Let me spell it out for you: the uses and perils of acronyms, initialisms, and abbreviations.
So you’re hard up against the word limit and you want to make your manuscript shorter by contracting a few of your commonly used phrases into a single word. To do this, you can make an initialism out of the first letters of the phrase, turning “ribonucleic acid” into “RNA”. As Penn & Teller define it*, an acronym is “an initialism that you pronounce like a word”. So, DNA is an initialism, but BLAST is an acronym.
Great, right? Not so fast– in making your manuscript shorter, you run the risk of making it unreadable.
First, and most egregious, some writers fall prey to AES (abbreviate everything syndrome). Initialisms and acronyms, especially uncommon ones, can make it hard for the reader, especially if there are a lot of them to remember. We generally suggest defining an acronym or initialism only if you use it three or more times– remember, this isn’t NASA**. Spell the acronym out on first occurrence, unless it’s a commonly accepted term like DNA (or NASA), and then use that initialism consistently throughout.
Second, some initialisms can lead you down the wrong path– for example, some have different meanings in different contexts, such as “HR” for “homologous recombination” or “hypersensitive response”. Fortunately, we have yet to come across a paper that examines the effect of homologous recombination on the hypersensitive response. Also, if FT means FLOWERING LOCUS T, then does FD mean FLOWERING LOCUS D? No, FD doesn’t have an extended spelling and FLD means FLOWERING LOCUS D.
Third, there is “ATM machine syndrome”– where the initialism becomes so common that one forgets what the letters represent, leading to duplications. Spelled out, ATM machine is “Automatic Teller Machine machine”. In biology manuscripts, we often see PCR reaction, but other examples we’ve seen include: MITE element, MYA ago, BLAST tool, and EMSA assay.
Defining initialisms can help your paper flow– because really, who wants to read “Ribulose-1,5-bisphosphate carboxylase/oxygenase” more than once in a paper? They can also
get your manuscript under that all-important word limit. So, use your initialisms wisely and avoid AES. Also, if you had to look back to see what “AES” meant, then you see our point about initialisms being hard on the reader.
*Caution, profanity!! Penn and Teller on Acronyms and Initialisms
** If it were NASA, we’d want to work with the people who devised this fake news story for the crew of the space shuttle: http://www.universetoday.com/38913/fake-but-funny-nasa-press-release/