When it comes to language, I am a lover and a fighter. I’m no great expert but I know what I like and do try to take a bit of care every time I lay out my little handkerchief of prose here on Nature Network.
So today, when I spotted that The Guardian’s report on the award of the Nobel prize for Chemistry to the three crystallographers who determined the structure of the ‘rhibosome’ (I kid you not), I fired off a tweet of correction. This weird mis-spelling of ‘ribosome’ didn’t look like a forgivable typo. No, the deformity rankled as a bad guess.
But last week I was myself pulled up for offences against the English language. This occurred when I received an email from an editor at the Journal of Molecular Biology inviting me to revise our recently submitted manuscript (on the structure of a protease-peptide complex) “in the light of the referees’ comments”.
Now my first reaction was one of delight since, if past experience is anything to go by, this circumlocution means the paper should be accepted subject to minor revisions. I was also pleased because this means we will probably have a paper in JMB in the year that this venerable publication celebrates its 50th anniversary.
Then I turned my attention to the requested revisions, three of which referred to my use of language.
To the first charge, the use of ‘apoenzyme’ to refer to the unliganded form of an enzyme, I have to plead guilty. That was sloppy of me. An aopenzyme is, of course, a protein catalyst without its co-factor.
In the case of the other two charges, however, I think I will fight my corner. The referee claims that ‘complex’ is not a verb in English. But it seems to me to be in common parlance, at least among crystallographers. We had written ‘prior to crystallisation we complexed the peptide with the protease’. I was relieved to find that ‘complex’ is indeed defined as a verb in the dictionary on my computer, and one of my co-authors found it in the Merriam-Webster online dictionary. Case closed, I think.
Finally, and most surprisingly of all to me, we were taken to task for using the term ‘protein expression’ to refer to the synthesis of our protein in bacteria. The reviewer pointed out that genes may be expressed but not proteins (!) and went on to bemoan the deterioration of accuracy in scientific language. Well that was a first for me. I can see where the reviewer is coming from but is there really any ambiguity in ‘protein expression’? It is a phrase I have used and heard used without confusion for nigh on 20 years.
Now I don’t want to row with the reviewer. (By which I mean don’t want to argue, not that I am averse to taking a trip with him or her in a boat equipped with oars. My goodness, this English language is a slippery thing. Look at the stacks of alternative meanings building up for just one little word, row upon row… but I digress). After all, this person has done me a great service by reading our manuscript very closely and politely suggesting improvements. But I have to dissent from their rather static view of language.
When it comes to the ways that we create meaning with words I am bound to say that I am firmly in Stephen Fry’s camp. Language is a living, breathing thing. It grows and develops. And, as long as meaning is not obscured, anything goes.
That’s what makes writing fun. Innit?
So what did they suggest instead of “protein expression”? “RNA translation”?
Because if they insist on “gene expression”, that doesn’t really say much about the protein levels.
Much talk about language on NN this week, by the way.
I’m interested in the same question- what did they suggest? This seems like an editorial issue!
Take some advice from a wily old editor, son: let the referees have their say on these minor linguistic matters. There are bigger battles to fight.
And, er, well, ‘protease-peptide comples’? Shurely Shome Mishtake?
as long as meaning is not obscured, anything goes.
No.
Using ‘complex’ as a verb might be ‘right’, but it’s bloody ugly. There is a beauty in language, especially the written word, that willy-nilly verbification is in danger of emulsifying. I’m with reviewer 2 on this one, but not for their reason.
The good Mr Fry is mostly right. But language is much more than a tool; it’s an expression of ourselves.
Well that’s just it Eva and Sabbi – no alternative for ‘protein expression’ was suggested and I can’t think of a good one. I don’t really think I’ll have too much trouble from the editor on this.
Thanks for the advice Henry (and for spotting that typo – it was a late post!) – BTW does Nature have a view on protein expression?
Plus it’s JMB. I’d guess that about a third of the papers use the phrase.
@Richard – I agree and disagree. Some mindless conversion of nouns into verbs is unpleasant. But in this case I don’t find ‘complex’ inelegant (beauty is in the eye etc). But there should be no absolute diktat. Who ruled that this rule should rule?
And ‘verbification’? Yeuch! I hope that was ironic…
I had exactly the same obection to protein expression on a paper some years ago and just backed down. I can’t even remember which paper it was. I think I changed it to “the gene for the protein was expressed and the protein purified…” Strictly genes are expressed and proteins translated but maybe we just had the same old fashioned referee?
I’m not convinced by complexed. I would have written “the protease-peptide complex was prepared and…” but I agree its a matter of taste rather than grammatical correctitude.
Ironic? Moi?
@Tina – many thanks for your comment and a warm welcome to Nature Network!
@Eva – I’ve been a bit dilatory in my blog reading this week. What discussion on language were you referring to?
@Richard – Oui. Toi.
@Cameron – Technically the reviewer has a point but I think the language has moved on. As they pointed out themselves (clearly with a heavy heart), there is even a textbook titled Protein Expression, all about how to express genes to make protein.
I may give ‘complex’ some more thought though…
I don’t know if Nature has a particular view (perhaps Dr M. C. of Kinston-upon-Thames would know) but to me ‘protein expression’ is an elision that might – might – give rise to misunderstanding. So I’d be against it. I’m also not fond of ‘complex’ as a verb.
Stephen, I have to say I definitely maybe support your stance. I’m painfully learning that we have to communicate our scientific ideas as clearly and efficiently as possible. Therefore, we should accommodate changes and simplification of our language to do so.
Otherwise, we’d still all be writing about science in Latin
However, the case of ‘complex’ is obviously still causing confusion for an expert here, so while it may be more efficient, it isn’t necessarily clearer.
Does that clarify anything?
About the Grauniad’s typo, maybe they were thinking about rhizome?
Regarding the two expressions you want to have a fight over, I would agree with you. A search on the Nature website for “complexed with” returned ~600 hits, so we wouldn’t have a problem with that. Additionally, the Oxford English Dictionary says it can be used as a verb, giving the example “the DNA was complexed with the nuclear extract”, although that might not fly with American reviewers.
Protein expression is OK too, everyone knows if is shorthand for “the gene coding for protein X was expressed” and variants therof. I see it a bit like “boiling the kettle”, an expression that greatly surprised me when I first moved to the UK and interpreted it literally.
Language is a living, breathing thing. It grows and develops.
Most definitely, mind you I listen to the ways in which our girls use words and do have wonder into what exactly it/they will develop…
Just to note that Nicolas is one of Nature ‘s subeditors, so far better qualified than Dr M. C. of Kingston upon Thames to comment on Nature ‘s style on these matters.
I, for example, would have a problem with using complex as a verb in this instance, though I am in agreement with you on expression.
Which all goes to show…………
(At Nature, our subeditors have the very useful, sensible rule of thumb – would the reader (Jill scientist) understand what is meant? If so, they can be a bit flexible on grammar – just look at the blood that has been spilt over the years on the topic of the split infinitive for example. And at Nature, I think it is highly unlikely that we would hold an author to points of style and grammar that referees consider to be correct, as we’d regard those decisions as ours to make (though referees’ advice is always very gratefully received and considered). I guess some people will have read Lynn Truss on subs overruling each other constantly on commas. Of course that never happens at Nature ;-), but it is certainly likely that a referee might advise on some style or grammar point that did not accord with the subeditorial view, whether or not the referees’ opinion was passed onto the subs in the form of the revised, accepted ms endorsed by the accepting editors.)
Mike – I don’t think the reviewer was confused. He or she took exception to using ‘complex’ as a verb. This is a a view clearly shared by come others, though as Nicolas points out, the verb ‘to complex’ appears commonly in Nature papers.
Thanks to Nicolas for pointing out that ‘boiling the kettle’ example. English is famed for its ability to confuse which I guess is why we have to exercise a degree of care (while still allowing evolution of the language).
@Kate – I also hear linguistic innovations at home from the young ones, some of them more felicitous than others. I quite like the development of ‘random’ as a term of disapprobation.
I’ve not read Truss’s book Maxine, though perhaps I should because I do stumble over commas, sometimes. Though I’m not overly fond of grammar Nazis… (thanks to my bro’ for that cartoon).
By the way, well done to The Guardian for fixing their typo.
this means we will probably have a paper in JMB in the year that this venerable publication celebrates it’s 50th anniversary.
Speaking of language, would it be churlish of me to point out that you’ve used “it’s” incorrectly? (Perhaps you were posting from your iPhone, which “corrects” this automatically!)
I’ve never used ‘complex’ as a verb but see no inherent problem with it — but then, I’m a Yank and Americans are more fluid with making nouns verbs.
@Stephen I quite like the development of ‘random’ as a term of disapprobation
Heh, ‘random’ in SE16 can also mean ‘cool’ – isn’t language fun?
@Jenny – oops! Thanks for that. I do know the difference (honest, guv!) but somehow the message doesn’t always get through to my fingers.
@Kate – yeah. Totally random.
“Random” means weird, or unexpectedly funny.
See also urban dictionary , although it’s full of “random” examples and people complaining about the use of the word. The picture of the girls with the cheese, though, is definitely “random”.
I confess to having occasionally semi-irritated colleagues in meetings by picking them up on the ‘protein expression’ one, and might argue that I’m with the reviewer here. Yeah, it’s a convenient shorthand, accepted and understandable all over the place, seemingly since whenever, but is nonsense nonetheless. Genes are expressed; mRNAs (not proteins) are translated. A protein only expresses itself in terms of its function, no? I’m not sure on an alternative that makes for less clunky sentences, though. Produced ?
Stephen, the tongue in cheek thing still doesn’t come across well in my typing.
If a ref is going to criticise anything in a paper, including grammar, they should probably check their facts first. As ‘complex’ is includified verbaciously in commonly consulted English and American English dictionaries, you’re probably pretty safe standing by your guns.
You’re just as bad as the grammar nazis if you give in. “I was only following orders” simply won’t cut it anymore.
Style is subjective, grammar is not. I don’t really have a problem with “protein expression” but it’s not grammatically incorrect.
Let’s not get onto potatoe’s next.
I agree with Lee. I can’t believe I wrote that. I’ve come over all dizzy. Must … sit … down.
ahhh the good old expression or production of proteins 😉
I’m sort of in the corner of saving space and words when writing articles although, I must say that I would add on the extra words of “the gene was expressed and protein purified”… it is more accurate but mainly because I would assume you made a construct where the gene is not in its “normal environment” (or whatever one calls the genome position rather than in a vector).
…then again, I’m not an English major and was drilled in the whole “genes are expressed, mRNA is translated and every word is important not to mix” 😉
I have to say at the moment I am more curious what protease-peptide complex is described in the article! Guess I’ll have to wait for a while to read it.
bq. “Thanks to Nicolas for pointing out that ‘boiling the kettle’ example. English is famed for its ability to confuse…”
And long may it so remain… life would be so dull without all the little linguistic curios.
A personal favourite, now seen almost everywhere, is:
I can’t ever walk past one of these without muttering under my breath:
@Henry – I think Lee may need to sit down to recover from the shock too!
Many thanks to everyone above who has contributed to the discussion. I have to say I am looking at both ‘complex’ and ‘protein expression’ in a new light. No final decision yet but I will weigh up these views when getting down to my revisions.
Åsa – I’ve already blogged about this manuscript which gives some clues as to the protease we’ve been working on. You’d have to know your amino acids pretty well to work it out from the pictures I posted. But since I’ve already talked about it in public, I guess there’s no need to be coy: it’s (did you see that Jenny?) the 3C protease from foot-and-mouth disease virus.
@Austin – har, har!
Stephen: many thanks for the insight! It would be a special day for me to make out which protein that was studied based on a close picture of some amino acids 😉 It’s a nasty disease. Interesting though,but nasty. I hope all goes well with the next peptide-protease complex!
maybe they were thinking about rhizome?
Rhizobome, perhaps?
Re. the protein issue, of course it is not strictly correct. However, it is much more convenient, and pretty, to write e.g. “The 3C protease was expressed in E. coli K12…” rather than “the gene for the 3C protease was introduced in E. coli K12, where it was expressed and translated”, especially if you have a reference to point to where the procedure has been described in detail.
For the complexing issue, I guess the problem with your sentence ‘prior to crystallisation we complexed the peptide with the protease’ is that you didn’t do the complexing, the proteins did. An easy way around this would be to use the passive voice: ‘the peptide was complexed with the protease prior to crystallisation’. It doesn’t even increase your word count.
And now, my tea break is over, bye!
Thanks for the suggestions, Nicolas.
Am sorry to learn how bad the tea-breaks are at Nature!
I would have made the same error in regards to the use of ‘protein expression’.
I am shocked the reviewer did not have you change crystallisation to crystallization (even the proof reader in your comments wants to change it). 😉
Re ‘protein expression’, I am rowing back from my initial position, partly in some sympathy with the reviewer’s views on accuracy but also because I can use ‘protein production’ as a viable alternative.
On the matter of crystallisation vs crystallization, either is acceptable (though some journals will insist on one form, usually with a ‘z’). But in our case, we use the former spelling because we wanted to grow crystals and not crystalz!
For the record, manuscript was re-submitted earlier this afternoon. Conceded the point on ‘protein expression’ but stood by ‘complex’ as a newly minted verb.
Well, crystallization is the English preferred spelling, according to the One True Dictionary.
Well done on the resubmission.
(PS. If you’re going to invent new verbs, you’ve got to know how the current ones work…)
@Richard – Crystallisation may be preferred but I guess that gives me enough latitude to stick with my own inclination, which is to eschew z’s (except when sleeping).
Not sure what your comment about inventing new verbs refers to. ‘To complex’ wasn’t my neologism – it’s been around for quite a while. I’m not in the habit of unnecessarily complexificating the language… 😉
Oops! – of course I meant to write ‘Crystallization’ in the first line above. Old habits die hard…
Reactionary Guardian reader. Feh.
But if I didn’t read The Guardian, where would you get the best bits of the Lablit podcast from…
Please: No more barcode ‘experiments’!
:-p