Lape R, Colquhoun D, Sivilotti LG. On the nature of partial agonism in the nicotinic receptor superfamily. Nature 2008;Jul 16. [Epub ahead of print]:1-7

What I like about this paper? Even though this is not my area of expertise, I can understand the paper without great difficulties thanks to the plain language used. An example is the introduction that starts with the following sentences:

Agonists are small molecules that bind to a receptor and activate it. The best understood receptors are ligand-gated ion channels.

The paper also has a clear structure and the logic can easily be followed. It helps that the model propoed in the paper is straighforward and that the experimental data support the conclusions without great difficulties.

Adding a paper that we want to discuss should be easier. We already use Connotea (link to the tag here), but the process could be better integrated. Digg-style votes (I like/I don’t like), also used in FriendFeed would be an easy-to-implement feature – something that is already used in Best of Nature. One step further would be a web form to fill out the basic information needed for a journal club discussion: summary, strengths and weaknesses and some more specific items for the Good Paper Journal Club (title, abstract, language, overall structure, figures and tables).

Even better would be the integration of the full text of the manuscript. We already discussed the legal aspects of this, but there should be enough interesting papers where the copyright allows this. It would be a big help if we could annotate the text directly in the Forum (e.g. to highlight examples of good writing) and to show figures and tables. This feature would obviously need much more work, but it would make an interesting project for the Article 2.0 contest.

Spalding KL, Arner E, Westermark PO, Bernard S, Buchholz BA, Bergmann O, Blomqvist L, Hoffstedt J, Näslund E, Britton T, Concha H, Hassan M, Rydén M, Frisén J, Arner P. Dynamics of fat cell turnover in humans. Nature 2008;453(7196):783-7

What I like about this paper? The authors try to address an important problem (obesity) by asking a number of simple questions. Instead of using the traditional IMRAD format (introduction, methods, results and discussion), the different structure of the paper allows the reader to easily follow the experiments. A lot of the experimental details are put into the supplementary information and don’t distract from the key research findings.

The title is short and interesting, but I would have put the main research finding in there, e.g. fat cell numbers remain stable during adulthood independent of body weight.

We have set up a project called Journal of Diabetes Forum, using an editorial team to help researchers formulate their study designs before they submit manuscripts to journals for peer review. It’s not pre-publication and does not deal with results. It’s not about posting and ranking authors, and it’s not about rejecting or accepting them. Rather, the project is about providing no strings editorial feedback on study designs. It aims to help a growing group of new researchers get some good paper basics right and optimize their chances of surviving triage and peer review once they do submit to a journal. After feedback, researchers are free to submit to any journal they wish.

This is a somewhat philanthropic project upstream from the standard journal peer review process as a “good paper” engine (somewhat philanthropic because there are obvious branding objectives for the journal). It’s an experiment we launched just recently, and at this stage, we don’t have enough submissions to draw solid conclusions, but we think we are onto something.

What do you think of this?

Best wishes, Neil

Kawaguchi et al., “Biochemistry 2008, 47:5387-5395”http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/2008/47/i19/abs/bi8002082.html.

I read this yesterday in a field whose toolset is fairly unfamiliar to me. So here’s an opportunity to see if a well-written paper can appeal outside of its discipline. (Spoiler: it can.)

This paper appeared as one of a tandem, the other, equally well-written but with a more genetic slant, appeared in May’s Journal of Biological Chemistry.

What I liked (I’m not having success in formatting my bullet list here):

1. Their clear, succinct explanations as they proceed through the results section of why they did certain controls and how it helped promote or eliminate certain hypotheses. This helped an intelligent but uninstructed neophyte in the techniques, like me, to understand their justification.

1. The authors made some new, testable hypotheses in their discussion (future directions). I like that a lot. Whether or not I would test them myself, it demonstrates a generosity of scientific spirit.

1. The figure legends are pretty much self-sufficient. You don’t have to flip between methods, results and the figure itself to understand what it’s about. Unless you want to know how many repetitions they did to calculate their error bars.

1. Overall, they say what they mean, and clearly.

What I didn’t like (but the former outweigh the latter by far):

1. The abstract, while clear and parsing well, is a little heavy on the -ize and -ility words.

1. The statistical quibbling above.

And it also lets you organize your ideas a little more coherently before you set off on the adventure of writing the actual paper.

But does it increase your chances of acceptance? Will the journal’s editors take more notice of you if they already know your name from pre-submission emails (or phone calls)?

Any views on the value of presubmission enquiries?

Gelman A., Pasarica C., & Dodhia R. Let’s practice what we preach: turning tables into graphs. American Statistician 56, 121-130.

I think it is worth reading as an encouragement to draw figured rather than write tables: they are generally easier to read. Sometimes a bit of thought is needed, and a few blind alleys explored, before a good figure is produced.

I’m curious about this, though. How easy do other people find it to interpret the figures? Would you draw any of them differently?

It seems to me that the aim of a forum on good papers is to stimulate that many more good papers will be written.

Diversity
The vehicle that is mostly used in this forum to achieve this goal is that of posters pointing out – what they consider to be – examples of good papers. I have no doubt that these papers are of indeed very high quality. The problem I have is with the diversity. Let us restrict ourselves for the time being to the Nature journals. Their scope varies wildly from medicine, biology to astronomy and climate science. The culture in these disciplines differs considerably. So my view is that pointing out an excellent paper on global warming is not going to help very much a physics postdoc who wants to write a good paper.

Dissect a paper
My suggestion for referencing a good paper is to do, what old-fashioned biologist know very well, dissect it.
A paper has a title, a list of authors, a list of affiliations, a corresponding author, an abstract, paragraphs, figures (graphs), figure captions, tables, table captions, conclusions, equations, acknowledgements, a list of references, footnotes, appendices, etc.

Example: Figures
It would be worth while to identify examples of good figures and captions. Criteria could include: use and abuse of arbitrary units, absence of spaghetti text in captions (caption saying: “see for explanation text”), good labeling, sensible color coding, self-explanatory caption.

Benefit
I could imagine that many more junior scientists from all science disciplines could learn and profit from such atomic examples.

But maybe this change of focus would be beyond the scope of this forum.

Ad Lagendijk
sciencesurvivalblog

Lämmermann T, Bader BL, Monkley SJ, Worbs T, Wedlich-Söldner R, Hirsch K, Keller M, Förster R, Critchley DR, Fässler R, Sixt M. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature 2008;453(7191):51-5

I think that the paper is easy to read, and the frequent use of the active voice is part of the reason. The paper also has a clear structure. The discussion puts the importance of the findings into a larger context. And this is again a paper by authors whose first language is not English.

This paper again made me realize that it is much easier to write a well-written paper when the data are strinking and the findings relevant.

Jones P, Jones S, Stone D. Accuracy of comparing bone quality to chocolate bars for patient information purposes: observational study. BMJ. 2007;335:1285-7.

The title is a tad too complicated and doesn’t state the main finding of the paper, the obervational study part could have ben ommitted. I like the structured abstract which is short and clear. The paper makes ample use of tables and figures that help to illustrate the research findings. Two additional features of BMJ papers are helpful: a box that summarizes What is already known on the topic and What this study adds and a clear statement of author contributions. What is missing is a statistical analysis of the findings, that probably slipped through the peer review process. And there was no ethical approval, this kind of study would not have been possible in Germany.

And as a bonus, the PDF version of the paper includes the summary of another important study: Dissent of the testis.

Wells WA. Me write pretty one day: how to write a good scientific paper. J Cell Biol. 2004;165:757-8

The paper starts by discussing the most important point: clearly state the take-home message of a paper. The rest of the short text deals with the structure of a paper and with specific style issues.

Feel free to add other good papers about paper writing in the comments of this post.

What I like about this paper? A simple title. An abstract that is understandable. A detailed discussion that puts the results into a larger context. A cool research finding that increases our understanding of a fascinating biological phenomenon.

Earth-shatteringly, the paper also includes an author summary. I wonder whether this summary is really needed.

The waggle dance in action can be seen here.

Cumming G, Fidler F, Vaux DL. Error bars in experimental biology. J Cell Biol. 2007;177:7-11

Wilbert-Lampen U, Leistner D, Greven S, Pohl T, Sper S, Völker C, Güthlin D, Plasse A, Knez A, Küchenhoff H, Steinbeck G. Cardiovascular events during World Cup soccer. New Engl J Med 2008;358:475-83.

What do I like about this paper?

• The title is short and clear
• The structured abstract is like a mini-paper, containing all the relevant information in a concise format
• Figure 1 is a wonderful representation of the data. After looking at the figure (and figure legend), you no longer need to read the manuscript

There are a few other things to like about this paper. It is difficult to imagine a better experiment to test the hypothesis that stress leads to heart attacks. The conclusions are also quite interesting: aspirin, betablockers and behavioral therapy before football games. The alternative of not watching the game is not even considered.

So, be it resolved that good writing results in an ease of reading, is it possible for an article to be at the same time well-written and incomprehensible outside of a small sphere of specialists?

Wager E, Middleton P. Technical editing of research reports in biomedical journals. Cochrane Database Syst Rev. 2007;(2):MR000002.

The authors looked at the effects of technical editing on the quality of peer-reviewed research papers. They identified 18 papers. The main findings are:

• Peer-review and editing increases the readability of a paper as measured by the Flesch Reading Ease Score
• Detailed author instructions improve a paper
• Structured abstracts can improve a paper
• Technical editing improves the accuracy of references

This is a very detailed review and worth reading. For a shorter text on the same subject, look at the 2002 JAMA article by the same authors.

I thought it might be an interesting exercise for the forum to examine our own writing. To start things off, here is my pre-print version of a review I wrote last year. The published article is at ELS , which is not open access.

What do you think?

Ditzen M, Pellegrino M, Vosshall LB. Insect odorant receptors are molecular targets of the insect repellent DEET. Science 2008;319(5871):1838-42.

The title and abstract are written clearly. The structure of the paper, from hypothesis to behaviorial studies, to electrophysiological studies, to conclusions from the findings, is logical. Of course it helps that everybody can relate to the topic from personal (in the true sense of the word) experience.

Alison R. Frand, Sascha Russel, Gary Ruvkun. Functional Genomic Analysis of C. elegans Molting. PLOS Biology 2005:3;e312.

Experiments with guinea-pig lung suggest that some of the therapeutic effects of sodium salicylate and aspirin-like drugs are due to inhibition of the synthesis of prostaglandins.

This paper was nominated by Martin Fenner. It is not yet available online, but is in the process of being digitized, and along with the rest of Nature New Biology and Nature Physical Sciences, should be online in the next few months. You can download a PDF of the whole paper at this Nautilus post .