Recent replies to "Laying myself bare"

Reply from Richard Grant

Richard Grant — Wed, 23 Apr 2008 04:05:48 -0000

except that he links to other reviews, a practice I find anathema unless the number of references becomes prohibitively large.

I agree; when you’re writing a review, you should cite primary literature,
For the ZNF article, we were limited to 10 citations and 10 ‘further reading’. So, yes, ‘prohibitively large’ was a given ;)

Reply from Heather Etchevers

Heather Etchevers — Tue, 22 Apr 2008 08:46:43 -0000

I prefer to separate the activities as Maxine has said – following up threads and delving into new areas via comprehensive review articles, and getting precise technical information from research articles.

I find the “Trends in…” series really helpful for this, although in the long run, reviews don’t survive long in my reading list. They get me started, and I prefer to keep source materials thereafter.

Rather than having linked keywords, an approach Nature Reviews journals take, I like having linked articles with the indication of the subjective weight the review writer gives to each. That helps me give priorities to the follow-up reading.

That said, I’ve been known to read Nature Reviews in Genetics ;-) but I think it has a dismayingly high impact factor relative to the original articles in Nature or Nature Genetics themselves. That is, reviews should serve to get someone to the source materials that a person in the field thinks are most important. But that is another kettle of fish and not much to do with Richard’s review, except that he links to other reviews, a practice I find anathema unless the number of references becomes prohibitively large.

Reply from Maxine Clarke

Maxine Clarke — Tue, 22 Apr 2008 08:01:50 -0000

I am sure you are not alone, Hawley. I am interested, though, in to what extent Review articles (literature reviews or short reviews of one recent advance) satisfy this need. Do readers of peer-reviewed research articles like to go off into these byways, or do they not have the time when scanning the literature for what’s new, and instead reserve their “byway investigation” to when there is a bit more time, and can read a review-style article? This is a fascinating question.

Reply from Hawley Rigsby

Hawley Rigsby — Mon, 21 Apr 2008 21:31:12 -0000

In response to Ms. Clarke’s question “is this kind of exercise … useful? And if so, to what type of reader?” I think it depends on how you define the term useful. I love links to keywords because it allows the writer more space to flesh out their ideas while I learn new terms by checking back on their definitions. This, of course, being the case in well written articles; the device can be a pitfall should the author, instead, use it to allow more jargon to enter their writing. That said, it is a guilty pleasure I have, delving further into subjects than is absolutely necessary, and sometimes to my detriment when I find myself miles away from my initial research interest, following cues and curiosity. But I don’t believe that I am alone in this. Am I?

Reply from Richard Grant

Richard Grant — Sun, 20 Apr 2008 23:05:39 -0000

Really? That’s a damned shame actually, not least because there’s more chance we’d have had an institutional subscription to a Nature stable journal!

Reply from Maxine Clarke

Maxine Clarke — Sun, 20 Apr 2008 19:56:35 -0000

If you are a camp-follower, like me (not a camp follower), the preprint version is clear enough in the introduction and conclusoin for me to get the drift of what zinc fingers are, how we think they work, and why they might be important. My only stylistic caveat with the intro and conclusion is the use of “ligand” as a verb in the conclusion.

One rider is that this article is written for the Encyclopaedia of Life Sciences, that is, a relatively low-level review for the interested non-specialist. ELS was started by Nature Publishing Group with the intention of linking its entries to technical articles in the journals. NPG did not pursue this course, and ELS was sold to another publisher (Wiley).

My question is, is this kind of exercise (linking between terms such as “zinc-finger domains” in technical papers and review/teaching-style articles explaining these entities) useful? And if so, to what type of reader?

Reply from Richard Grant

Richard Grant — Sun, 20 Apr 2008 04:12:28 -0000

A table at the end of the introduction with the major classes of zinc finger proteins would have been nice.

Ah, I had a table, but it was too complicated for my liking. I might have been able to simplify it. If I ever re-write then I’ll certainly consider it, thanks.

Interesting article, Martin. Thanks. It seems to be becoming more widely accepted that the vast majority of malignancies arise as a result of environmental factors. Familial genetics is not as important (numerically) as once believed, although that doesn’t mean we shouldn’t stop looking for them; if nothing else, understanding cancer neogenesis is going to help.

Off topic but related to the aboce: Think before you pink . Check out the section on Cosmetic Companies.

Reply from Martin Fenner

Martin Fenner — Sat, 19 Apr 2008 19:19:28 -0000

Richard, that is a brave step you take here. We cannot guarantee for the consequences…

I don’t have access to the published article, so I can only comment on the pre-print version. The title is obviously short (which I like), and the writing is clear and concise. The structure of the paper makes sense for someone not involved in the topic. A table at the end of the introduction with the major classes of zinc finger proteins would have been nice.

On a sidenote, MLL is not only a zinc finger protein, but also one of the most interesting molecules in leukemia research. Did you know that the diet of a mother during pregnancy can increase the risk of leukemia for her child by inducing DNA breaks in the MLL gene?

Reply from Henry Gee

Henry Gee — Fri, 18 Apr 2008 10:07:58 -0000

I think it’s a good idea, Richard, provided that one is prepared to take criticism on the chin. The NN is all about collaboration, after all, and one can always communicate privately as well as in the forum.

I thought the article was fine. Given the subject material (necessarily dense) and the target audience (people who’ll be reading it for information, rather than for pleasure) it does what it says on the tin. You’ve kept the sentences short and simple, avoiding too many relative clauses.

Heather – being an editor I shall try to respond to your challenge.

The ADP-ribosylation factor (Arf) GTPase-activating protein (GAP) family contains a single treble clef ZnF domain that mediates the hydrolysis of GTP bound to Arf

As Richard has pointed out, this looks worse than it is because of the entities within it, not because of what they are doing to each other. One could translate it as

The Futtock family contain a cordwangle that mediates the hydrolysis of grunts bound to moolies.

The problem is that the Futtock family contains elements of grunts and moolies, which makes the initial problem of interpretation harder, because some of the concepts seem nested within each other.

Reply from Richard Grant

Richard Grant — Fri, 18 Apr 2008 08:07:31 -0000

Thanks Heather. You make interesting points.

The thing is that this was never intended for a layperson. Even so, I do remember sweating over that sentence – probably not for long enough.

Syntactically it’s straightforward.

“The thing-family contains a doodah that does something.”

It’s a problem with all this stuff we work with – multiply compound nouns and modifiers. Eyuk.

Reply from Heather Etchevers

Heather Etchevers — Fri, 18 Apr 2008 07:37:19 -0000

Hey there – I think to be honest that this is unlikely to work, Richard. We won’t want to demolish people with whom we get along online, in public. How about we post what we think is good and send an e-mail to the author (if we do this) with what is bad, with the understanding that the author is supposed to post a paraphrase of that criticism at some point?

I had given this some thought what with the manuscript that we should finally send back TODAY to another journal, having been refused by Nature way back when, and all ;-)

It’s definitely been a learning process for me, if a little harrowing for my postdoc.

This is gentle criticism, but “mélange” for “variety” (this coming from a French speaker) comes across as only slightly less affected than “de novo” for “new”. Otherwise, good clear abstract, to start.

And I learned what RING stands for – here I thought it was a structure!

I defy anyone – in particular, you editors looking for clarity out there – to take this sentence and make it any clearer. Nonetheless, it’s pretty impenetrable for a layperson. “The ADP-ribosylation factor (Arf) GTPase-activating protein (GAP) family contains a single treble clef ZnF domain that mediates the hydrolysis of GTP bound to Arf.”