Analogies to describe science to nonscientists

From an Edtiorial in the current (April) issue of Nature Genetics (40, 375; 2008):

Communicating the details of science to nonspecialists is intrinsically hard because research entails specialized techniques for empirical testing of counterintuitive ideas. Public imagination may be more readily seized by stories that fit with preconceived models, and distortion can happen when communicators employ the most transmissible ideas. But when new concepts are successfully represented in everyday imagery, there is no reason the public cannot follow in detail the excitement of doing research. When engaged in the details of the analogy, nonspecialists can ask questions from a perspective that will be useful to the expert.

In an interview with Robyn Williams on Australian Broadcasting Corporation’s Science Show [15 March 2008 edition], Oxford University researcher Kim Nasmyth explained molecular mechanisms of chromosome segregation with a riddle. In his allegory, chromosomes are represented as pairs of socks.

Continue reading

Good paper journal club: stomatal signalling in plant guard cells

This is a paper under discussion at the Nature Network forum for good, clearly written papers.

SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling

Triin Vahisalu et al.

Nature 452, 487-491 (27 March 2008) | doi:10.1038/nature06608.

Download PDF here

To discuss this paper, please visit the Nature Network good paper journal club.

Making research papers clearer

Professor Linda Cooper writes at her Time for a Change blog on Nature Network about initiatives in which authors write a one-page initial summary to explain their research paper to a wide audience. She makes the argument that clearer writing of the paper itself serves a better purpose, for the following reasons:

Scientists need to communicate clearly -“when scientists write manuscripts that accurately communicate their important findings, then everyone benefits including the researcher’s colleagues, educated readers, science journalists, and civil society. In other words, it isn’t the journalist’s role to reinterpret a scientist’s writing; scientists should learn how to communicate effectively in the first place.”

Explain specialized terminology – “a relatively easy thing to do. More egregious are articles that contain lapses in logic, assumptions about what readers know, and omissions of essential information. These issues can be easily addressed by careful editing” [by the journal office].

Compressed language — “it’s not obvious why this should necessarily lead to poor writing. Several editing techniques exist to make writing more efficient by eliminating clutter and simplifying awkward constructions. Better editing also gives the writer space to include information that is essential for the non-specialist to understand the author’s story.”

The crucial question is whether research articles can be made more accessible. Professor Cooper writes that “little will be gained if researchers fail to conquer errors of style and are simply made to write more. Greater effort by both authors and journals – rather than Authors’ Summaries – will go a long way to increasing a paper’s readability. Authors could do more to revise their manuscripts while journals could apply more rigorous writing standards. Delaying the publication of papers until they meet established criteria for clear and accessible writing could provide a strong incentive for scientists to write with greater care.”

Please add your views to those being expressed by scientists at Time for a Change blog.

In addition, Dr Martin Fenner and Dr Richard Grant have started a ‘good paper journal club’ at Nature Network, to promote good scientific writing by posting examples of well-written papers, and by discussion of these papers. Please do join this group, add examples of papers you consider to be well-written, and comment on those examples arlready under discussion.

Nature Network journal club for well-written scientific papers

For discussion at the Nature Network good paper journal club.

Holocene dwarf mammoths from Wrangel Island in the Siberian Arctic — download article as PDF

Nature 362, 337 – 340 (25 March 1993); doi:10.1038/362337a0

Holocene dwarf mammoths from Wrangel Island in the Siberian Arctic

S. L. Vartanyan*, V. E. Garutt† & A. V. Sher‡

*Wrangel Island State Reserve, 686870 Ushakovskoye, Magadan Region, Russia

†Zoological Institute, Russian Academy of Sciences, 1 Universitetskaya naberezhnaya, 199034 St Petersburg, Russia

‡Severtsov Institute of Evolutionary Animal Morphology and Ecology, Russian Academy of Sciences, 33 Leninskiy Prospect, 117071 Moscow, Russia

THE cause of extinction of the woolly mammoth, Mammuthus primigenius (Blumenbach), is still debated. A major environmental change at the Pleistocene–Holocene boundary, hunting by early man, or both together are among the main explanations that have been suggested. But hardly anyone has doubted that mammoths had become extinct everywhere by around 9,500 years before present (BP). We report here new discoveries on Wrangel Island in the Arctic Ocean that force this view to be revised. Along with normal-sized mammoth fossils dating to the end of the Pleistocene, numerous teeth of dwarf mammoth dated 7,000–4,000 yr BP have been found there. The island is thought to have become separated from the mainland by 12,000 yr BP. Survival of a mammoth population may be explained by local topography and climatic features, which permitted relictual preservation of communities of steppe plants. We interpret the dwarfing of the Wrangel mammoths as a result of the insularity effect, combined with a response to the general trend towards unfavourable environment in the Holocene.

Nature Network posts, events and good reading

A few useful links and some weekend light reading suggestions via Nature Network:

Who’s got an opinion on public engagement with science? asks Nature Network London editor Matt Brown.

An overview of science-related “stuff” at Second Life, by T. Troy McGonaghy of Science in the Metaverse. Via the link, you can see the slides and a video of Troy’s presentation at the recent Virtual Worlds: Libraries, Education and Museums conference.

On the Visualization and Science forum, Hilary Spencer posts what she calls a “rant” about powerpoint, public speaking and blog posts. I’d define it as a strongly opinionated article: it contains her reactions to presentations at a recent conference she attended, and provides some useful advice about how to make and how not to make helpful slides. In a post with a related theme, Nuruddeen Lewis at his blog Lab Daze provides a very useful primer about how to give a talk: ‘Tips for nailing your next presentation’.

Martin Fenner on his excellent blog Gobbledygook writes on the “complicated” aspects of paper writing: all those policy and format requirements, ethical bodies’ requirements, and international nomenclature committees’ pronouncements. And Richard Grant, at The Scientist blog, hosts a discussion on writing style: ‘On the care and training of students, especially the training.’

Stew at Flags and Lollipops picks up on various recent posts and articles about the lack of take-up among scientists of the online commenting facilities often offered by journals on the papers they publish. Stew takes previous suggestions with a pinch of salt, homing in on the two main reasons he believes inhibit people from writing comments on published papers.

LabLit publishes the first installment of Private Investigations, a four-part story about the adventures of a very special scientist-for-hire. The author? He or she is not unknown to Nature Network, as a small amount of detective work will reveal.

What is the best way forward for Eastern Europe’s science? asks Mico Tatalovic at Cambridge Student blog, in an article featuring the new life-sciences institutue MedILS at Split, Croatia.

If you are in reach of London, there are some unusual science-related events coming up, listed by Li-Kim Lee (see links for further details): Elizabethan Sea Charts and Maps (behind the scenes); Francis Crick – DNA and beyond; Leonardo’s philosophical anatomies; and my favourite, Prince Rupert, Cavalier and Scientist.

Today (14 March, which in the US style is 3.14) is Pi day; see Gobbledygook for links to the Pi day website, but also to some music, including the American Pi song — as Martin points out, best listened to at 1:59 today.

And finally, again from Matt Brown, Nature Network’s ten most prolific bloggers over the past six months, with links to the blogs concerned. They’ll give you a good taste of the lively discussion on the network – do join us there.

Language of scientific publishing

Frank Gannon in his EMBO Reports editorial this month (9, 207; 2008), Language barriers, writes about the stark contrast between his own ability to write in English and “the difficulties faced by scientists for whom English is a second language, and who have to cope with the much more restricted style of a scientific report.” Dr Gannon goes on to discuss the differences between standard English language and the arcane, depersonalised style favoured by (or taught to) many when writing scientific reports, quoting the view that “the public would not bother to read scientific papers even if the journals were lying around for free, simply because scientific prose is largely unreadable for the non-expert—and often only barely readable for the expert.”

Although English seems set to be the main language of science for the foreseeable future, it is worth noting that the Nature journals do encourage authors to use direct, plain prose. Our subeditors and copyeditors help authors of accepted manuscripts who are not native English speakers, and we provide advice on our website which we hope will be useful to scientists preparing a paper before submission to one of our journals. Advice is also available at Nature Network, for example at Linda Cooper’s excellent advice blog Time for a change, and Ai Lin Chun’s forum Nature Nanotechnology — Asia Pacific and beyond.

See related article in the same issue of EMBO Reports as the Editorial discussed here:

Six senses in the literature: the bleak sensory landscape of biomedical texts by Raul Rodriguez-Esteban and Andrey Rzhetsky (EMBO R. 9, 212–215; 2008).

Write about science books today, World Book Day

Via Scott Keir on Nature Network:

Today (Thursday 6 March 2008) is World Book Day in the UK. Elsewhere in the world, the day falls on 23 April, traditionally held to be the anniversary of Shakespeare’s birth and death — but on this later date, the target audience of school students is usually on vacation in the UK.

Scott suggests that scientists with blogs, on Nature Network or elsewhere, write today about science books. And wearing his hat as manager for science book prizes at the Royal Society, Scott is offering to give a book to five people who write about science books on their blogs today. Henry Gee, on his Network blog End of the Pier Show, has followed suit by offering copies of his book Jacob’s Ladder: The History of the Human Genome, to the first few people who drop him a comment.

Scott has started the process of writing about books with an entertaining story about science books that have changed his life on his Network blog Mixed miscellanies. And Brian Clegg, on his Network blog PopSci, writes about how SF stimulated his interest in science.

Nature Network advice on writing style

Senior Nature editor Henry Gee writes on Nature Network’s Ask the Editor forum about writing a scientific paper.

“In my experience, the best-written submissions to Nature come from people whose first language is not English – and who have therefore been taught English, properly, as it no longer is in England……..I had a paper recently that was written in a most peculiar way, so much so that I had to turn to the author list – and found that both authors were English, working in England. In general, though, Nature editors aren’t looking for English that is beautiful (though it’s nice when it happens) but English that is comprehensible and clear, and whose meaning is unambiguous. If you are attempting to write in clear English, I find it’s best to adopt a few simple rules: the same rules that journalists use to improve the clarity of their prose.” Here are Henry’s rules:

1. Look at the lengths of your sentences. If you can split them into shorter sentences, do so.

2. Don’t use words or phrases in print that you wouldn’t use in conversation: write as you would speak. I find that if you’ve written something and you think it doesn’t make sense, speak it out loud. If it still seems like it doesn’t make sense, then it probably doesn’t.

3. Use simple sentence constructions that start at the beginning and progress in a stately and linear way to the end.

4. Avoid relative clauses.

5. Avoid the use of double negatives (cell biologists absolutely adore double negatives).

6. Avoid compound nouns (ditto).

7. Avoid neologisms (very popular in the United States).

8. Avoid creative-writing classes.

9. Audit English Literature classes. When looking for models of good writing, study writers who could really write. If you are English, read Jane Austen. If in the United States, read Hemingway.

The Nature Nanotechnology group Asia-Pacific and beyond (also on Nature Network) features some technical style tips with examples of how to shorten sentences, and lazy phrases to avoid. There is also excellent advice, including worked examples, at Time for a Change, the blog of Linda Cooper.

Nature Network bloggers feature in anthology

Four Nature Network bloggers feature in an anthology of selected science blog posts of 2007, Open Laboratory 2007. Out of more than 450 nominated entries, 52 were chosen for publication, including these from Nature Network bloggers:

Deanne Taylor, a research scientist with the Harvard School of Public Health, describes what changes need to be made to boost faculty diversity in science.

Kristin Stephan, a Tufts graduate student, discusses how difficult, but necessary, it is for PhD students in grad school to learn about careers outside academic science.

Henry Gee writes about how his 9-year-old daughter’s Asperger’s syndrome might help her become a good scientist.

Jennifer Rohn, a postdoc at University College London, documents in a series of four posts her return to the lab and academic science after four years as a journal editor. Required reading for anyone contemplating a career change.

In a short review of the book in Nature‘s 24 January issue (Nature 451, 401; 2008), Nature’s Books and Arts editor Joanne Baker wrote: “If you are overwhelmed by the surge in science-related blogging and don’t know where to start, then this compilation may help you steer a course through the sea of perspectives on offer — or inspire you to start a blog yourself.”

The book is available either as a PDF or a printed paperback, from Lulu.com.

What’s in a Jane?

Martijn J. Schuemie and Jan A. Kors (Bioinformatics doi:10.1093/bioinformatics/btn006 ) have created a freely available web-based application that, on the basis of a sample text, can suggest “journals and experts who have published similar articles”. Their aim is to help scientists to determine which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work. The application is called Jane (for journal/author name estimator).

I inputted some sample text to Jane, and was told that the Saudi Medical Journal was my top choice. No disrespect to that journal, but I know (because I am a person and not a computer) that this journal would be inappropriate for my test sample in at least two ways.

I would not primarily recommend an automatic selector to authors trying to decide where to submit their articles. When someone is ready to submit a paper, she or he will have given talks about the work and circulated drafts for comments from others in the field. That is a good time to ask for suggestions and advice about journals in which to publish. The scientist is then well-advised to read the author guidance on a few journals’ websites, to find out about editorial scope, impact factor and so on.

I think it is possibly counter-productive to use this kind of text-based comparison system on its own for making decisions about journal submission. At Nature, for example, we are looking for novel results, not something similar to what we have just published. Other journals are the same – most of them are looking for distinctive articles, not incremental repeats.

Rather than relying on computer searches to choose where to submit, I highly recommend looking at our free Author and Reviewers’ website for writing and submission advice. From there one can go straight to a great set of articles written by professional journal editors about how, where and why to submit and publish at the free science-information website SciDev.Net.

In addition, scientists can upload a draft manuscript into a community preprint server, where others in the field can comment and suggest. (Nature Precedings is one such, which provides meta-features such as alerting people in the field when new preprints have been uploaded, but many others. ArXiv is another, for the physical sciences.)

I think it will be a sad day when science journals publish “articles selected for us by computer”.

(I first read about Jane at Nature Network in a post by Graham Steel.)