JOURNAL CLUB: Functional Genomic Analysis of C. elegans Molting
Martin Fenner
Sunday, 06 April 2008 21:29 UTC
I’m reposting the article suggested by Linda Cooper:
Alison R. Frand, Sascha Russel, Gary Ruvkun. Functional Genomic Analysis of C. elegans Molting. PLOS Biology 2005:3;e312.
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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.
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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 -
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…
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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?
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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.
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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. -
“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.
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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.
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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 -
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.
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