Punctuation is extremely important in your writing. It tells the reader when to breathe, when to pause, it adds flourishes and flavour, and it keeps ideas organised. If you use run-on sentences (i.e., a sentence spanning 4-5 lines without punctuation) the reader will quickly run out of breath, or lose track of the point you were making. By properly couching your writing in well-placed punctuation you can make it much clearer and more readable, so we’ll spend a little time here going over the key elements of punctuation and how to spot where they’ve been used incorrectly. Native-English speakers may, at this point, start sweating and/or screaming internally, since our collective aversion to formal grammar training is ingrained from a young age. The good news is that you probably know most of the rules intuitively even if you don’t know all the official names. You will do soon, anyway.
Introduction
stock image: Min An/Pexels
If you want a bit of light bedtime reading, I recommend the book “Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation” by Liz Truss for a wry, pedantic ramble through the vagaries of English grammar. In scientific writing, it isn’t necessary to adhere rigidly to every rule as long as your meaning can be clearly understood by your readers. Indeed, every journal has their own style guide so the minutiae vary from one journal to the next. It is quite literally impossible to please everyone. The rules of punctuation are changing continuously, albeit at different rates depending on which country you live in. Even worse, punctuation usage vary wildly around the world, and this can create conflicts when you are publishing in English-language journals. There are even conflicts between British-English and American-English. So no matter where you want to publish, check the style guide of your chosen journal to see if they have any particular requirements – whether or not you’re a native speaker. It’s easy to make mistakes by accident.
The best advice I can give is to become familiar enough with the most important rules that you can get away with using the bare minimum needed. Then you don’t have to think too hard about it. After all, you don’t have to get it perfect. You just need it to be good enough to help, not hinder, the clarity of your writing. If you are unfortunate enough to get a “Reviewer 2*” then even the most perfectly punctuated manuscript won’t save you from a scathing review. Use the following handy links to jump down to a specific section:
*NB: “Reviewer 2” is a state of mind. One that is unconcerned with helping your paper to become the best version of itself. Most reviewers are not “Reviewer 2”.
Giving your paragraphs structure
I’m going to assume that my readership knows that a full stop (sorry, Americans) should be used to end their sentences. What I’d like to talk about instead is sentence length. There’s something seductive about the comma that makes many scientists want to use it all the time, and it often leads to sentences being twice to three times the length they ought to be. Sometimes, I see sentences a whole paragraph in length, and good luck to the reader trying to untangle them! At that point you might well huff and say “well, I really like my long sentences!” under your breath. If you have any left from reading a paragraph-length sentence, that is. Long sentences may feel satisfying to some authors from a literary standpoint, but they make it far more difficult for your readership to understand the structure in your argument. Especially if they have to read the same sentence multiple times to fully extract your meaning.
Your sentences should never be longer than about one lungful of air if you’re reading aloud (which typically corresponds to about two lines of text in a single-column format). So, if you have got very long sentences in your text, try reading them out loud. If it turns out you need to breathe more than once per sentence, wherever you start to get out of breath will be roughly where you need to try and put a full stop. You’ve probably already got a comma there, so use this natural break to put a full stop and split the sentence in two. This will often require slight rewording, but it’s worth taking the time to do it. You’ll usually end up with something that’s more concise, legible, and interesting than what you started with.
When to use commas (or go back to index)
Once you have your full stops in their most natural place we can worry about the commas. The point of commas, really, is to tease apart all the different clauses (“chunks”) of a sentence and impose some order on them. Let’s start with the easy ones first. In general, when you read over your text (whether aloud or in your head), you should insert a little pause wherever you see a comma – not quite long enough to take a breath, but long enough to separate one chunk of text from the next. For native English speakers or those approaching native fluency, this will usually help you figure out where you need the comma. For the rest, these are the main rules you’ll need!
Lists: If you want to list some objects in a sentence, you have to separate each of them with a comma (these are called “serial commas” a.k.a. the Oxford comma). Any adjacent words not separated with a comma will be assumed by the reader to belong together, which can lead to ambiguities. Since we in the sciences really want to avoid ambiguities, the Oxford comma is our friend. For example, in Fig. 1, are the bacon and spam supposed to be one item, or two? Without the Oxford comma, we have to assume they belong together as one item, but that may not be your intention. The safest (and clearest) course of action is to use a comma before the final “and” … but if the bacon and spam are indeed meant to be considered as a single item, put them further back in the list. Consider: “Spam, egg, bacon and spam, spam, and spam”. It doesn’t sound as satisfying to say, but it’s no longer ambiguous!
Surrounding an adverb: In the sciences it’s common to use adverbs to introduce a sentence. Just to keep things tidy, adverbs that modify a clause should be flanked by commas (unless it’s at the start of a sentence, where you just have one). Evidently, in this case I’m talking, specifically, about the words that, usually, end in -ly, but can also include words like “however”, “nevertheless”, “still”, and so on.
Joining two sentences: Ideally, we would be splitting up sentences rather than joining them together, but sometimes it just reads better to have two sentences joined by a conjunction (and/or/but/so, etc.). In this case, put a comma before the conjunction to mark the separation between them.
This is a complete, independent sentence. We can add another sentence to it.
This is a complete, independent sentence, and we can add another sentence to it.
(If you want to take out the “and”, you can still do that as long as you use a semicolon (;) instead of the comma.)
Surrounding an aside: If you’re describing something and want to interject a detail that isn’t really necessary, but might add some interest, you can encase that interjection with commas to separate it from the essential part. If your detail can be removed completely and you wouldn’t lose anything of value, then your clause is “non-restrictive”, or non-essential. It’s always your call to decide whether you want to keep or delete non-essential details, but if the sentence could stand on its own without it, put that detail in a little nest of commas. There is usually a lot more room for these in a Ph.D. thesis than a journal article.
Commas and clauses (or go back to index)
A relative clause is one that contains a relative pronoun, such as: “who”, “what”, “which”, and “where”, and they may be preceded by a comma. These clauses can be either restrictive (essential) or non-restrictive (non-essential), so it’s important to think about what the comma implies in these cases, otherwise you can introduce a lot of ambiguity. If the clause is restrictive, i.e., if it contains essential information that can’t be removed without completely changing the meaning of the sentence, you should not use commas. If the information isn’t really essential, and you can remove it without affecting the meaning of the sentence, then the clause is non-restrictive. For example:
- Restrictive: The participants who were over the age of 50 had their blood pressure checked every 3 hours.
Implies that only the participants over the age of 50 were checked every 3 hours, which tells us there are participants under 50 years old who were checked at a different rate. - Non-restrictive: The participants, who were over the age of 50, had their blood pressure checked every 3 hours.
Implies that all the participants are over 50 years of age, and that all of them were checked every 3 hours.
If we remove the italicised clause in both cases, we are left with “The participants had their blood pressure checked every 3 hours”. In the non-restrictive case this doesn’t matter, because the implication is that all of the participants were checked every 3 hours, which is fundamentally the same meaning as when the clause is still there. However, in the restrictive case this has completely changed the meaning (and implications) of the sentence, which means that the clause was essential to our understanding. So, if you have a relative clause, think very carefully about whether the clause it introduces is essential or non-essential, and use your commas accordingly.
Incidentally, there can be confusion around whether to use “that” or “which” to introduce a relative clause. British-English can be more of a loosey-goosey free-for-all, so the more rigid American-English rules are arguably easier to remember and follow. In American English, restrictive clauses take “that” instead of “which”, and “that” doesn’t need a comma. So our above example would be “The participants that were over the age of 50 had their…” for the restrictive case, while the non-restrictive case remains the same. A tidy alternative, especially if you are trying to cut down on your word count, is to remove the relative pronouns altogether. This can only be sensibly done in the restrictive case, so indirectly, it also makes a good test for whether your clause is restrictive or non-restrictive. In our above example, the restrictive case becomes: “The participants over the age of 50 had their…” versus the non-restrictive case: “The participants, over the age of 50, had their…”, which the reader needs to read more than once to make sense of.
On the subject of numbers… I can’t think of any journals that don’t use SI as the default for units and numbers. If you have a choice, it’s best to use the SI system if you can, to avoid conflicts between different international methods of presenting numbers. For instance, in the UK and US it’s common to separate thousands using a comma, but in many other countries, this is done with full stops (periods). The standard way to separate thousands in the SI system is with spaces (if you’re using LaTeX you can create half-spaces using a backslash-comma (\,) command which produces a more pleasing appearance than with full spaces). Full stops in the SI system are reserved for denoting decimals. If you want more guidance on how to follow the SI system, you can download the brochure for free from the BIPM website (the International Bureau of Weights and Measures).
Colons and semicolons (or go back to index)
Colons are less commonly used in the sciences than in more literary works, and usually, they aren’t necessary at all. We would typically only used a colon (:) to precede a list (including bullet lists), an explanation, or before the introduction of an equation.
A semicolon (;) is usually placed between two separate clauses (as discussed in “joining two sentences” above), but if you are in this situation, ask yourself if there isn’t a neater way to express them instead, perhaps as a single sentence. You may also need to use them when you are listing objects, where the list also contains commas (especially if the list was introduced with a colon) as demonstrated in Fig. 2. Using semicolons in this way prevents the sentence from degenerating into a confusing mess of commas; the semicolons (circled in green) act as separators between list items (underlined), and the commas can then be reserved for structuring any additional details or comments (for example, providing the make/model of any specific equipment).
Brackets/parentheses
As per usual, British and American English differ in their terminology, if not their usage.
- ( ) Round brackets (UK) or parentheses (US) are used to surround non-essential information in the same way that commas can. There’s no real hard-and-fast rule about whether to use commas or brackets in these cases, but if your sentence already has too many commas, you can drop some sneaky brackets in around any comments or asides you want to make to the reader. This can help to avoid what I like to call “comma-fog”, which is where you have so many commas surrounding all the different clauses in your sentence that the reader gets distracted or confused trying to keep track of what bits belong to which.
- [ ] Square brackets (UK) or brackets (US) are used less often in scientific writing and are usually reserved for interjections that explain something or add small details for the reader. They are much more common in literary fields where the editor or writer may use them to clarify statements from interviewees, etc.
Dashes (or go back to index)
These unobtrusive little marks can be a surprising source of frustration. Despite there being no strictly definitive rules about them in English, some people take the rules very seriously. More than with any other form of punctuation, it’s absolutely critical to refer to your chosen journal’s style guide if you care about getting these “right”. In some situations, you can avoid them entirely by using alternative punctuation, which I do recommend if you can get away with it.
Since there is so much overlap between the different dashes (and the hyphen) and the usage isn’t remotely standardised, I’m not going to break down each of them. Instead, I’m going to look at the different situations where one or more of them might apply in the context of scientific writing, and explain which ones you are permitted to use (and how). If you see more than one is allowed, check your journal’s style guide for the one they want you to use. If they don’t give you any guidance, then just make sure that whichever one you choose is used consistently throughout your manuscript. It’s generally acceptable to use the em-dash instead of the quotation dash (if you use LaTeX, this makes your life easier) unless you are specifically told otherwise. The swung dash is generally only used to indicate approximations in scientific texts.
| Dash name | Looks like | MS Word shortcut | LaTeX code |
| en-dash | – | Ctrl + Num - | -- or \textendash |
| em-dash | — | Ctrl + Alt + Num - | --- or \textemdash |
| quotation dash | ― | \hbox{---}\kern-.5em--- | |
| swung dash | ~ | $\sim$ |
- Parenthetical (i.e., to replace brackets/parentheses, or parenthetical commas): You may either use a pair of en-dashes (with spaces either side of each dash), or a pair of em-dashes (with no spaces).
a. (with em-dash) It is most common—especially in literary circles—to use dashes if you want a stronger pause than commas can provide.
b. (with en-dash) It is most common – especially in literary circles – to use dashes if you want a stronger pause than commas can provide. - Replacing a colon: the em-dash may be used to full replace a colon, or to act as its opposite. For example, “Em-dash, en-dash, and hyphen: A great deal of confusion surrounds their use”.
a. (replacing the colon) Em-dash, en-dash, and hyphen—A great deal of confusion surrounds their use.
b. (opposite use) A great deal of confusion surrounds their use—Em-dash, en-dash, and hyphen. - Separating the author of a quote: you may use either a quotation dash or an em-dash here. In both cases, it should have spaces either side (the only time an em-dash takes spaces). For example: “Stuff can do two things.” — Jake Peralta
- Redaction: Usually for the purposes of anonymising data, you can use the first letter of the word followed by an em-dash (R—), use the first and last letter with en-dashes replacing the middle ones (R––––a), or use three consecutive em-dashes to completely replace a word (———). If you need to redact information, your thesis advisor should be able to give you guidance on what method to use.
- Indicating ranges or spans (of dates, numbers, etc.): An en-dash is usually used for this, but some style guides prefer a hyphen; in either case, do not use spaces between the numbers and the dash. It’s considered to replace the word “through”, “and”, or “to” when discussing ranges of numbers, but if it adds ambiguity you should spell the word out (for example, if you’re dealing with negative numbers where the dash may be confused with a numerical minus). Some style guides only allow ranges to be presented like this outside of the body text (in tables etc.).
Hyphens (or go back to index)
These are more widely used, especially to help prevent ambiguity. However, give ten copy editors a single document, and you’ll be given back ten different lists of words that should or shouldn’t be hyphenated. Partly it depends on which dictionary (and even what version of it) you use, and partly on personal preference. What might be clear to one reader may seem ambiguous to another. It’s basically a lawless, Mad Max-style wasteland, is what I’m trying to say. Compounds that used to be hyphenated ten or twenty years ago may not be any more, as they become so common and familiar that the hyphenation is no longer necessary (e.g., “e-mail” and “web-site” are now “email” and “website”). So don’t get too hung upon making sure you hyphenate everything 100% correctly, because you will definitely get “corrections” back from your copy editor. So, when can we use hyphens?
- To join two words where the first word is represented by a letter (like X-ray, Y-direction).
- To show a broken word that continues on the next line (this is usually handled by software these days).
- To give clarity where not using a hyphen could lead to mix-ups when words have multiple meanings. For instance, predate/predates (from the verb meaning “to prey upon”) could be easily confused with pre-date/pre-dates (suggesting a prior occurrence) if not hyphenated!
- To separate a prefix from a word. There are no solid rules about prefixes, for example, “anti-” may or may not take a hyphen with a word that follows it depending on which dictionary you look in. Usually, if the word that follows it is capitalised you will use a hyphen between them (e.g. anti-Christmas, ex-President), but otherwise you need to check each one in the dictionary used by your chosen journal. There has been a recent trend against hyphenating with some publishers, even where it makes a word awkward to read because of double vowels (e.g. “antielliptical”).
- To leave out words from a compound we don’t want to repeat. For example, these two phrases are equivalent: “You may use either Harvard-style or Vancouver-style referencing”, and “You may use either Harvard- or Vancouver-style referencing”.
- To join two (or more) words in compound (you can also use en-dash), like “off-axis”, “freeze-frame”, “native-English-speaking” etc. This is usually done to remove ambiguity, but is where most of the controversy starts blowing up. I would recommend checking on your final run-through of your manuscript for every place you have a hyphen or en-dash and make sure that your phrasing definitely says what you want it to. You might need to use more than one hyphen if it’s really fuzzy.
- To join two compounds in a super-mega-compound-combo. This is not recommended except as a last resort, but it is sometimes unavoidable. Usually you would use an en-dash to join the two compounds, with optional (clarifying) hyphens between the two component compounds. For example, “Nobel Prize–winning research” is a compound of two compounds, so we’d join them with an en-dash to imply which bits belong together. In this case we wouldn’t need to use hyphens because it’s obvious that we’re referring to research that won a Nobel Prize, but you might need to use them, if you were talking about (for instance) the pro-GMO–anti-GMO debate. The difference in length between the hyphen and en-dash can make it easier to tease out the different parts of your text and keep them organised for the reader where just using hyphens would make it confusing.
If you’re in any doubt, just try to make sure that you have your manuscript read by someone before you submit it, and if they point out any ambiguous parts, try to clarify your intentions (either through rewording or hyphenation).
Apostrophes
Mastery of the apostrophe is central to the possessive case, but it often trips people up (especially native English speakers who learn to speak first and read second) as a quick jaunt down any British high street would show. Apostrophe use is more easily mastered by non-native English speakers, who are usually given far more comprehensive tuition in formal English grammar. Figure 3 gives us a quick-and-dirty guide, so let’s go through it in more detail.
The humble apostrophe can be used to denote either possession or a contraction. In a contraction you have two words, usually a subject and verb, that get commonly smushed together in speech (because we’re lazy) and the apostrophe shows where these two words have been joined. For example, it is or it has becomes “it’s”, she is goes to “she’s”, and let us becomes “let’s”. So, if you’re not sure whether to write “its” or “it’s”, ask yourself if you mean to say “it is” – if you do, then you want to use the contraction “it’s”. “Its” is the possessive case, indicating “the thing belongs to it“. Ironically, “its” is the only example of the possessive case I can think of that doesn’t have an apostrophe.
It’s also common to contract a verb with “not”, and in this case the apostrophe sits in the middle of the “not”, e.g. is not turns into “isn’t”, can not becomes “can’t”, and will not becomes “won’t” (not “willn’t”, because we still retain vestigial remnants of Ye Olde Englishe today, probably for the purpose of confusing…well, everyone, quite frankly). When it comes to scientific writing, it’s generally considered safer and less headache-inducing to just not use contractions at all unless you really, really have to. In this way, you’ll be able to avoid these questions altogether.
The apostrophe is never, ever, used to make a plural noun, so if we have more than one of a single Something all we need to add is an “s”, so the plural would always be Somethings. If you were to mistakenly write Something’s, it wouldn’t make sense to the reader. In our Fig. 3 example, you can see that the plural of our noun “corgi” should be corgis. If we wrote instead: the Queen has a pack of corgi’s, and the reader tried to expand the contraction, it would read as “the Queen has a pack of corgi is”. What?! This makes exactly zero sense!
With the possessive case, things can look a little more complicated until you pick the sentence apart and realise that actually, it’s deceptively simple. The possessive case can be either singular or plural, and the one you use depends upon whether your subject is singular or plural, and the number of objects is irrelevant. What does that mean? The object is a “Something” that gets acted upon (in this case, being owned) by a “Someone”, who is our subject. Let’s look at Fig. 3 again, this time paying attention to the possessive sections. It’s worth mentioning that the noun doesn’t have to be a physical object, it can also be a property that describes the subject – this is the most common sense in which you will use the possessive in scientific writing (e.g. “the particle’s velocity”).
In the case of the singular, the Queen owns corgis, so she is the subject of the sentence, and the corgis are the objects. Whether we talk about one corgi, or a whole pack of them, doesn’t actually matter. In the possessive case, there is only one Queen that we’re talking about so we use the singular possessive ‘s to show that she owns the corgis. The same rule applies to the possessive plural. If you have more than one subject (two Queens, for instance) then the subject of the sentence is plural, so it doesn’t matter if, for example, the Queens are having a joint party (the Queens’ party) or each of them is having a party (the Queens’ parties). Since the subject is already plural, you use s’ to denote their ownership over the object(s) – in this case, the party or parties.
In a more useful example, say we have run a test that gives us multiple results. The correct form of the possessive would be the singular, since we ran only one test: “the test’s results”. If we run multiple tests that each give us three results, we would use the plural form: “the tests’ results”. Just be wary of using the possessive case in more complicated situations where ambiguity might arise as a result of using it. If you’re in doubt, don’t use it – there’s nothing inherently wrong with saying “the results of the test” if it’s the clearest way to express what you mean to say. Brevity should not come at the expense of clarity.
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