Recent replies to "JOURNAL CLUB: Functional Genomic Analysis of C. elegans Molting"

Reply from Martin Fenner

Martin Fenner — Thu, 17 Apr 2008 20:13:51 -0000

Linda, I can follow the arguments of the discussion without great difficulty. One small problem I have is inherent to this kind of functional genomic paper. It is sometimes difficult for me to grasp the vast amount of information. Table 1 and the model in Figure 5 are a big help, but subheadings in the discussion would probably increase my understanding.

Reply from Maxine Clarke

Maxine Clarke — Thu, 17 Apr 2008 07:27:56 -0000

Good point, Linda, I have emailed the corresponding author.
I’ll try to read the discussion and post a comment on it.
All best
Maxine.

Reply from Linda Cooper

Linda Cooper — Wed, 16 Apr 2008 17:35:24 -0000

Hi Maxine,
I agree that the text could be strengthened by tighter editing, but I’m glad that you think the Introduction works. And simple terms like “new” always seem better to me than more unusual (and potentially alienating) ones like “de novo”.
If you have a chance to check out the Discussion section, I’d be interested to know what you think.
What I appreciate the most about the paper is that it’s fairly accessible to the non-expert AND sepcialized enough for the expert – a difficult yet crucial and possible balance to strike.
(And may be we should alert the authors that this discussion about their paper is going on!!)
Linda

Reply from Maxine Clarke

Maxine Clarke — Mon, 14 Apr 2008 14:39:03 -0000

Hi Martin, Agreed that not all journals disallow the practice (of a number at the beginning of a sentence) – I was explaining why other journals, eg Nature, don’t do this. So far as I am aware, it is a universal rule of grammar that a sentence has to start with a captial and that a number doesn’t “count” as a word. I suppose that there is a subjective element as to which style the reader finds more elegant.

I am of the view that there is no one correct writing style, or even one grammar, though others may disagree. Certainly there is US (American) English and English English, which have diverged in many ways. There are a plethora of dictionaries and style guides, all with variants. Take split infinitives, for example: some people rigorously excise them all whereas Hart’s Rules, Jane Austen and many others are more relaxed.

I think all agree on the aim, though, which is clarity. Our rule at Nature is that if a certain phraseology makes sense to the reader (as judged, say, by the sub(copy) editor), we like it. Apologies as I am drifting off onto general topics here instead of sticking to this paper. So, to return to the topic, I think the first paragraph below is very clear, though I would have hyphenated larval stage in the first sentence; I am not sure that the phrase “the most abundant and diverse group of animals on the planet” is in the best place there. Although it is useful background, I think it is a slight distraction here. Would “Although molting is universal in these animals…...” have been shorter and just as clear? Also not sure about the adjective “de novo” in the last sentence. Is it necessary? Or, if so, could it be “new” instead? But, all in all, a very clear paragraph in my opinion.

Ecdysozoan animals, including nematodes and arthropods [1], develop through periodic larval stage molts when the exoskeleton is shed and synthesized anew. Although molting is the hallmark of the most abundant and diverse group of animals on the planet, including a wide variety of human pests and pathogens, the endocrine circuits that regulate molting in response to environmental and physiologic cues are not well understood. Moreover, little is known about the molecular mechanisms for release and de novo production of the exoskeleton.

Reply from Martin Fenner

Martin Fenner — Mon, 14 Apr 2008 11:01:18 -0000

“Numbers at the beginning of a sentence” is one of those topics for long discussions. Not all journals disallow it – the paper we discuss here was not in a Nature journal.

I was told in writing class that it is OK to use if you are consistent and I personally prefer this. Having a long number like sixty-seven thousand one hundred forty-nine at the beginning or rewriting the sentence to avoid the number at the beginning can also be awkward.

If I think about it, is there always one correct writing style, or are there sometimes variations that can all be used? English or American spelling comes to mind. A house style is probably the only possible solution to this dilemma.

Reply from Maxine Clarke

Maxine Clarke — Mon, 14 Apr 2008 08:34:23 -0000

Martin—On the “number at the beginning of sentence”: at Nature our house style is not to allow this because it isn’t grammatical or pleasant to the eye. To elaborate a bit: a number isn’t a word, so to be grammatical, if we had a number at the beginning of a sentence, the next word would have to be captitalised, which would look jarring or ugly to the reader. Hence, our style is either to avoid having a number at the start of a sentence, or to write out the number as a word. I imagine other journals have similar policies as English grammar is universal (supposedly!).

Yingfeng—I am afraid very few manuscripts are well-written when they are submitted to Nature. The final version that one reads after publication has been vastly improved by the editors, the peer-reviwers and the sub (copy) editors. Another problem with what you suggest is that most papers are written by many authors: if someone was the main “writing author” on one paper, that same person may not be on another paper: not all his or her papers are automatically going to be of the same standard.
Hence, I suggest that for the purposes of improving one’s writing style, it makes more sense to identify well-written papers (as opposed to “good authors”) and to note online (for others to benefit) how those papers use language well.

Reply from Martin Fenner

Martin Fenner — Sat, 12 Apr 2008 15:53:01 -0000

Yingfeng,

you could start with the authors of the papers we have already posted. You could use this Connotea tag to find these papers. Pick the first or last author of a paper you like and look at some other paper from the same author. And please report what you found out.

Reply from Yingfeng Zheng

Yingfeng Zheng — Fri, 11 Apr 2008 02:49:29 -0000

My experience is that good paper is indeed helpful, but the style could be varied and the good points could be difficult for the novice to perceive. Why not give a list of good writer name so that we could learn systematically and know how the authors went through all kinds of scenarios?

Reply from Martin Fenner

Martin Fenner — Thu, 10 Apr 2008 20:38:23 -0000

But I like the use of numbers at the beginning of a sentence:

…(Figure S2). 69% (148/216) of constricted larvae expressed…

Better than

Sixty-nine percent (148/216) of constricted larvae expressed…

Reply from Linda Cooper

Linda Cooper — Thu, 10 Apr 2008 15:34:28 -0000

Martin, Let’s start a campaign to banish “respectively”. This word forces readers to back track if they want to understand the writer’s frame of reference. While back tracking can slow down readers, the “respectively” construction can also confuse them.
Linda

Reply from Martin Fenner

Martin Fenner — Wed, 09 Apr 2008 21:31:26 -0000

I agree with Linda that the structure of the paper is nice and logical. The introduction is clear and informative. This Journal Club makes me read papers I would otherwise not considered.

One small annoyance: I don’t like respectively – used 11 times in this paper.