specify the source of that special reagent, which isn't available commercially, but you or your supervisor scrounged it (sorry - obtained it as a gift) from someone. You might not be very popular for revealing your source (but you could tell your benefactor that there's a profit to be made). Appropriate details (e.g. purity) of special materials should be included, especially if they were used as analytical standards.

Instrumentation

Many academics have a poor understanding of the equipment in their laboratory, knowing little more than what it's called, who made it, how much it cost and who funded its purchase; everything else is left to the long-suffering lab. technician. Not surprisingly, inappropriate information finds its way into manuscripts for papers, which is not a good example to set to research students. It is likely that the poor description will go unnoticed, since the referees probably know even less about the technique and the equipment than the authors of the manuscript.

The information which is almost always included in methods - and which is usually of little importance - is the manufacturer of the equipment. Would you be put off trying to do an HPLC analysis just because the authors of the method you want to use specified a Waters HPLC system? Of course not. Similarly, it doesn't usually matter which electrophoresis power supply, spectrophotometer or centrifuge you used. In some cases the equipment will be unusual or have some special specification, in which cases it would be appropriate to specify the manufacturer and model.

Consider a simple example in which gas chromatography was used to measure something or other. Having decided that it is not necessary to advertise the manufacturer, what information should go in the Methods section and what should be omitted? Details of the chromatography column (dimensions, details of stationary phase), carrier gas, detector type, temperature and, possibly, split ratio should be included. Assuming that the machine is used according to the handbook, there is no need to include such details as the hydrogen/air flow and injection port/detector temperatures for the flame-ionization detector.

Miscellaneous

It is common to find see reference to 'an adaptation of A's method' or 'a slight modification of the procedure described by B'. This is useless and inexcusable: you should either give details of the changes or decide that they are too trivial to merit comment.
'Room temperature' is another worthless description, since the reader's crystal ball may be away for repair. An approximate value or range should be quoted.
It is common in reports and theses to describe, in detail, standard methods, but this must be avoided in the manuscript for a paper. Here it is appropriate to cite the appropriate reference, along with details of any modifications (provided that there are no major differences). Be sure to cite the paper which describes the method because it is infuriating to find just another reference to the source of the method! The best (or worst) example that I have found (so far) was when I had to plough through a series of six papers before locating the recipe for a reagent for electron microscopy.
It is generally accepted that rpm should be converted into g force (note that it is customary to quote maximum rather than average g force) when describing the use of centrifuges. Conversion tables are generally available; if not the g force can be calculated using the from the speed and maximum radius for the rotor.
Descriptions such as 'phosphate buffer' must be avoided - this might mean potassium phosphate, sodium phosphate or Sorensen's buffer (which contains both these cations!). Similarly, salts should not be referred to as acetate or succinate and it should be clear, throughout your thesis, report or paper, whether concentrations refer to the salt or to the free acid. And was it di-sodium EDTA or tetra-sodium EDTA that you used? You have, no doubt, had to make educated guesses when trying to follow your predecessors' work, so take the trouble to remove ambiguity from what you write (and this doesn't just apply to Materials & Methods).
The Materials & Methods section should be the easiest part of a document to write, since there is nothing controversial, unless you forgot to make adequate notes when you did the work. I'm sure that you would like to be remembered as the creator of the Grand Unifying Theory, rather than as a scientific fraud because none of your experiments could ever be repeated by anyone else!

Mounted by Peter J. Large. Last revised 18 February, 1998.