For those interested in consistency of nomenclature, Jennifer Rohn (Mind the Gap) posts about some of the challenges, after discoverinng that a particular "gene’s ‘official’ symbol was ZNF265 according to OMIM, but ZRANB2 according to NCBI Entrez and HGNC." As well as the challenge of researchers agreeing on common nomenclatures for entities such as genes and viruses with many variants (subtypes, polymorphisms and so on) and depositing the information in an appropriate database, the databases themselves sometimes do not update frequently. It does not get better, as Jennifer writes: "Looking up your new gene of interest in PubMed is not an easy way to grasp a coherent idea of what’s been published in the literature. Abstracts are littered with synonyms (and some pairs of different genes have the same synonym), but there is no unique gene identifier, as far as I can see, associated with the abstracts." And, as Euan Adie remarks in the comment thread: "even if you used database identifiers instead of HGNC names you could run into trouble – in the abstract did you mean the gene as we knew it in 2000, or in 2002, after we discovered those extra exons? In the position it was in on the initial genome assembly, or a million basepairs further down in the latest version? The same gene in different contexts needs different identifiers (or at least version numbers), but you still need to be able to pull all that together somehow and pull out the information you need." Further discussion continues, to which you are welcome to contribute. Views from authors (past, present and future) on topics such as this one are invaluable to journals in helping them to shape their policies.

So you use Nature Network, but what do you really think of the impact of Web 2.0 (the 'social' web) on research? The TalkScience team at the British Library has set up a group Scientific researchers and Web 2.0, posing a few questions about why busy scientists should invest in Web 2.0; using the web to share data and preprints; whether concern about confientiality will lead groups to set up "gated communities"; relevance of taxonomies, folksonomies, semantic web and other Web 3.0 concepts; and user-participation, necessary to keep these new web services alive. There are already discussions on scientific method in the era of big data, advertising by stealth, open notebook science, Web 2.0 in neuroscience, and more. Please join the group, which will be providing details of the TalkScience evening at the British Library in London in September, where some of these issues will be debated. Keep an eye out for the notice on this group to attend this free event.

The official programme for Science Blogging 2008 is now up. Whether you are a blogger and regular user of the Internet, or whether you have never written an online comment but are interested to learn more, this meeting is for you, so please head on over to the Nature Network group to find out more about the programme, contribute to the make-up of the sessions, discover where to find cheap accommodation, and sign up for some science-themed outings. As a taster, here is the abstract for one panel: "Mistrust of scientists is common, and misinterpretation of scientific results rampant. Science blogs can serve as a bridge between scientists and the general public. Blogs build a community of scientists in which they can discuss the peculiarities of their jobs, their work, and their results. More than that, science blogs have the power to demystify the scientific process for the public and to reverse deeply held stereotypes of scientists. In this session, we will discuss how science blogs can change the public’s perception of scientists and provide a support framework for scientists themselves."

Previous Nature Network columns.

How long did it take to plan the fieldwork?

Two years elapsed between getting the project approved and setting sail. We wanted to use a particular vessel, the RRS Charles Darwin, which was already in the Indian Ocean and had the scientific capability that we needed. Unfortunately, we had to join a rather long waiting list. Coordination was a nightmare — our scientific instruments were all in different parts of the world, taking part in experiments that were also subject to scheduling changes. When we finally had our chance, the build-up to the Iraq invasion resulted in several changes to our port of embarkation. It was a huge relief when we finally set sail with all the equipment onboard!

See Nature Geoscience's website for the rest of the Backstory.
The paper featured is: The relationship between rifting and magmatism in the northeastern Arabian Sea, by Timothy A. Minshull, Christine I. Lane, Jenny S. Collier & Robert B. Whitmarsh (Nature Geoscience 1, 463-467; 2008).

During his first year as a graduate student, Nuruddeen Lewis at his Lab Daze blog was advised by a mentor to read at least one journal article every day. Reading a paper every day is tough, but keeping up to date with recent publications is an essential part of scientific research, writes Nuruddeen. Is the key to read as much as you can? Is there an optimal way to read the scientific literature? Nuruddeen would be interested to know your views, at Lab Daze blog.

The rENNISance woman, Cath Ennis, proposes that online networking tools such as Nature Network could be used for forge links with biologists "whose proteins of interest interact with our own". She cites a case of two people who met, discovered that one worked on an enzyme and the other on its substrate. They are now married.

Appealing to the emotion is a fundamental aspect of successful writing, says Brian Clegg at his blog PopSci. What he does not like, however, is the use of a term such as "pornography" as a substitute for this emotion. "When someone refers to a property show or a book on the impact of climate change as pornography, what they really are doing is demonstrating their own emotional insecurity, and diluting and corrupting the English language to boot", he writes. Thirty comments (at time of writing) follow, as the scientists on Nature Network respond to the concept.

Research integrity is a hotly debated topic this week, as the discussion of last week's Nature Commentary and Editorial continue at the News and Opinion forum. But "Photoshopped gels are nothing", writes Euan Adie , in a fascinating historical post about Sir John Herschel and a newspaper's stunt with bipedal beavers.

Martin Fenner continues his quest for his "paper-writing dream machine" by turning to reference management software and providing a useful brief review of what is available. "Not quite there yet", is the verdict of the post and the commenters.

Bob O'Hara describes how he is outdone by misprints. He investigates a classic paper in his field, and finds that the number of its mis-citations result in an h-index of 12, a level that the inventor of the metric, Hirsch, suggested might be a typical value for advancement to tenure.

The world's first internet balloon race is taking place, reported by Scott Keir at Mixed Miscellanies blog. In the competition, websites can be recommended by users and balloons representing subject areas race across a world map (disclaimer: I may have misunderstood the details). Scott points out that science, in the shape of Charles Darwin, is not doing very well, so nominations of science websites are required to assist. Charles Darwin himself, of course, is blogging at Nature Network, commenting on science as it is reported in the popular "prints". This week he is none too impressed at the latest genome sequencing project -- chocolate.

Finally, for those interested in how journal editors spend their days, here is an account by Henry Gee, A day in the life of a senior editor. It is impossible to summarise this eclectic account, but it is engrossing, as well as very funny, so do read it.

Previous Nature Network columns.

As stated in the retraction text, all nine of the paper's authors have agreed that the paper must be retracted. However, Tae Kook Kim, the principal investigator and corresponding author, did not agree to the retraction statement signed by the other authors and asserts that any scientific irregularities are limited to a subset of the paper's experiments. Although circumstances did not allow complete agreement among the paper's authors and the text does not list all of the scientific concerns that were raised in the initial inquiries, the published retraction statement and 'Editor's note' provide abundant explanation for why the paper must be removed from the scientific literature. We commend CGK scientists for raising the initial concerns with the Science and Nature Chemical Biology papers and the KAIST investigating committees for their efforts to date. It is reassuring that Korean institutions are taking a hard line on scientific misconduct. However, we do question the timing and content of the KAIST press release of February 29, 2008, which was made public without advance notice to the journal. It is not unusual for an institute to announce that an investigation is underway and to make another announcement at its conclusion. Ideally, though, investigating committees contact journals well in advance of making public statements, thereby ensuring that the information communicated is accurate at all stages. The potential negative impacts of scientific misconduct allegations on the accused and on the public perception of science cannot be underestimated. Statements to the press are useful, but first priorities should always be determining the facts quickly, giving due process to investigators under suspicion and correcting the literature.........As the KAIST committee completes its deliberations, we urge them to provide a full accounting of the case and make their findings widely available in English. This example would serve as a model for future investigations committed to maintaining the integrity of science and the scientific literature.

The following speakers have kindly agreed to participate:
• Jim Loftus, Research Recruitment Manager, Pfizer
• Matthais Haury, Coordinating Manager, EMBL International Centre for Advanced Training
• Zonya Jeffrey, Biomedical Scientist, Central Manchester and University Hospitals NHS Trust
• Stijn Oomes, Assistant Professor in Human–Computer Interaction, Delft University of Technology
• George Schlich, Chartered and European Patent Attorney & founder of Schlich & Co
• Jonathan Yearsley, Postdoctoral Researcher, Department of Ecology and Evolution, University of Lausanne.

Already in the Nature Network Source Event forum there are questions and answers about moving from academia to industry, what participants hope to gain from the event, which recruitment and other companies will be exhibiting, how to upload your CV, and more.
Please join this free Nature Network group to ask your questions and to obtain further careers advice from the panel of experts.
The Question and Answer sessions are here.

Many researchers would like to believe that scientific misconduct is very rare. But news reported in this issue (see page 969), and the survey results reported by Sandra Titus and her colleagues in the Commentary on page 980, challenge that comfortable assumption. Titus's team found that almost 9% of the respondents in their survey, mainly biomedical scientists, had witnessed some form of scientific misconduct in the past three years, and that 37% of those incidents went unreported.
The results suggest a research climate in which scientific misconduct, although uncommon, is certainly not an anomaly. Titus et al. outline a number of measures to address this situation, including better protection for whistleblowers, and promotion of a 'zero tolerance' culture in which scientists have just as much responsibility to report others' misconduct as they have for their own behaviour.

The Science Blogging 2008 conference, to be held in London on 30 August, is taking shape, not least in the form of this logo, created by Euan Adie. Further updates about the meeting can be seen in the forum; where you can sign up for poster sessions or talks, and book for a science walking tour of London with Nature Network London Editor Matt Brown on Friday 29 August.

Should laptops be banned from conferences during presentations, asks Andrew Hudson-Smith of Urban Nature blog? When presenting his work, he finds it disheartening to look up "only to view a sea of laptops and people typing", using their laptops to check email, surf the web or write blog posts rather than listen to the presentation.

As part of her job, scientist and rENNISance woman Cath Ennis is receiving more and more requests from colleagues to provide lay summaries of research projects for grant submissions and websites. What bothers her is the trend towards making nouns and adjectives into verbs, for example: “please can you lay this language for me”, and “if you could just laymanise this technical abstract”. She asks Network users to suggest a better term than "lay".

The latest paper for discussion in the Good Paper Journal Club is up: Dynamics of fat cell turnover in humans. Martin Fenner's view: "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."

Karesh Narasimhan, in the structural biology group, suggests that the raw data underlying experiments reported in peer-reviewed work is published online by the authors, at their institution's or laboratory's website, allowing others to "reconstruct the pieces of experiments done by a lab – the biggest beneficiaries would be graduate students – who can learn many subtler aspects of data processing and manipulation that is of publication quality."

Previous Nature Network columns.

At Nature Publishing Group, which produces some of the world's leading science journals, image guidelines were developed in 2006, and last year the company's research journals began checking two randomly selected papers in each issue for image tampering, says Linda J. Miller, U.S. executive editor of Nature and the Nature Publishing Group's research journals. So far no article has been rejected as a result of the checking, she says. Ms. Miller and other editors say that in most cases of image tampering, scientists intend to beautify their figures rather than lie about their findings. In one case, an author notified the journal that a scientist working in his lab had gone too far in trying to make figures look clean. The journal determined that the conclusions were sound, but "they wound up having to print a huge correction, and this was quite embarrassing for the authors," she says. Ms. Miller wrote an editorial for Nature stressing that scientists should present their images without alterations, rather than thinking polished images will help them get published. Many images are of gels, which are ways to detect proteins or other molecules in a sample, and often they are blurry. No matter, says Ms. Miller. "We like dirt—not all gels run perfectly," she says. "Beautification is not necessary. If your data is solid, it shines through."

Nature journals' image guidelines can be found here. Also on this page are links to free-access editorials in the Nature journals about our policies and why we have them, together with an invitation to authors and other scientists to comment online.

1 NAT REV MOL CELL BIO 31.921
2 NAT REV CANCER 29.190
3 NATURE 28.751
4 NAT REV IMMUNOL 28.300
5 NAT MEDICINE 26.382
6 NAT IMMUNOLOGY 26.218
7 NAT GENETICS 25.556
8 NAT REV NEUROSCI 24.520
9 NAT REV DRUG DISCOV 23.308
10 NAT BIOTECHNOLOGY 22.848

The Impact Factors of the Nature journals that publish original research are:

1 NATURE 28.751
2 NAT MEDICINE 26.382
3 NAT IMMUNOLOGY 26.218
4 NAT GENETICS 25.556
5 NAT BIOTECHNOLOGY 22.848
6 NAT MATERIALS 19.782
7 NAT CELL BIOLOGY 17.623
8 NAT NEUROSCIENCE 15.664
9 NAT METHODS 15.478
10 NAT NANOTECHNOLOGY 14.917
11 NAT PHYSICS 14.677
12 NAT CHEM BIOLOGY 13.683
13 NAT STRUCT MOL BIOLOGY 11.085

(Nature Photonics and Nature Geoscience are not old enough to have been awarded an Impact Factor this year.)
Readers can create their own lists of journals by subject area, title, Impact Factor or publisher, at ISI Web of Knowledge.
There is a free-access account at the ThomsonISI website which explains how the Impact Factor for journals is calculated.
Discussion of the 2007 Impact Factors, and of citation in science in general, is taking place at the Nature Network Citation in Science group, which you are warmly invited to join.