Scientific Practices & Ethics/Scientific = Writing

Scientific Writing: Ethics and = Style

Dr. Kent T. HayGlass
Updated = August 10,=20 1999; October 2, 2002; April 30, 2004

(See also the Grantsmanship = articles=20 which are posted on the University of Toronto's web site.

Citing information from others' publications is common. = However,=20 except in rare instances, these should not be verbatim quotes (ie. = copied=20 out). In all cases, the concept or sentence you use must be = referenced to=20 the individual who wrote/thought of it. You do not wish to take = the chance=20 that you look like your are trying to take credit for someone = else's=20 original ideas as one of your own -- plagiarism.

Review articles are very useful but they should be read, = digested and=20 synthesized by you rather than directly copied in your writing. = Aside from=20 the question of who did the original writing (you or the review = article=20 author), you may not want to agree with the bias expressed. Review = articles are always written with a bias that you need to identify. = Your=20 own publications (papers, essays, exams etc.,) should reflect your = own=20 interpretation, and not just reflect someone else's.

Writing the Results section of a poster, = paper etc.,=20 is a learned skill that you will acquire in the lab, usually after = quite a=20 bit of practice. Basically, you want to be sure that the data you = choose=20 to show is representative of the whole picture. This is (i) to = avoid=20 misleading others and (ii) to protect yourself when others try to = repeat=20 your work. There is no problem in selecting a particular = experiment (for=20 instance, one out of 4 performed) which clearly demonstrates your=20 findings. Not all experiments work out identically and you = shouldn't=20 expect them to. At the same time, you do not want to choose the = one=20 experiment which gives much bigger differences between groups than = all the=20 others, because it is "nicest", because this would be misleading.=20 Basically, you need to ask yourself if the data you show fairly = represents=20 your observations. It's not technical, just honest.

It can be permissible to exclude some experiments from = consideration=20 if you can justify the reason for doing so (ie. enough mice died = by=20 accident or from bleeding over the course of the experiment that = you are=20 concerned about the validity of the conclusion; the positive or = negative=20 control failed to work; the viability of the cells was low; the=20 radioisotope was old; the culture was contaminated, etc). These=20 experiments would clearly be misleading, so excluding them is = appropriate.=20 Ask yourself if excluding data is going to falsely enhance (or = detract=20 from) the "impact" of the data that you do show. This is worked = out in=20 discussion with your advisor at the time by looking at all the = relevant=20 data.

Often, the best resolution in cases of uncertainty is to add = an=20 additional independent experiment to increase your confidence in = the=20 conclusions you are drawing.

Do you know why you are using the statistical approach that = you are?=20 You needn't be a statistician, but you need to know why you chose = the=20 method you did, and the assumptions it is based on (ie. normal=20 distribution for parametric tests such as Student's T tests, = usually=20 non-parametric such as Mann-Whitney for highly variable data such = as that=20 obtained with human populations). If in any doubt, do not make=20 assumptions. It is best to consult Mary = Cheang (789=20 3730), Senior Systems Analyst and biostatistician in Community = Health=20 Sciences.

Other common points regarding = writing:

Misspelled reports/theses or overheads are terribly=20 unprofessional. Use a spell checker before showing your document = to=20 anyone. Make sure that your figures and tables are clear = and=20 easily interpretable.

Discussions should not be a chronological recitation of your = data =96=20 they are intended to discuss it. This is your opportunity to = demonstrate=20 your critical ability to synthesize and interpret scientific work. = Check=20 an issue of the Journal of Immunology. In general you = will find=20 that there is a brief recitation of the main findings (ie., not a = list of=20 observations made but a synthesis of the data) which are intended = to (i)=20 highlight the conclusions that have been drawn and (ii) focus the = reader's=20 attention on the novelty of the study. This is followed by an = attempt to=20 integrate your observations into the literature. This means a=20 demonstration of your critical analysis - extracting the key = points of=20 difference / agreement/ weakness, etc., from the literature that = you need=20 to buttress your argument. It is not a recitation of "George found = it went=20 up 87%, Sally found it went down 19% and Sue didn't even look." = That is=20 just a compilation that can be done by a student who is asked to = make a=20 list of observations without commenting on them. Particularly = since we=20 know that one can find evidence for and against absolutely = everything in=20 the immunological literature, you need to make your conclusions = =96 your=20 judgement =96 clear.

A common problem as one appreciates the complexity of the = literature=20 on the topic they study is that some people attempt to cite every = possible=20 related study (both pro and con), something that can give the = impression=20 that you are arguing with yourself or haven't made up your mind = and want=20 to list all possible outcomes to be safe. It is much better to = decide on=20 the point you want to make for each paragraph, then state your = hypothesis,=20 assemble your evidence (your conclusions/ others data which you = may=20 synthesize and refer to or refute with a valid reason) and, if = necessary,=20 restate your conclusion at the end. Everyone will not agree, but = if your=20 argument is clearly presented, the reader will enjoy discussing = the=20 scientific merits of your case rather than spend most of their = time trying=20 to figure out what you believe yourself. Brief, simple writing is = always=20 better, and more difficult, than covering every single=20 eventuality.

Novelty: This is difficult. You obviously = don't want=20 to overstate your case, claiming novelty for something already = well known.=20 At the same time, the summary paragraphs in initial drafts of = theses are=20 sometimes written to make it appear that you have successfully = repeated=20 what others have done and not much new. Is this the impression you = wish to=20 convey? It is natural to take comfort in the fact that you find = what=20 others do (reducing the probability that a prof will ask an = awkward=20 question), but you need to clearly identify what you have done = that is=20 novel. Be explicit about what you have discovered/contributed or = they'll=20 safely assume that the answer is nothing. Particularly = for=20 theses, you know much more about your data and the literature in = your area=20 than do the readers. Be explicit about your contributions and = don't assume=20 that the reader will intuitively grasp the significance of your=20 work.

Once you have completed a draft that you feel you can be = proud of,=20 ask a colleague (post-doc or senior student in the lab) to read it = and=20 critique it for you. This will benefit both of you.

General points concerning the preparation = of a=20 scientific paper or report

Developed from Instructions to=20 Authors published in Infection=20 and Immunity.

Organization and Format

One of the best ways to improve your writing is to examine = carefully=20 good papers that you have read, paying particular attention to = their style=20 rather than just reading them for content, as you usually=20 do.

Regular Papers

Regular papers/theses/research reports should include the = elements=20 described in this section.

a). Abstract

Usually limit the abstract to one double-spaced page, two = pages for=20 theses.

Concisely summarize:=20

the background - Why did you bother to do the study?=20
the intent - What did you set out to do?=20
the results obtained, without presenting extensive = experimental=20 detail=20
their significance.

b). Introduction

The introduction should supply sufficient background = information to=20 allow the reader to understand and evaluate the results of the = present=20 study without referring to previous publications on the topic. The = introduction should clearly provide the = rationale=20 for the study. Choose references carefully to provide the most = salient=20 background rather than an exhaustive review of the topic. Often = the last=20 paragraph is a brief summary of the major findings of the work. An = explicit statement of the hypothesis you will test is an excellent = idea.=20 You don't want to give the mistaken impression that you were just = working=20 along, hoping something would jump out at you.

An important point is to ensure that your introduction is = focused and=20 does not ramble. In theses where this can be a common problem, a = good=20 trick is to use subheadings for each subsection so that the reader = can see=20 the focus of each section in advance.

c). Materials and Methods

The Materials and Methods section should include sufficient = technical=20 information to allow the experiments to be repeated. When = centrifugation=20 conditions are critical, give enough information to enable another = investigator to repeat the procedure: make of centrifuge, model of = rotor,=20 temperature, time at maximum speed, and centrifugal force (X = g=20 rather than revolutions per minute). For commonly used materials = and=20 methods (eg., media and protein determinations), a simple = reference is=20 sufficient. If several alternative methods are commonly used, it = is=20 helpful to identify the method briefly as well as to cite the = references.=20 For example, it is preferable to state "cells were broken by = ultrasonic=20 treatment as previously described (9)", rather than " cells were = broken as=20 previously described (9)". The reader should be allowed to assess = the=20 method without constant reference to previous = publications.

Assays for cytokines, Ab etc., should provide explicit = detection=20 limits and state clearly the specific activity of the standard = used so=20 that comparisons can be made with other literature.

Your subjects, animal or human, should be clearly identified = in terms=20 of their characteristics, number of experiments, number per group, = etc.=20

d). Results

In the Results section, begin most paragraphs with the = rationale=20 or objective of that section. Follow with the specific = experimental=20 approach taken. It is an often good idea to highlight the reasons = for your=20 choice of this method in preference to others. Do not assume that = the=20 reader will know why you made the choice of strategy that you=20 did.

What are the main findings that you want to focus their = attention on?=20 Identify the one or two major points that are important in your=20 figure/table. Do not bury your audience with extensive = presentation of=20 everything that can be seen in your experiment.

Reserve extensive interpretation of the results for the = Discussion=20 section. However, you should include a single sentence identifying = what=20 you believe to be the relevance of this experiment and how it = connects=20 with the plan of your research. Do no assume others will = necessarily=20 derive your implied conclusion. Be=20 explicit.

Present the results as concisely as possible in one of = the=20 following: text, table(s) or figure(s). Don't make filler figures = to beef=20 up a paper. It is better to have a short report with one very = important=20 figure than nine figures of fluff that obscure your one important = finding,=20 and make the reader skim your paper so quickly they miss it. Avoid = extensive use of graphs to present data that might be more = concisely=20 presented in the text or tables. Think carefully about which means = of=20 presentation will most effectively convey your point. All tabular = data=20 should usually be accompanied by standard errors of the means = (SEM). The=20 number or replicate determinations (or animals/humans) used for = making=20 such calculations must also be included. All statements concerning = the=20 significance of the differences observed should be accompanied by=20 probability values given in parentheses. The statistical procedure = used=20 should be stated in Materials and Methods.

e). Discussion

The Discussion should begin with a brief one paragraph = summary of the=20 novelty/importance of your findings. It should provide an=20 interpretation of the results, not merely a restatement of = your=20 observations, in relation to previously published work and to the=20 experimental system at hand. It should not be a reiteration of the = introduction. It is in the discussion in particular that you have = the=20 opportunity and obligation to critically analyse your own and = others'=20 findings, and demonstrate your ability to do this well. What are = the=20 important differences between your own and previously = published=20 work? How does it affect our view of the field? You must make = clear your=20 contribution. If you just exactly repeated someone else's work, no = one is=20 interested. Therefore, the discussion should explicitly state what = is=20 different or novel and important about your work. It = is ok,=20 sometimes important, to criticize specific aspects of others' = work, but=20 his needs to be done carefully and with grace. You should also be = sure of=20 your facts. Re-read the particular papers very carefully to be = sure you=20 have not misinterpreted.

There will usually be many small discrepancies between your = work and=20 that of others. It is usually best to ignore these, unless they = are=20 critical or your discussion becomes bogged down in trivial = details. If in=20 doubt, discuss it with your supervisor.

Your paper or thesis should tell a coherent story that is = connected=20 from beginning to end. Some observations will not fit and will = "require=20 further research" but after reading your work, your reader should = feel=20 able to give a brief statement of what you wanted to do, what you = found=20 and why it matters.

Common problems that drive your readers = crazy...=20 like your supervisor!

Make sure your subject and verb agree: Conditions=20 are tested, not = is=20 tested.

As your sentences get longer (and they should = not), it=20 becomes easy to forget the subject of the sentence. Identify it = and make=20 sure that it agrees. It is very boring for your supervisor to do = this=20 for you.
Use a spell checker before giving your report to anyone, = including=20 your supervisor!
Keep your sentences short or your point becomes obscure. = Resist the=20 temptation to add too many modifying clauses. If you find a = sentence=20 becomes too long, break it into two or three. It is better to = have two=20 short, clear sentences than one that is long and = confusing.
After you have proof-read your document carefully, read it = aloud, to=20 an empty room if necessary. This will make you break up the = run-on=20 sentences into more manageable ones. Note that where you pause = in your=20 reading, a comma should be inserted. One sentence equals one = thought.=20 Remember not to add so many modifying clauses that it becomes = impossible=20 for the reader to get the point.

Specific faults:

We effect = changes and=20 their consequences affect=20 us.
We measure effects.
Cells or animals are=20 not primed. They are=20 immunized.
Mice = are not cultured (Unless, of = course, they=20 have been to the opera lately!)
Spleen=20 cells from mice immunized with xyz are=20 cultured.
We don't measure=20 IL-4.
We measure IL-4 production, levels or = synthesis.=20

=20

Questions? Comments? Broken=20 Links?
Contact the Web Master at kmorrow@cc.umanitoba.ca
Latest=20 revision: April 30, = 2004

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