Nautilus

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

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.

Posted by Maxine Clarke on July 04, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

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.

Posted by Maxine Clarke on June 27, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

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.

Posted by Maxine Clarke on June 20, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Barbara Axt, at her blog Baxt, asks how Internet videos can be used in science communication and science journalism. The subseqent discussion ranges over podcasts, movies of protocols, and videos of experiments as training aids.

In the good paper journal club, Neil Blair Christensen describes his journal's new project, Journal of Diabetes Forum, in which an editorial team offers to help researchers formulate their study designs before they submit manuscripts to journals for peer review, providing "no strings" editorial feedback on study designs. The service 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. For more details, please see the Nature Network forum.

A discussion at Richard Grant's blog The Scientist has blossomed into an example of how networking using the Internet, and Nature Network in particular, can help scientists. Sebastian Gonzalez, a Masters' student from Chile, "a little country at the end of the world" containing not many scientists, entered the conversation because he is interested in web-based collaboration but thinks it doesn’t work for some stated reasons. Some inches later, he has changed his position, thanks to a Chile-Australia-UK-Finland-Switzerland five-way sharing of information and ideas.

"A paper came across my virtual desk the other day that’s got Instant Classic written all over it." Nature editor Henry Gee reacts to a rather special submission: "Without giving anything away, it’s a genuinely new and startlingly simple insight into a problem that’s been perplexing people for ages; backed up by a novel, simple and apocalyptically powerful new technique; written like a dream; and from (now get this) a single author. I’m bound not to say any more. Indeed, I might have said too much. But this is one of those papers that gave me gooseflesh and threw my editorial spidey sense into fibrillation; one of those lightning-from-a-clear-sky manuscripts that as an editor I have the opportunity and privilege to be able to read and review perhaps once in a decade, and make me feel glad to be able to do the job I do. When I look at a manuscript and can’t decide whether I should send it to review or not, I ask myself one question, in particular: does this manuscript have the potential to make me see the world in a completely new way? This one does. Oh boy, it does."

In the wake of the annual Society for Scholarly Publishing, Nature Network editor Corie Lok asks whether it is the role of a scholarly society to be setting up and running groups on Nature Network or Facebook, or even building their own networking site?

Meandering Scholar (Ian Brooks) tells us what it is really like to be a mentor, and raises a toast to a first data point.

Previous Nature Network columns.

Posted by Maxine Clarke on June 13, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

A necessarily brief round-up this week, due to lack of time.

Ai Lin Chun, at Nature Nanotechnology: Asia-Pacific and beyond, explains how the journal's Research Highlights come into being . "Every week, each editor reads a list of journals in their area. We scan through all the articles published within the past week and pick out the most interesting two articles. A picking session occurs mid-week and we spend about 1-2 hours to read and write about the selected article. The criteria for Research Highlights are not as stringent as selecting papers for publication. They are meant to highlight a new idea or interesting preliminary findings published in other journals. Sometimes they are papers that we would publish and sometimes they are not. So, if you want to get into our radar, post your most recent publication on our network group. We will most definitely see it!"

Why would a researcher who has access to most journals himself be bothered to submit a paper to an open access journal and pay the publication costs when there are similarly ranked “closed” journals that are supported by subscriptions and cheaper to submit to? So asks Eva Amsen at Expression Patterns blog. The question has led, inevitably, to a lively comment thread.

Andrew Hudson-Smith, one of the newer bloggers at Nature Network, writes at his blog Urban Nature: "Blogging research thoughts and outcomes to me at least seems the most natural thing in the world, after all the current buzz around universities is outreach and breaking down silos. As such, Web 2.0, with its shared videos via services such as YouTube; its virtual environments such as Second Life; and real-time research updates via Twitter have all been welcomed and indeed become central to my work. The embracing of Web 2.0 by academics is not however universal and by many it can be viewed as trivialising research." (Some pros and cons have been discussed recently at Peer to Peer.)

Previous Nature Network columns.

Posted by Maxine Clarke on June 06, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

The citation in science group's discussion is continuing after the meeting at the British Library last Tuesday (27 May), which was attended by a range of scientists, publishers, funders and others. Please join this group to provide your views on the use and misuse of citations in assessing research output. Forum topics include Metrics: the art of counting, a useful summary by Ian Mulvany of how metrics such as the Impact Factor and the H-index are calcluated. Ian concludes: "David Colquhoun’s admonition that we should just read the papers to determine the quality of the work is a great ideal, and it is certainly the only way that scientists can determine the value of the contributions of their peers in the published literature. However there remain many of us who are interested in what is happening in science who are not conversant with the details of particular fields, and we depend on derivitave indicators. Beyond the published literature there are many growing areas of contribution that at present are almost totally ignored." (See also Turning web traffic into citations, a post by Noah Gray at Action Potential, the Nature Neuroscience blog.)
In another discussion on the forum, David Colquhoun asks whether publication metrics are appropriate for assessing people and/or institutes? "There are three separate problems that need to be kept distinct.
(1) Are any sort of publications metrics suitable for assessing people?
(2) Are any sort of publications metrics suitable for assessing institutions?
(3) How accurately can each sort of metric can be measured.
There is little point in discussing (3) unless the answer to (1) or (2) is yes. It is very easy to see that the answer to (1) is no, simply by applying the proposed measure to someone who commands universal respect in you own field. The answer to (2) is perhaps more difficult. The argument against using methods like that is partly their undemonstrated worth, but also the distortion of science that their imposition will undoubtedly produce. The pressure to produce cheap headline-grabbing work will be enormous. The long-term reputation of science will surely be damaged by this sort of bean-counting approach."

In brief, some other Nature Network news:
From the recently re-named Lo Scienziato blog of Richard Grant, a conversation on the nature of networking, on the ways in which scientists communicate to collaborate (and other, unsummarizable topics).
William Burns asks "Are presubmission enquiries useful?" I have replied on behalf of the Nature journal editors, the short answer from our perspective being "not really": the editors prefer to read a full paper at initial submission, rather than just an abstract, for the reasons provided in my reply.
In a forum post, James Millington highlights an article A Young Scientist's Guide To Gainful Employment, containing "wise words for any junior researcher starting out on their academic career. It’s written with ecologists and biologists in mind but much of the advice is likely to apply to other fields."
Bob O'Hara draws attention to a paper on "turning tables into graphs" and asks readers whether they think it helpful to create figures instead of presenting data as tables in their papers.

Previous Nature Network columns.

Posted by Maxine Clarke on May 30, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Today, the National Portrait Gallery in London unveils a portrait of Nobel laureate Sir Paul Nurse, who shared the prize for Medicine in 2001 for his work on cell division. Matt Brown asks Network readers to nominate their suggestions for whose portrait they would like to see in the gallery.
Good news for crystallographers: Hariharan Jayaram reports how a new generation of wikis, mostly based on the mediawiki platform, are being "constantly updated with crystallographic tips and tricks and plain old documentation by everyone from the creators of these powerful packages to seasoned users and even beginners."
In the Good Paper journal club, William Burns writes: "Perhaps we’re trying to be too scientific about defining what is good and bad writing? I think as scientists we hear about “a rule of writing”, and our eyes light up as if we have been given the keys to getting in Nature every week. We like to have some certainty, some “laws of physics” in the writing game. But I do feel a lot of the “rules” are snake oil." Bob O'Hara had addressed a similar theme in his blog post 'The hierarchical structure of bad writing', to which several people have made their suggestions about constructing (rather than the process of writing) a scientific paper, including Brian Derby, who writes "is no correct way to write a paper because the context is important." But, as Martin Fenner warns, "irony is a dangerous rhetorical device, because it can confuse the readers." (Examples provided.)
Allan Sudlow alerts readers to a debate called Citation in Science, to be held next week, 27 May, at the British Library in London (all welcome, but register in advance via this link), and proposes continuing the debate at Nature Network. He suggests a few topics to get started, including: ‘Tools for the Job’: does use of a single-citation search tool (PubMed, UKPMC, Google Scholar, Web of Science) bias the results? Is there a call for the use of mutiple tools?; and ‘Don’t Quote Me on That’: Even when the “original” paper is cited it is often misquoted. Do those citing not always fully understand the meaning behind a paper? Is this form of mis-citation more a case of misinterpretation rather than misrepresentation? For more on these and other similar, pertinent topics, visit the Citation in Science forum.
Senkei Umehara asks Nature Nanotechnology editor Ai Lin Chun: "Based on your experience, do you agree that there is a certain degree of “seasonality” in the number of submitted manuscripts? Could the acceptance rate differ between high and low seasons, if any?" See the editor's reply here.

Previous Nature Network columns.

Posted by Maxine Clarke on May 23, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Ennio Tasciotti writes a delightful account in the Nature Nanotechnology forum of the journey of his paper, from the experiments to final publication. I think it is a lovely account, one point of interest (among others) being that the author is not a native English-speaker.
In response to a discussion started by Cath Ennis about the obligation of authors to answer (sometimes frivolous) questions and comments from readers, Charles Darwin responds, helpfully: "take it from one who spent many years worrying about the questions and sensitivities of one’s correspondents and critics that they are rarely completely satisfied. By answering in detail you do them a great courtesy: some may be enlightened and informed, some may be grateful, some, I remember will then write a poisonous review of your work.
I wrote some years ago that ‘he who wastes an hour does not know the value of life’. Are the questions about which you fret worth an hour of your life or are there other waters to be – I ask this to a fellow seafarer – paddled?
These days I would have written ‘he or she’, of course."
At the Good Paper Journal Club, Martin Fenner starts a discussion of good papers about scientific writing. His first pick is Me write pretty one day: how to write a good scientific paper by W. A. Wells (J Cell Biol. 165, 757-758; 2004). "The paper starts by discussing the most important point: clearly state the take-home message of a paper", writes Martin. "The rest of the short text deals with the structure of a paper and with specific style issues." Half a dozen further articles and books are referenced, linked and discussed by forum contributors.
Cover letters are dissected at The Scientist, Richard Grant's blog. Richard writes that a well-written covering letter shows respect for the editor and might be useful in persuading them to send the manuscript out to review. "But — just like writing papers and giving seminars — cover-letter writing is one of those things that we are, as far as I can tell, supposed to acquire by osmosis. I wondered if you have hints or advice you’d like to share. If so, you should leave a comment." Twenty-seven comments follow, providing various degrees of detailed advice as well as a link to some humorous examples for those needing light refreshment.
The Science Blogging conference (London, 30 August 2008) plans are beginning to form, so if you are interested in coming along, whether you have a blog or are just interested in the topic, see here for suggestions about accommodation; volunteer to give a talk here; see here to offer a poster or a short presentation; and go here to make your suggestions for topics you'd like to be included on the agenda.

Previous Nature Network columns.

Posted by Maxine Clarke on May 16, 2008
Categories: Nature Network round-up | Permalink | Comments (1)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

An early collaboration between academics and industry is revealed in Scott Keir's news article. In a unique collaboration between crystallographers and designers, the story of Festival of Britain's Pattern Group is told for the first time at the Wellcome Collection’s London exhibition From Atoms to Patterns, which runs till 10 August. All but one of the contemporary (1950s) crystallographers took part anonymously and are unmasked here for the first time. “It does seem to have been perceived as a risk to venture outside academia—and to associate with trade and commerce”, comments co-curator Emily Jo Sargent.
Charles Darwin continues his assessment of science as discussed in the media, this time turning his attention to television. So far as the UK terrestrial channels are concerned, he found one factual science programme in 6 days, stimulating some acerbic comments, for "what now appears is – if I may coin a phrase – parascience. It does not deal with the raw work of our noble trade, but its applied results in society and the environment."
The University of Rockefeller Press, publisher of Journal of Cell Biology and other journals, has joined the publishers who no longer ask authors of research papers for copyright. The new policy is highlighted by Richard Grant at his blog The Scientist, and there is a comment thread that includes clarification of Nature Publishing Group's licence to publsh policies. And at Nature Precedings forum, the discussion of search, self-archiving, citations and "findability" started last week, continues apace.
Some journals apparently send unsolicited emails to authors asking them to submit their manuscripts. This practice is discussed at Gobbledygook blog, particularly in relation to open-access journals. The blog's author, Martin Fenner, advises potential authors so approached to "first check whether the journal (if it is a biomedical journal) is indexed in Medline and either has a reasonable impact factor or (for new journals) receives enough citations" before deciding whether to submit a manuscript.
Many journals do not approach potential authors in this way. Senior Nature editor Henry Gee addresses the question of Editors and the Research Agenda at his blog End of the Pier Show, in a post stimulated by Pedro Belatro's comment: "I also would like to see editors having a stronger say in the research agenda. They spend so much time reading, researching and deciding what should be interesting for a certain community, why not be more vocal about their ideas?" Henry writes: "What editors don’t do is go on the stump, making general statements about the specific subjects they’d like to see papers cover, and what they don’t like. There are many good reasons for this. The first is that all papers are welcome, simply because some of the most important papers are the most unexpected. Another, I think, is that to be too specific about what sort of things we like is to throw the game of science: editors aren’t in the business of shaping science, they are there to select the best papers for their journals. The two are not mutually exclusive, but they are distinct."
In a previous post, Henry tackles another topic of perennial interest: science careers and sexism. In commissioning a series of scientific profiles for Nature, Henry writes: "I scrupulously invited as many women as men to participate, so it was a surprise to me to learn (as perhaps it should not have been) that women featured disproportionately rarely in the published result." He goes on to question why this should be.
While on the subject of careers and training, debate continues at the News and Opinion forum on education: are we training too many scientists? ; and what's the value of molecular evolution training? Michael Thain, a UK biology school teacher writes: I have long lamented the almost complete lack of any developmental biology, certainly of non-human animals, in school biology. Indeed, as my colleagues are keen to complain, it is difficult at present to see how any school biology student can appreciate from their studies that there is a biosphere filled with non-humans. Extraordinary, isn’t it? And disgraceful." Please join us there to provide your views on these provocative Nature Commentaries.
Finally, at the Good Paper Journal club group, now numbering more than 100 members, the topic of definition of error bars is currently under the microscope.

Previous Nature Network columns

Posted by Maxine Clarke on May 09, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Who gets most credit when publication of two (or more) papers is simultaneous? Hilary Spencer asks this question in the Nature Precedings forum. Is credit correlated with being the first (even if by a few days)? And is the most cited paper the one with the most impact? Opinions about visibility, findability, impact and citation practice vary among those participating in the online discussion.
Many people feel that visualization began with Charles Minard’s 1861 map/graph of Napoleon’s march to Moscow and back, writes Rob Cogan in the Visualization and Science forum. He asks readers if they have any favourites milestones and highlights of visualization that were conceptually advanced for their times. Some attractive pictures have been posted in response.
Brian Derby has just "read and assessed (we don’t use such 20th Century termas as marking any more) a number of 1st year student projects. I am sick to the core of seeing an axel of a car.... Why can't students spell?", he asks. Referring to an article in the New York Times on mobile text language making its way into the class assignment paper, one commenter asks: "What’s the science paper of the future titled? afawk, amygdala activation assoc w/ alol, rotfl, and rotflmao" (a translation is subsequently provided).
On a similar theme, in her post 'In which I deconstruct the publication process', Jennifer Rohn initiates a discussion on stock phrases in manuscripts. "Why is it, for example, that adverbs like ‘interestingly’ seem always to be deployed for the most boring results?" Various words, phrases, use of abbreviations and aspects of grammar are deconstructed in the comment thread. Meanwhile, Charles Darwin continues his entertaining analyses of how science is reported in a different forum from the peer-reviewed literature: today's newspapers.
New blog of the week on Nature Network is A Meandering Scholar, in which Ian Brooks writes: "I hope to document the path of change: The continuing evolution of the Postdoctoral Fellow within academia."
Volunteers are needed for the 2008 World Science Festival in New York from 28 May to 1 June. Chris Wiggins writes that 4-hour volunteer shifts are available each day, at various locations throughout New York City. Volunteers will receive a festival T-shirt and free entrance to some festival events. The group for planning the Science Blogging 2008 conference Science Blogging 2008, set up a few days ago, already has 36 members. If you are interested in blogging and the social web, or if you have a blog about science, please join the group and help to shape the form of the conference, which will take place in London on 30 August. You can also enter the competition to design a logo.

Previous Nature Network columns.

Posted by Maxine Clarke on May 02, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

With his experience of writing about NIH policy for Nature, Paul Smaglik writes at the Nature Jobs careers forum, " I believe a fair peer-review grant system is the best way to distribute funds to the most-deserving science. Having said that, one must wonder how some senior investigators are six, or ten or 22 times more deserving of merit than promising young investigators, or the extent of the problem, as seen by the young investigators...... Please let me know if you are the victim of what appears to be an imbalance in the system—or if you have suggestions on how to either fix it (beyond an unprecedented NIH budgetary boost) or deal with it."

Discussion about clear writing style continues at the Good Paper Journal Club. Linda Cooper's view: "I know scientists are capable of writing clearly about highly complex research. Students in my classes do this all the time once they have the tools to transform their original confused drafts into articles that both the specialist and non- specialist can understand." Hawley Rigsby describes how rewriting a "long, obscure, and jargon-filled" account allows the reader to find the point even though some detail is missed; yet how courses in science writing can provide too much focus on simplifying concepts, and so over-simplify complex ideas. He asks whether it is possible for an article to be at the same time well-written and incomprehensible outside of a small sphere of specialists. In another discussion thread, Heather Etchevers contrasts readers of review articles, who may follow up threads and delve into new areas, with readers of research articles, who need precise technical information, quickly.

Further views on the publication process, as practised by Nature, are provided by senior editor Henry Gee at his blog End of the Pier Show, where he opines that "a purpose of the Nature Network.... is to make the whole publication process less mysterious and less frustrating for authors whose years of painstaking research are met with a form letter that says ‘no’, albeit with great politeness and much circumlocution. We know from experience that many authors see Nature as a Black Box and crave some human interaction, hence the frustration and anger when the Black Box is all they get......the Network has been adorned with many interesting discussions about editorial policies, accessibility and publication, in which editors and scientists have all taken part."

And finally, a bittersweet post from Anna Kushnir of Lab Life, about finishing her dissertation and why she won't be returning to the lab (for now).

Previous Nature Network columns.

Posted by Maxine Clarke on April 25, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

In the longest-yet comment thread on Nature Network, part of the conversation has turned to open science. Jean-Claude Bradley writes: "For my research group, switching to Open Notebook Science has been extremely beneficial for finding some great collaborators (and friends). We’re working on making anti-malarial compounds so I would be quite happy if someone branched off from our ongoing results to do something useful or even point out another interpretation or error." Jason Kelly, on the other hand, is of the view that "in “open science” discussions is that there are going to be people who think it doesn’t make sense in their (‘very competitive’) field to be open about their work. However, there are many, many scientists whose principle problem isn’t being scooped—it’s that no one notices their work. This is especially true among younger scientists still making a name for themselves or folks in smaller fields. I think there is already significant incentive for young scientists to publicize what they are doing as openly and early as possible. This open group will either be scooped out of existence, or will be more successful thanks to all the unintended benefits of making your work accessible early." These are but two small samples of a broad discussion on "open science", its desirability, and tools to achieve it (as well as tools to achieve plain old archiving). There's further discussion at Deep Thoughts and Silliness blog about the financial viability of open access publishing models.

Ai-Lin Chun describes a day in the life of a Nature journal editor in Tokyo: how she handles manuscripts submitted to the journal Nature Nanotechnology and other important matters.

The news feature from last week’s Nature about how collaborations can go bad, ending up in disputes about data ownership, is followed up by Corie Lok. Would you sign a ‘pre-nuptial’ agreement to try to avoid potential conflicts?, she asks. Further discussion on drawing up an "agreement template" for international collaborations is taking place at the News and Opinion forum.

Structural resolution is under the microscope at The Scientist blog, in a post and discussion about metrics to judge crystal structures.

Previous Nature Network columns.

Posted by Maxine Clarke on April 18, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Jennifer Rohn has once again sparked a vivacious discussion, this time about how to document an ever-expanding plethora of files, information and notes -- on paper and, as mostly described in the long comment thread, electronically. There is much to note here about the practical problems of date-stamps, peer-review, wikis, plagiarism and data sharing - from and for those at the sharp end.

The theme of electronic and web-based research and teaching is taken up in a blog post by Bob O'Hara. The pros and cons of online tools for collaborative research are discussed, both in the post and in the comment thread, with links to several services that are currently available.

Philipp Selenko reports on the Nature Network Berlin group's evening with Alison Abbott of Nature, and urges local students to join. "The basic idea of Nature Network Berlin is to also give students the opportunity to participate in activities that they would otherwise not have access to (like talking to a senior Nature editor over a glass of beer, for example)."

On 2-3 June, there will be a Royal Society meeting (free to attend) on synthetic biology, a field covering the design and construction of novel artificial biological pathways, organisms or devices, and the redesign of existing natural biological systems. Synthetic biology has developed from the convergence of other disciplines such as systems biology, genetic engineering, engineering, information theory, physics, nanotechnologies and computer modelling. Advances and applications of this exciting technology will be discussed at the meeting.

Jose Manuel Otero gets stuck into another myth of industrial (as opposed to academic) research, that "if you join an industrial research center, you can kiss good-bye the exciting days of the pursuit of knowledge, teaching students, working on large consortium projects, or in fact, having individual impact. Essentially, you will be relegated to a number inside what are often large organizations, and find moments of happiness reading the Dilbert Comic Series, only to realize you are Dilbert." Among many other points, he discusses the lack of training in management and human resources in the academic community, and the rights of the individual in large-team collaborations.

Some useful advice to the scientist who has never submitted to an international journal is provided by the ever-engaging Paul Smaglik, emeritus Editor of NatureJobs.

Finally, an historical note. On Monday (14 April) a meeting at King’s College will mark the fiftieth anniversary of the death of Rosalind Franklin. Molecular geneticist Noreen Murray will discuss Franklin’s inspiring role for women in science (also celebrated by the Rosalind Franklin Award), Ellen Solomon will speak on Franklin’s legacy for genetics and medicine, and Franklin’s co-worker Ray Gosling will recall their work in elucidating the structure of DNA. Read more about Franklin's work at Nature Network London News.

Previous Nature Network columns.

Posted by Maxine Clarke on April 11, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

If you are in Berlin on 8 April, join Alison Abbott from the Nature office in Munich at an informal gathering to discuss your ideas about scientific publishing, Nature’s activities in Germany, catch up with fellow scientists from Berlin and take the opportunity to meet the people behind the Nature Network Berlin Group (further details at the link).

Here are some thoughts about how to use the tagging options at Nature Network to encourage new scientific collaborations.

Joanna Scott, Nature Publishing Group's expert on all matters Second Life, announces a new nature.com website: Second Nature. Second Nature is also the name of Nature's home on Second Life: Joanna describes how the new Second Nature at nature.com website is a starting point for newcomers, an introduction to what Second Life’s all about and what we’re doing there, as well as providing listings of all our upcoming events and guides to the best science-related places to see in Second Life,to make it easier for people who have heard of Second Life to see what it can be used for and to help experienced users follow activity.

Read here, in the good paper journal club, how some recent papers fared on a test that correlates with the US school-grade level that can follow the text.

New group of the week is NYC, a Nature Network hub for scientists and engineers in the New York City area interested in sharing protocols, interesting publications, ideas and possibly beer. The goal of the group "is to become loud enough so that we get out own tab right next to Boston” - that's right, to become the next Nature Network official hub. The first non-virtual meeting will take place at Lucky Jack's on 9 April (details at the link). In the same group, Chris Wiggins draws attention to the five-day World Science Festival in New York City from 28 May to 1 June 2008 -- list of speakers here, including many eminent scientists, prominent media figures and others.

While on the topic of conferences, Matt Brown in his Editor's blog draws attention to the British Association's scientific communication conference on 19-10 May, in a post that offers bursaries to allow 32 scientists to attend free. To qualify, you need to fall into one of the following categories: UK science communication students; freelancers/microbusiness (fewer than 10 employees); campaigning groups; or scientists/engineers involved in public engagement. For further details of how to apply, see Matt's blog post.

Finally, Brian Clegg on his blog PopSci reveals the answers to his challenge to recognize the opening lines of five famous novels after being "babelized". (Here is one: No relation of transformation of the point, in the name of the station of the work, of that that not worried, the end still to call it, one gentleman did not live between little hour, one, of one entrerrosca and the old sample in small fine squeezes of a cremagliera of the horse and have more and more to lévier more for the packing.) There are some further challenges in the comment thread.

Previous Nature Network columns.

Posted by Maxine Clarke on April 04, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors. The Nature Network week column is archived here.

In the science writers' group, Angela Saini asks what science stories would be great for television, given that her non-scientist friends frequently tell her that "there is not enough science on TV". Among the responses so far are suggestions about heirloom tomatoes, better science for children, fun science and a magazine show. Matt Brown , who provides a weekly round-up of UK science TV on the network, comments that his favourite science programme on TV is "the recent BBC4 documentary about the lead singer of Eels discovering his father’s pioneering work on parallel universe theory. In other words, rock star learns extreme physics." Read on, and add your suggestions, at the Network forum.

At the NatureJobs careers forum, Paul Smaglik provides advice on roles in clinical trial programmes and starting a research career.

At the good paper journal club, Linda Cooper asks why so many scientific articles are difficult to read, and Heather Etchevers encourages more suggestions of well-written papers for dissection. Continuing the theme, Richard Grant at his blog The Scientist asks why most scientific papers are so boring. There is a very nice blog post by Mico Tatalovic, providing a student's perspective on students' science-writing skills -- including a round-up of undergraduate science journals.

Anna Kushnir initiates what has turned out to be a very informative debate about PubMed searches, at her blog Lab Life. There are plenty of tips and links in the long comment thread. You can also read an article on Partial Immortalization blog, "How to filter and read PubMed articles through RSS feeds", complete with screen shots, by Attila Csordas.

Jose Manuel Otero has started a Nature Network blog to discuss the difference and similarities between academic and industrial research. He is setting out to destroy some common myths. One such is that industrial research environments are not focused on problem understanding, but instead exclusively concerned with project milestones and product delivery, and therefore, will punish any type of mechanism-based efforts towards enhanced and deeper understanding. Wrong! Unsurprisingly, this blog is attacting stimulating discussion, which doubtless will continue.

John Willbanks writes about creative works, copyrights and publishing, providing some further thoughts after his talk at MIT on the question of how to extricate the “non-creative facts” from the creative, copyrighted work.

Perhaps the most intense and long comment thread for the week is Jennifer Rohn's post and discussion on Mind the Gap, "In which I utterly fail to conceptualize". Initially on the use of Excel spreadsheets to analyse genome-wide screens, the discussion becomes a full-blown debate on the contributions of bioinformaticans and "wet" (laboratory) biologists. And perhaps the most significant Nature Network group that started this week is called Collaboration: bringing Nature Network members together, set up by Bob O'Hara in direct response to this discussion. Can Nature Network create collaborations between its members? How can NN facilitate this process? Here you can discuss these details, and look for other people who are interested in working on the same topics as you are. I encourage you to sign up.

Previous Nature Network columns.

Posted by Maxine Clarke on March 28, 2008
Categories: Communication, Nature Network round-up, Partners | Permalink | Comments (0)

Corie Lok, Nature Network's Editor, was in Toronto over the weekend attending the world’s first Scibarcamp, where 120 scientists, writers, artists, technologists and business people discussed topics ranging from science '2.0'; science and art; and whether can technology can make us happy. Corie highlights a session led by Eva Amsen on '10 things everyone should know about science'. Eva asked conference-goers to write down their ideas for what everyone should know about science on a board, which is photographed at Corie's blog, together with a list of her favourites.

In a post called The condition of Denmark, Nature editor Henry Gee writes on scientific literacy and how "Selecting papers for publication in Nature is rather like standing in front of a firehose and picking out a few choice drops of water. Even then, Nature’s subeditors remain hardpressed, given that papers these days contain volumes (volumes) of accessory and supplementary material—none of which existed a decade ago. Online publication means that papers are published round the clock, rather than just once a week. And things are unlikely to get any easier."

The Fiction Lab, coming soon to the newly refurbished Royal Institution, will be a reading group dedicated to lab lit and other science-related or inspired literary fiction, introduced by Jennifer Rohn at her blog Mind the Gap. The first book to be discussed is The Sun and Moon Corrupted by Philip Ball, who will also be making a personal appearance.

In response to a question at the NatureJobs career forum from a Network user who has a medical degree and wants to start a job in research, Paul Smaglik advises that "it’s perfectly acceptable to start as a technician, learn a few skills, decide whether or not you like what you’re doing, and, if you do, seek further training. That’s perhaps a more rational approach than in investing seven years in a PhD, a few more in a postdoc, then learning you despise benchwork."

Posted by Maxine Clarke on March 21, 2008
Categories: Communication, Nature Network round-up, Partners | Permalink | Comments (0)