Writing a Scientific Paper (M. Dickinson)

Dickinson Lab Guide to Writing a Scientific Paper

Disclaimer

This document represents my own personal views on writing a scientific manuscript. It is meant as a helpful guide for students or post-docs who feel overwhelmed with the process of constructing a paper from scratch worthy of submission or presentation to one’s PI. Many excellent writers will disagree with much advice in the document, and there is no single perfect way to write a clear and compelling scientific paper. If this guide stimulates debate and discussion among senior authors and students alike, that will be good, as it would indicate that people are at least thinking about the various decisions that one must make while preparing a paper. My most important message is that if you have never written a paper before or struggled with those you have written, it is useful to formally organize a set of guidelines that will, with time, evolve into your own personal style. In this document, I will use the second person singular to address the aspiring author, although of course many manuscripts are written in collaboration. Usually one person is responsible for writing the first draft of a paper, and this document is written with that individual in mind.

Make a figure storyboard

The best way to start writing a manuscript is to construct the sequence of figures, which will constitute the narrative arc of the paper. The figure sequence is critical to the results section, which is usually the best place to start when you begin writing. The final version of any figure may be quite complicated, consisting of multiple panels and images. It is therefore tempting and seductive to spend hours on the computer perfecting each figure in sequence, but this is not the most efficient strategy. It is far better to think through the entire figure sequence schematically. Take a blank piece of paper and sketch cartoons, panel by panel, of every figure in the paper as you envision it initially. This process is analogous to the storyboards drawn by directors of movies or television programs. The purpose of this exercise is to free yourself of the mental constraints imposed by whatever preliminary plots you might already have constructed – perhaps for lab meetings or conference presentations - and envision instead what the perfect paper might look like. What sequence of figures would make the best case? Will a reader be able to follow your story from figure to figure without awkward conceptual gaps? Do you actually have all the data necessary to create the set of figures you need? Sketching the storyboard may send you back to the bench or field when you realize that one more experiment will make the sequence tighter and more convincing. You might find that your story is really best divided into two papers, or perhaps there are sections of your story that just do not fit well within an otherwise crisp narrative. Either way, this is the best way to hone your project into a manageable structure.

When constructing your storyboard, bear in mind that most readers will know much less about your project than you do, and that the goal is to provide all the information needed to interpret your data and make the scientific points you wish to make. I always suggest to my students that they use Figure 1 to succinctly illustrate the basic experimental paradigm used in the study. Panel A might be a picture of your experimental apparatus or field site, for example. You then use subsequent panels of Figure 1 to hold the hand of the reader as you go through the steps of data analysis employed in the paper - from a representative example of raw data to a highly derived representation that you may use in subsequent figures. Showing an example of raw data is both scientifically honest and instructive. You might feel that it is unnecessary to show raw data, especially if your basic paradigm has already been presented in prior publications. A little redundancy is helpful however, in making each paper stand on its own. How many times have you been confused by a histogram, ANOVA table, bar graphs or heat map because you cannot understand how raw data were transformed into a high-order representations? We often blame ourselves for this lack in understanding, when it is more likely that the authors have not made an effort to explain and show what they are doing. Walk the readers carefully through the process in a series of panels so that they can see how you collect and handle your data. You may need to do this repeatedly throughout the manuscript whenever you introduce a new analysis method.

After introducing your methods, the next sequence of figures need to tell the basic story of your paper. A critical task at this stage is to determine the correct order that accomplishes this task most effectively. Sometimes the narrative within a manuscript is quite linear and working out the right sequence is very easy. Some manuscripts are more complicated, and it may not be immediately obvious whether experiment B should be described before or after experiment C. Like editing a Hollywood movie, you can sketch out the alternative storyboards and see which one seems to work best. Sometimes this will not be clear until you start writing the text of the results section, but it is better to start with alternative storyboards in hand than none at all.

In constructing your storyboard, it is not necessary that you present you data in the same chronological order in which you collected them. Many times, scientists may put off performing a critical control experiment at the end of a project, but this does not mean that these data should be displayed in the final figure. Choose the sequence that optimizes narrative clarity, even if this scrambles the actual timeline of the experiments. Of course, you should not manipulate the temporal sequence to the point of misrepresenting your analysis or providing a false impression of what you have done or why.

At the end of the paper, it is a great help to provide a summary diagram – one figure that pictorially displays the basic results of the paper. This is the figure that readers will remember and your colleagues will reprint when they write reviews and textbooks about your paradigm-changing results. Even if the summary figure does not make the final cut, the time and thought invested in constructing it is never wasted because you can use it in seminars, job talks, or review paper for many years.

The point at which you are happy with your storyboard is a good time to get some feedback from your PI or collaborators. Once you and your coauthors have agreed on a tentative sequence, then you can begin to construct the final version of the figures. I am quite persnickety about figure construction (ask anyone who has worked in my lab!), but much of that is beyond the scope of this writing guide. Here are a few suggestions that should make the process easier:

1) Have a target journal in mind before you start making the figures. Most journals have an ‘instructions for authors section’ that provide specific details about figure and text formatting, such as the suggested or required font type and size that you should use in your figures. Follow whatever formatting instructions are provided so that you do not waste time later.

2) Create your figures at the final size at which they will be printed in your targeted journal. Most journals use either a two-column format, and figures can be printed 1, 1 1/2, or 2 columns wide (there are also some three-column journals). Try to fit your figure panels into an efficient aspect ratio such that it can fit in either one or two columns, with the figure legend below. Within these constraints, use all available space possible, i.e. scale your figures out to the column boundaries. Do not use 1 ½ column format unless it is absolutely necessary. This strategy with save awkward and (for the journal) costly whitespace and will increase the likelihood that the journal will not shrink your figures to some incomprehensibly small size. Another reason for properly formatting your figures at final size is that is allows the referees to see the data as they will be viewed by your readers, which permits them to offer the most accurate feedback during the review process.

3) Obey the fundamental rule of scientific illustration: do not add anything to your figures (line, dot, word, image, arrow, etc.) that is not necessary for the interpretation of your data. In other words, keep things clean and try to remove unnecessary redundancies, such as multiple scale bars or axes that are all the same size. Do not use color just because you can, use it only in the service of clarity.

Figure Legends

Writing figure legends is easily the least exciting part of writing a paper, but they have to be written at some point and they are crucial. I often work on legends when I know I need to make progress on a paper but am too tired or distracted for focused composition. After the obligate ‘Figure 1’, I try to write one crisp summary phrase or sentence that provides the take home message, so that even a casual reader will know what the figure is about, e.g. ‘Measurement of aardvark bronchial flow using endoscopic micro particle image velocimetry’, or ‘Pre-natal exposure to dopamine induces risk-taking behavior in naked mole rats, but not meadow voles.’ According to journal instructions, each panel should be referenced in sequence with an ‘(A)’ or similar notation, followed by a clear description of the panel contents and relevant information such as statistical tests. Some authors write legends that are too sparse such that data interpretation is difficult, others write legends that are too long and redundant with information provided in the text. Finding the right balance takes some practice. The technical requirements of figure legends may inhibit the use of elegant prose, but try to make them as readable as possible.

Composing a Title

While composing the storyboard and in preparation for writing the results section, it is useful to have an idea for the title of your manuscript. A good clear title may help you focus your narrative and prioritize the data presentation. If you get stuck – for some reason first time authors have a hard time with titles - just work on something else and come back to it later. When you are in a good place to think about the title, write down a list of several alternatives. Titles basically range from purposely vague, ‘The effects of swamp gas on the mating behavior of feral hogs’, to clear statements of the results, ‘The ratio of methane to hydrogen sulfide in swamp gas modulates the sexual receptivity of feral hogs’. Aim for the latter, i.e. a clear statement of your results. It is always preferable if a reader can deduce the main conclusion of the paper from the title. Sometimes, however, the results of the paper simply do not justify a claim of causality. When possible, stick to the active voice. For example, ‘Swamp gas components modulate the sexual receptivity of feral hogs’ is preferable to ‘The sexual receptivity in feral hogs is modulated by swamp gas components’. I will discuss issues related to active and passive voice in more detail below.

Results

Once you have your figures (and perhaps a title) in hand, it is usually most natural to start by writing the results section. Most students will find this easier than beginning with the introduction, and you already have your figures to help lead the way. Although it is tempting to simply chronicle the sequence of experiments you performed, well-written results section exerts a strong narrative pull. In most cases, you will write about a paragraph of text that explains the result associated with each panel of each figure or table, in the sequence in which they are presented. (Most journals are adamant about this, you have to present the data in the figure in the same sequence they are first mentioned in the text.) One way to insert narrative, as opposed to just listing results, is to explain what you learned from the last set of experiments and what drove you to do the next set of experiments:

‘The data displayed in Figure 3B demonstrate that aardvarks cannot discriminate among different color M&Ms. Color selectivity cannot, therefore, explain the results of Fig. 3A, which show that the spiders exhibit consistent preferences for different types of Halloween treats. One possibility is that the aardvarks are selecting candy based not on color, but rather on shape. To test this hypothesis, we repeated our choice task using peanut M&Ms and plain m&ms with the same color coating.’

Sentences of this type serve as segues among components of what is otherwise a dry part of a paper and make it much easier to read. The reason you are presenting the results of experiment L after experiment M may be clear to you, but make sure that it is also clear to the reader. You may find that adding segues make it easier to write, as it forces you to organize you results in the proper sequence. With the above strategy as a guide, you just need to work your way through the entire figure sequence until the results of all you panels have been described.

There are several words you should avoid when describing your results. These include, ‘interesting’, ‘amazing’, ‘astonishing’, ‘surprising’ and above all ‘incredible’. (I cannot imagine a reason for why authors would want to imply that their results were not credible.) If your narrative is clear and compelling, you may indeed compel a reader that your results are ‘astonishing’, but it is poor practice to explicitly describe them as such. Used sparingly, I think the term ‘surprising’ is OK when used to describe a result that both you and a reader would find unexpected, although ‘unexpected’ might be a better choice.

Another common pitfall within the results sections is the repeated use of certain words, especially when they are employed multiple times in the same sentence. Particularly problematic words include, ‘difference’, ‘change’, ’cause’, ‘response’, and ‘effects’. For example:

‘The differences in the song preferences of the individual whip scorpions was correlated with differences in their size.’

Although this sentence may make sense, several problems arise when using the same word multiple times. First, multiple use of the same word obscures the logic within a sentence making it harder to follow. Your argument may appear tautological, even if it is fundamentally sound. In addition, prose laden with repeated use of the same words is mind-numbingly monotonous, and may induce your reader to lose interest and drop your narrative thread. It is good practice to start with the goal of never repeating the same word in any sentence. This may be impossible in some cases, but at least the attempt will make you more aware of the words you are using.

The above sentence contains another common problem, that of ambiguous antecedents. Does ‘their size’ refer to the size of the whip scorpions or the size of the songs? We are typically juggling so many concepts, variables, stimuli, and results in paper that it is tempting to rely on pronouns or other devices to simply the text. When you use terms such as including ‘these results’, ‘this effect’, or ‘the response’, make sure that the reader can easily infer which results, effect, or difference you are talking about, because chances are you have just described many. Avoid using pronouns without pristinely clear antecedents. In other words, do not write ‘this’ or ‘that’ unless you are sure the reader will know what you are referring to. It is a bad habit to start the first sentence of any paragraph with a pronoun for which the antecedent is in the previous paragraph.

Another potential problem with the previous example text is that it employs the passive voice. I dedicate an entire section to verb tense below, but try to employ the active voice as much as possible when writing your results section, as it is the section of a paper in which the passive voice exerts its strongest pull.

Discussion

It will no doubt be a matter of taste, but I find it easier to write the discussion of a paper before the introduction, because it is a more natural extension of the results. Also, whatever you say in the discussion will constrain what you need to say in the introduction, which reins in the natural tendency to start a paper with bloated prose. The discussion section is the part of a paper that seems to cause the most stress for first-time authors. To avoid boilerplate, I suggest a rough boilerplate that works well for most papers is to start by organizing the discussion into three unequal parts.

Part one is a paragraph or so that succinctly describes what you found in your study. Make a list of what you think are the most important results and observations, remind the reader what these are, and give a reference to the figure, panel, or table form which these results are drawn:

‘By using miniature headphones, we were able to provide precise auditory stimuli to freely crawling Drosophila larvae. The results indicate that listening to popular music as juveniles influences food preference as adults (Figure 2C-F). The rhythmic structure, and not simply the spectral content, is critical for this effect (Figure 3B, C). Unlike prior research with head lice, Drosophila can discriminate between Beatles and Stones songs, the latter inducing a strong adult preference for papaya (Figure 4A)…..’

The next part of the discussion is a series of sections of one or a few more paragraphs, each of which addresses an import consequence of the research. A good way to organize this section is to start with subsection headings, i.e. ‘Importance of rhythmic structure’, ‘Ecological relevance of pop music’, ‘Relevance of current findings to prior research’, ‘ Neural mechanisms underlying auditory influence’, ‘future work’, etc.. In the final version you may delete these subsection headings (and will have to if they are not allowed in the journal you choose), but they provide a helpful scaffold for your discussion as you write it. As you flush them out, you will find that some sections really aren’t necessary, some may fuse together, and some new sections may be necessary.

The final short section of the discussion should be one final restatement of the main result, and its most important consequences, e.g. its relevance to work in other model systems or human health. Here is where you might find a place for a summary figure. For example, the summary diagram might be a visual representation of a causal model suggested by your results. Many first time writers end their papers with a whimper because they don’t make the effort to make one final stab at a good definitive summary. Remember, this is that last text that a reader will swallow as they read your paper. Do not end it on some less-than-critical experimental caveat.

Introduction

The introduction section is basically a conduit between some general question in science and the specific goals of your experiments. Preferably, you want to frame the general question in such a way that it interest a broad sweep of readers. However, you cannot begin with a scope that is so large that any attempt to place your results within this context will seem absurd and amateurish. For example, do not start with Darwin and end up with experiments of the effects of pH on sperm tail mobility. To start, try to accomplish this tasks with three paragraphs. The first is a general introduction to the topic:

‘Evidence from several phyla suggests that the style of popular music experience by juveniles strongly influences their food preference as adults (citations). For example, after experiencing 60’s British new wave psychedelia as pups, Bengalese civet cats display a strong preference for field voles, whereas syblings that experienced alt country preferred millipedes and worms (citations). Experiments with synthetic music suggest that it is the rhythmic structure, and not the lyrics, that induces the observed…..’

The second section serves as an introduction to your specific experimental system:

‘Until recently, there was little evidence that popular music influenced adult food preference in insects and other arthropods (citation). However, von Winkie and colleagues recently demonstrated that Velvet Underground baselines could change the food preference of Nepalese diving spiders from caddis flies to dragonfly nymphs…..’

The third section explains what you are going to do, how you are going to do it, and gives a brief description of what you found.

‘In this paper, we test whether the adult food preference of fruit flies is influenced by popular music played during larval stages. …To perform these experiments, we constructed miniature headphones that could deliver auditory input to maggots as they crawled across agar plates. ….The results suggest that whereas Beatle songs have no influence on adult food preference, flies are exquisitely sensitive to Rolling Stones music, particular songs from ‘Goat’s Head Soup’.

Introduction sections can be much longer and more complicated, but it is good to start with this simple architecture. Some authors do not like to hint at the results of the paper in the introduction, as it creates redundancy, but I think a little redundancy is good and it helps both the referees and future readers to know where you are going. A simple but helpful rule for the introduction, and every other section for that matter, is that the section should stand by itself if it were the only part of the paper that someone actually read. Each section should have a compelling narrative, and should provide the reader will the basic take-home message of the research.

Methods

If you are having writing block, it is often helpful to start writing the Methods section – it is the part of a paper laden with the least emotional baggage. The scientific importance of Methods sections cannot be overstated. Think of how many time you pick up a paper just to learn how an experiment was done. This is particularly important for a technology-biased paper, in which you have performed the experiments using new techniques or custom-built instruments. The best way to organize a Methods section is with subsections, e.g. ‘animals’, ‘electrophysiology’, ‘visual display’, etc.

Revisions

Very few scientists are natural writers. For this reason, the first drafts of our manuscripts are unlikely to survive peer review. Perhaps the most important skill in learning to write well is to learn to be a harsh self-critic. It is essential to develop the habit of reiteratively revising your own drafts, and in doing so identifying both major and minor flaws in your writing. The biggest challenge is to train yourself to read the paper as if you were a referee or colleague. The sentences we write are naturally clear to us because we wrote them, but many times when you read a draft written by a colleague (or indeed, a published paper) you encounter whole passages that are incomprehensible. The key kernel in good writing and editing is to not just be able to identify unclear text, but to be able to identify what is unclear about it. Two common practices that muddy text include run-on sentences and pronouns lacking clear antecedents. In run-on sentences it is easy to lose track of what are the subject and objects of actions, which is pretty critical if or purpose is to make causality clear. Often scientific text must juggle the discussion of many different processes, which is why it can be hard to know what an author means by ‘this’, ‘that’ or ‘the effect’. It is better to err toward being overly explicit.

Tense

Here’s an issue that causes much anxiety in first time authors (and much conflict with co-authors) – should you write in the past tense or present tense? There is no perfect answer to this, but it is very helpful to devise and maintain a strategy so you don’t get bollixed up every time you write. I suggest that if you are talking about past research and past experiments (even those in your paper) use the past tense. If you are stating a result or claim based on experiments (including yours) then use the present tense. Experiments were done in the past, but the results we draw from them should inform us how to think about the world now. Consider the consequences of this dictum in each section of the paper.

You may rely on the past tense often in the Introduction, because for the most part you will be discussing past research. However, if a general consensus or model emerged from the research, then describe this in the present, as it represent a current understanding:

‘Von Winkie subsequently demonstrated that holometabolous insects also exhibit this phenomonen. Collectively, these studies show that popular music influences adult food preference in a wide range of insects.

For the most part, the past tense works for the Methods and Results sections because you are describing what you did. However, if you provide narrative in the Results section by stating findings, then you may want to switch to present tense:

‘The results displayed in Figure 3 demonstrate that sun spiders cannot discriminate among different color M&Ms. To test whether they can discriminate Halloween candy based on shape, we repeated our choice task using peanut and plain M&Ms.’

The Discussion section causes the greatest problems with respect to tense, but try following the same rules as above. Mention results using the past tense, but as you synthesize the results together into claims, models or hypotheses, switch to the present. Animals and plant are alive, so present tense should be used when describing how they work.

Voice

Scientists seem to be most comfortable using the passive voice. Some of my colleagues even assert that it is the only proper voice to use, because it provides objectivity. Good writing is good writing, and any book on expository style (e.g. Shrunk and White) exposes the passive voice for what it is – an imprecise construction because it does not clearly identify the subject of an action. Most of the confusion comes from the fact that scientists are uncomfortable using first person construction in the Methods and Results sections:

‘Animals were placed in small round cages and provided with a choice of M&Ms’

Here’s my favorite example from a paper I read in graduate school,

‘Calcium ions had their concentrations changed’.

There is nothing wrong with saying that you did the experiments, unless in fact you did not, but in which case you are all the more under an obligation to say who did. After writing half the paper (Methods and Results) in passive voice it is hard to get out of the habit in the Introduction and Discussion, where overuse of the passive results in imprecise and compelling prose. I think Strunk and White were correct – start with the ‘plain style’. The clearest explanatory sentences follow the simple structure: ‘the subject verbed the object’. The importance of simple, active voice plain style is especially critical in the Discussion section when you are providing mechanistic explanations for the phenomena you have studied.

Avoid using pronouns without pristinely clear antecedents. In other words, don’t write ‘this’ or ‘that’ (or vague terms like ‘the effect’) unless you are sure the reader will know what you are referring to. It is a bad habit to start the first sentence of any paragraph with a pronoun for which the antecedent is in the previous paragraph.

Style Guide

A style guide is a document that standardizes writing practices for a particular institution, such as the New Yorker or New York Times. The following entries constitute the current style guide for my lab, which students and post-docs consult when writing papers. You may not agree with all the rules, but it is very helpful to have some set of defensible rules that you follow consistently when composing your own work. You may wish to use the following text as a scaffold for building your own style guide. The entries are ordered alphabetically.

acronyms

Acronyms should be capitalized and clearly defined the first time they are used, ‘e.g. Once the aardvark was anesthetized, we injected the virus into the locus obscurus (LO).’ From that point on in the text, you should write LO and not locus obscurus. In some journals, common acronyms such as CNS do not need to be defined.

among vs between

These terms are used quite frequently in scientific papers and the rules for usage are quite simple. You make comparisons between two things, but among many things. Typically people write between when they mean among.

colons

The most appropriate use of a colon is to introduce members of a list or provide an example, e.g. ‘Aardvarks dream of many things: pencil sharpeners, picnic baskets, and purple socks.’ It can be effective, especially when word or character length is of a premium. However, consider using ‘for example’ or ‘including’ instead. Do not rely on colons as a lazy means of translating concepts from an outline into prose, e.g. ‘The results of the aardvark exclusion experiments were as follows: ant populations rebounded’.

contractions

Don’t use them, it’ll drive me crazy.

dashes

Used properly, dashes can be very effective because they allow a writer to add emphasis to certain concepts – roughly comparable to changing tone when speaking. When used to offset a clause within a sentence, dashes bring attention to the information just as parentheses diminish the importance of the enclosed phrase. A reader should be able to skim a parenthetical phrase, whereas they should read the words between dashes carefully. Another effective use of a dash is to set off a phrase that would otherwise be confusing because the subsequent text contains many commas, e.g. ‘Everything that Batman did that morning – toasting bread, brewing coffee, frying an egg, and squeezing an orange – went horribly wrong. As with semicolons, dashes lose their utility in overuse. Note that a dash is longer than a hyphen and is typically made by typing the hyphen key twice.

first person references

Do not refer to work from your own papers by mentioning your name or that of your co-authors. For example, avoid writing, ‘In an absolutely seminal paper, Dickinson and coworkers (1997) tracked the movement of aardvarks within a controlled magnetic field.’ In these cases, state the finding and provide a reference to the paper at the end of the clause or sentence. When appropriate, it is ok to use another author as a subject, I just find it a bit rich to refer to oneself in the first person. Michael Dickinson would never write in such an obnoxious manner.

hyphens

Do not hyphenate an adverb and an adjective to modify a noun, ‘e.g. genetically-modified aardvarks’, or well-intentioned attempt’. Adverbs are what we use to modify adjectives so the hyphen is unnecessary. Hyphen should be used when a sequence of words functions as a single adjective, ‘e.g. take-off behavior’ or ‘blue-green abdomen’. Most style guides do not allow hyphens to be used when two words are used as a noun, e.g. ‘The take-off sequence consisted of a take off (not ‘take-off’) followed by a quick heading change (not ‘heading-change’)’. I have noticed that journals may differ a bit on the rules for hyphens.

in order to

There is no need to precede an infinitive with ‘in order’; simply start the sentence with ‘To’. This is a classic example of the type of text that can be extracted without any loss of meaning whatsoever.

figure legends vs results

Do not bog down your results sections by including detailed information that should go in figure legends. If you are mentioning the color or thickness of points and lines in your figures within the results section you are probably providing too much detail, which will be redundant with information in the legends. Occasionally, it is necessary to drill down to minutia of plotting conventions within the text of the results, but in general you should keep the content at a relatively high level and point the reader to the figures for details. The goal is to make sure that the narrative flow of the results section is not disrupted by extraneous detail that is available elsewhere. When possible, you should have completed a draft of your figure legends before you request feedback on your results section. This way, you will have a better sense of how you plan to parse your content between these two sections.

figure

This will vary from journal to journal, but generally ‘Figure’ should always be abbreviated as ‘Fig.’, unless you are using the term to start a sentence. This will save many characters within the manuscript. If referring to a particular figure, the term should be capitalized, e.g. ‘Fig. 6A’. If referring to a sequence of panels, use a hyphen between letters, e.g. ‘Fig. 7D-G’ or ‘Fig. 3A-C, E-F’. Journals vary with respect to whether panel letters are in lowercase or caps. Think carefully about how you reference information in figures. There are two basic constructions: ‘We found that the aardvarks avoided the killer whales by exhibiting a directed somersault (Fig. 5D)’, and ‘As shown in Fig. 5D, aardvarks avoided the killer whales by exhibiting a directed somersault.’ The advantage of the parenthetical reference is that it does not break up the prose – it sends the figure itself to the background and brings the conclusions to the foreground. In situations where you need to dig down into the data a bit, perhaps by describing individual traces in a panel, it may be preferable to bring attention to the figure itself. The important thing it to think about how and why you are referencing data in the figure and making sure that your prose is not repetitive.

numbers

Numerical data should always be written in Arabic numerals, with decimal places chosen appropriately with respect to measurement accuracy. However, if you are referring to integer amounts of items that are not data, please provide the word, unless the value is higher than ten, e.g. ‘We performed eight sets of trails on each species of kumquat maggot, for a total of 32 experimental runs’.

on the other hand

Do not use this phrase to emphasize a contrasting concept unless you have used the companion construction ‘one the one hand’. Something happening one hand does not make sense without the other. This construction is somewhat tired and you should probably avoid it anyway.

quote marks

Restrict the use of quotations to indicate quoted text, e.g. ‘In their pioneering study, Snodgrass and Wigglesworth (1953) described the mouthparts of these beetles as “freakish and downright disgusting” ‘. Do no you quote marks to indicate emphasis, I know of no journal that permits such usage. Do no use quotes to indicate that the standard meaning of a word does not apply in a particular example, the way that people use air quotes when speaking. In these cases, it is better to explicitly explain the ambiguity, e.g. ‘Although for convenience we write that the aardvarks flew through the maze like a bat out of hell, we do mean to imply that this species is capable of sustained flight or is capable of echolocation.’

repeating words

Unless absolutely necessary, try not to repeat the same word or phrase in a single sentence. Of course there are many times when clarity requires you need to use a word twice, but in most cases repetition is indicative of poor, convoluted construction. It is not that repeating words and phrases within the same sentence is so bad in itself –‘of the people, for the people, by the people’ is among the most eloquent phrases in political discourse – but the practice is usually a symptom of other problems. As you re-work your drafts, consider repeating words as a red flag indicating where you can improve the clarity of your text via simplification. In many cases, re-writing sentences in the active voice, breaking up run-on sentences, and reordering clauses will eliminate the necessity of using the same word twice. While editing drafts in the lab, I probably spend ~70% of my time re-writing sentences with repeating words or phrases.

semicolons

The main utility of a semicolons is to separate to phrases within a sentence that share equal weight, e.g. ‘The aardvark drove the getaway car; the chinchilla road shotgun.’ However, you should always consider an alternative construction, such as separating the two actions with a conjunction. Before using a semicolon, you need to convince yourself that stringing the two concepts together in a single sentence provides clarity above and beyond what would be conveyed by two separate sentences. Few potential uses of a semicolon will pass this test. Another traditional us of a semicolon is when to complete phrases are separated by a conjunctive adverb, e.g. ‘Batman did arrive at the dry cleaners on time; however, this did not stop the joker from ordering pizza.’ Semicolons are very useful in scientific writing when delineating item in a list that contain multiple attributes, ‘e.g. We conducted a survey of aardvark population density in four locations: Little Rock, Arkansas; Hoboken, New Jersey; Los Vegas, Nevada; Palm Springs, California.

short sentences

When you write a very short sentence, make sure you are doing so on purpose. Short sentence can be effective when used properly, because their very simplicity provides emphasis, equivalent to isolating text within dashes. Writing according to the tenets of plain style will result in relatively short sentences, but aware that extremely short constructions can be distracting, e.g. ‘We put each aardvark in a box.’ or ‘The results were not significant’. Although there is nothing intrinsically wrong with such simple sentences, in many cases they suggest under-edited writing, as if the prose was thrown together quickly from an itemized outline. In many cases, combining short related sentences together helps the narrative flow of the text, and sometimes reduces the word count by a tick or two.

since vs because

Use since only within the context of time, e.g. ‘Since the beginning of time…’ or ‘I was more careful ever since I licked the soldering iron.’ Use because to indicate explanation or causality, e.g. ‘I licked the solder iron because it was stuck to a chocolate bar.”. It is acceptable and often very convenient to begin a sentence with because.

so

Never begin a sentence with ‘So, …’. So, is that clear enough?

species references

The first time you reference an animal subject, you should provide the full species name, e.g. ‘We conducted all experiments on fruit flies, (Drosophila melanogaster)’. If you do not describe experiments on any other animal within that same genus, then you can drop the species designation in all further reference, e.g. ‘Drosophila’. If your paper involves more than one member of the genus, you must write ‘D. melanogaster’ and ‘D. hydei’. If you don’t know the species identity or you are describing results that apply to all species within the genus examined, you should write ‘Drosophila spp.’ Although some journal do not require italics for common genera including Drosophila, please follow conventional rules. If your paper deals with only one animal, it is appropriate to revert to vernacular terms such as ‘fly’ or ‘fruit fly’. Writing ‘fly’ or ‘flies’ can save a lot of space iterated over the whole manuscript, but use the binomial designation when it matters in contrasting the result with another species. Never refer to ‘the fly’ as if Drosophila is the only one, e.g. ‘as we know in the fly’. Such usage is barbarous and worthy of medieval torture.

that vs which

Employ these common words according to classic usage. That indicates more restrictive features, whereas which provides additional, non-restrictive information, For example, ‘The aardvark in the cupboard which is spotted’ implies that there is one aardvark in the cupboard and it happens to be spotted. ‘The aardvark in the cupboard that is spotted’ implies that there are many aardvarks in the cupboard, but you are discussing the one that is spotted. In scientific writing, that is typically required much more frequently than which. When editing your papers, you should expect to go ‘which hunting’ at some point.

though vs although.

Use although, not though. Yes, dictionaries make little distinctions between the two; I just don’t like though. Of course, though is fine for other expressions such as ‘even though’.

thus and therefore

Many writers tend to overuse these words, typically employed at the beginning of sentences in the discussion section. Paragraphs with excessive use of these words are very tedious to read. If your prose is tight and logical, you will not need these starters to indicate that the next statement follows the previous statements. This is a hard habit to break, perhaps because we want our prose to sound logical. It may be helpful to consider an alternative phrase such as: ‘Collectively, these results suggest…’ In nothing else, make sure that you have not fallen into a repetitive mode in which every other sentence begins with thus or therefore.

while vs whereas

Like ‘since’, ‘while’ should be used exclusively to convey things that happened simultaneously, e.g. ‘While the Keith Richards made omelets, Mick Jagger took out the recycling.’ Use ‘whereas’ to convey two concepts that related somehow but did not occur at the same time, e.g. ‘Whereas Ron Wood insisted on making pancakes, Rod Stewart was always open to cooking a large variety of breakfast treats.’ The goal here is to preserve the meaning of ‘while’ so that it can be used to unambiguously convey simultaneous action.