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July 30, 2008

Social ads and the appliance of science

Something odd is happening - it almost looks like Facebook has started delivering relevant, targeted ads to scientists.

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So far today I've seen ads for The Source Event (a scientific job fair run by NPG), ResearchGate, ScienceCareers (their page now has almost 2k fans) and a shop that sells mugs that have mathematical equations written on them. Admittedly that last one is a bit weak.

It's odd as up until now the only Facebook ads I've seen have been telling me that I've just missed buying an Xbox 360 for $10 and that I can gain a six pack in less than a week. Those ads are targeted too, of course, but in a much more general way - presumably to every male between the ages of 18 and 45. The Facebook ad buying interface lets you do that pretty easily.

Showing ads that match keywords on somebody's profile isn't anything special either. But my profile doesn't mention science explicitly. I'm a fan of the Nature and PLoS pages and a lot of my friends are scientists, but that's pretty much it. Is there some under the hood ad optimization going on at Facebook - my friends match the 'science' keyword so I probably do too?

If not should there be? To what extent are you defined by the company you keep?

I suspect that the reality is more prosaic and that it's a coincidence, or matching on keywords in group names or something. Still, for a moment I was almost tempted to click...

July 23, 2008

New look Neuropod

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On Monday we launched a new look for Nature's podcast pages (it'll roll out gradually - the ever popular Neuropod is first with the others to follow). One immediate benefit is that you can now embed a Flash player in your blog or website.

We're also experimenting with chapterization; once the MP3 has loaded in the player you can now skip straight to the part that you're interested in. Each chapter comes with a brief description and relevant links collected by the podcast team while they were researching the story, so if you want to explore the story in even more depth you can.

It's all fairly new, but do check it out and let us know if you have any comments, suggestions or notice any glitches!

July 22, 2008

Who comments on scientific papers - and why?

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Free drinks and nibbles - Cambridge knows how to discuss a paper

I drafted a long paragraph for here about how science publishers are generally rubbish at commenting implementations, but if you read journals online you already know this. Can you name three science publishers that allow online commenting? When last did you leave a comment on a paper? Have you ever?

We're planning on rolling out commenting on the rest of Nature.com relatively soon (the system is already up at News@Nature) so obviously we're interested in seeing how other publishers have handled things and what the results have been.

BioMedCentral (BMC) are one of the companies who have had some success on the commenting front. In publishing tech they're quietly innovative in lots of ways and they've allowed online commenting on all of their papers for the past five years. Over time they've built up a reasonably large database of user comments. Matt Cockerill at BMC kindly gave us access to a dump of all comments published since they launched in 2002 (the majority of BMC's data is open access). I figured it'd be interesting to do a bit of simple data mining.

So.... who leaves comments on BMC? How frequently? What are they about?

The basics

From November 2002 to July 2008 BMC journals accumulated 945 comments from 753 different users on 732 different papers.

How widespread is commenting at BMC?

BMC have published 37,916 papers since they launched. That means that (732 / 379.16) = ~ 2% of BMC papers have attracted comments. Most of BMC publishes low to medium impact papers (this is not a reflection of the quality of those papers, I hasten to point out), it'd be interesting to see if the percentage is any higher when you only look at their higher impact journals. I didn't have time to do that.

It'd also be interesting to see how this compares with somewhere like PLoS One.

The graph below shows the number of comments attached to papers grouped by the year of publication. Perhaps unsurprisingly there's an upwards trend. I guess this is partly because more people are becoming familiar with commenting and partly because there are more papers to comment on.

comment_times_small.png

(edit: Note that there are only 82 comments on papers published in 2008 so far, even though we're in July ie halfway through the year. It'd be interesting to see what the average time between publication of the article and publication of the first comment is. Are most comments in any one calendar year on the papers published the year before?)

Who leaves comments?

~ 1/3rd of comments on papers are left by the authors themselves, in order to present supplemental information, to make readers aware of errors or typos in the manuscripts, or to reply to an earlier comment by somebody else (authors added their comment to an existing thread 37% of the time).

64 people out of the 753 (~ 8%) commented on more than one paper. Only two dozen people have commented on more than two different papers. In other words it's not the same people commenting all the time (as you often find with blogs).

What are the comments about?

Broadly speaking the comments fall into one of seven categories:

bmc_comments_small.png

Updates from authors 24%

Authors providing corrections, updates and replies.


"As of 4/13/06, correspondence for Peter K. Rogan should be sent to:"
"Please DO NOT utilize the version of the software as currently available. It will not function as specified ... [we're working on a fix]"
"Please note that there is a typo in the phosphopeptide sequence in the METHODS section"

One reason this percentage is so high is that it seems authors are encouraged to comment on their own papers if they spot typos or other errors in their published manuscripts, as it can take BMC a wee while to sort out corrections in the PDF and HTML. By commenting readers can be made aware of mistakes sooner.

Requests for clarification 8%

Readers asking for more information from the authors.


"Were the PAO2 values directly estimated by sampling end tidal alveolar gas?"

Interpretation and see also... 22%

Readers suggesting how the results of a paper might be interpreted, often pointing towards additional relevant research.


"Recent research data suggests that the lethality of the H5N1 strain..."
"We would like to inform readers of this paper of our prior efforts in the area of PCR primer design"
"Researchers planning to follow the 'plan A' approach discussed in this paper may benefit from first checking out..."

Direct criticism 17%

Readers pointing out possible experimental flaws or errors.


"We think, however, that the authors have overlooked an important confounder when adjusting the relationship between exposure and allergic disease.."
"The fact that the network is trained on only 20 samples and validated on the rest 20 at the end of the flow schematic does not mean that a correct validation has been done"


Bonus material 17%

Things that could plausibly have been included in the paper. Quite common in the bioinformatics journals. Links to datasets, implementations and software downloads.

"The described method is available as an R script and can be found at..."
"The software described in this article is available online at http://dulci.org/sage/."
"I have made the test data we used for this paper available from http://biotext.org.uk/ on the Downloads page."


Other comments 8%

Appreciative comments.

"I feel that this is a timely commentary, addressing the issue of semantic enrichment of our scientific literature"
"This paper is, in my opinion, the by far most clear and up to the point paper I ever read on the analysis of microarray data"

Crazies 2%

Self explanatory.

Takeaway message?

The quality of comments at BMC is high and the vast majority add value to the paper, though the numbers involved are relatively low (would a larger audience reading higher impact papers be different?).

Perhaps unsurprisingly comments on papers are not like comments on blogs; they're far more formal (only 8% of comments were of the chatty, supportive variety) and it's not the same people coming back each time (with the exception of the crazy 2%).

July 14, 2008

Best of Nature Network for Monday, July 14: Stockpiling Flu Vaccines, Fair Play in the Blogosphere, and Is a PhD Just a PhD?

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A new blog focusing on alternative careers in science has spurred debate in the Careers Advice by NatureJobs forum about the value of airing concerns and complaints about current work situations. Ian Brooks says that leaving the traditional academic path is not easy, but one should, “direct your anger and mal-contentment towards building the future and career you want.”

In response to a commentary in Nature on the World Health Organization’s (WHO) program of stockpiling influenza vaccines in preparation for a potential flu pandemic, Brendan Maher asks, "Can a pre-pandemic vaccine curb a major catastrophe?" Steven Salzburg, the author of a related Commentary responds that, "What our governments can and should do is launch a crash program to create vaccines using non-egg based methods. This could allow us to get a new vaccine – if a pandemic strain appears – into production in a matter of weeks."

Deanne Taylor’s post about a talk given by Richard Hamming of Bell Labs spurred a conversation of what it means to be a great scientist, as well as obstacles which can stand in the way. Mark Tummers says that many scientists are afraid to voice their opinion for fear of being remembered for an objectionable or incorrect comment. “A bad impression will last longer than a good one. So why stick your neck out by asking a question that is potentially ‘stupid’ or a remark that might offend someone who can decided over your future.”

In a blog post, Corie Lok, the Editor of Nature Network Boston, asks whether science blogs are fulfilling their promise of fostering constructive debate about science, or are they being used for empty banter and rants without the threat of personal retribution? "So what do people feel is the right level of bantering/joking/silliness/criticism/insults/nastiness in the science blogo/commentosphere? Is there even a 'right' level?" A conversation about the various discussion threads on Nature Network and beyond follows.

A forum post in the PhD Students group asks whether there are differences between PhDs obtained in the United States as opposed to other countries in world. The conversation reveals that while the time to completion of a PhD varies wildly among countries in Europe and the States, sometimes a PhD is just a PhD. Eva Amsen notes that, "Once you have the PhD, it doesn’t seem to matter – people with those really short three-year UK PhDs seem to get North-American post-doc positions without any problem."

July 07, 2008

Best of Nature Network for Monday, July 7: Nobel Laureates in Berlin, Success in Science, and Science and Politics

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A summary of the week's best discussions on Nature Network.

With over 70 members, the Berlin group on Nature Network is gaining momentum. The group even has its own online calendar of upcoming NN Berlin events. The group’s administrator, Philipp Selenko, is organizing a series of dinners to take place during the International Congress of Genetics 2008 in Berlin this month, featuring speakers from the Congress. Eric Lander, Oliver Smithies, Mario Capecchi, and Elisa Izaurralde are among the speakers expected to attend.

As a graduate student, Nuruddeen Lewis has had ample opportunity to reflect on how science is done. He shares his reflections on the importance of reading scientific literature, balancing life and lab, and novel approaches to reading while exercising on his blog, Lab Daze. In his latest post, Nuruddeen asks readers for their Most Important Tips to be Successful in Science. Responses range from the philosophical to the practical.

In the Nature Network Italy group, Marco Boscolo asks, "…is politics a world apart from science?" The discussion addresses the relationship between science and politics in Italy and beyond.

The Consortium of Functional Genomics (CFG) is a "large research initiative… formed to define the paradigms by which protein-carbohydrate interactions mediate cell communication." The consortium is made up of seven scientific cores, including mouse transgenics and microarray, with participating investigators based all over the world. The CFG has recently formed a series of groups on Nature Network in order to ease communication between consortium members.

DIYBio is a Boston-based group which hopes to create an "Institution for the Amateur," devoted to promoting scientific experimentation by the general public. In a Q&A with Nature Network Boston, one of the group’s organizers speaks about the ethics of scientific experimentation outside of an academic lab, proposed projects, and plans for a future biotech workshop.

If you’d like to nominate a conversation you’ve read or taken part in on Nature Network for next week’s roundup, please email us at network [at] nature.com.

July 04, 2008

PLoS ONE: Take Two

Declan Butler's article about PLoS financials in this week's Nature has provoked a predictable – and many ways understandable – backlash from open access fans (see Bora's blog for links and summaries).

First, to deal with a few of the gripes raised in the various blog posts:

  1. Nature isn't anti-open access. Its coverage of everything from ChemSpider to PubMed Central and Wikipedia ought to make that clear. Heck, it even broke the original story about Eric Dezenhall's involvement in the debacle subsequently known as PRISM.
  2. Declan isn't anti-open access either. But like me, he's a realist. Here's what he wrote in 2003:
    Few people would disagree, in principle, with the ideal of open access. The question is whether the economics can be made to work.
    Quite so. We'll come back to this later.
  3. The idea that commercial publishers are inherently evil lingers on. I can understand why, but it's completely untrue. BioMed Central is for-profit and the American Chemical Society is not-for-profit. Now, tell me which is more progressive.
  4. There were also quite a few comments to the effect that the article was self-serving given Nature's business interests. That completely ignores the overall balance of Nature's coverage, which in my opinion is broadly supportive of open access even though Nature itself charges subscription fees. The calls for a disclosure of competing interests sound reasonable to me if there really is a danger that any reader might not notice the link. But in that case let's also have them on all those PLoS editorials espousing open access.

Anyway, enough quibbling. Let me come at last to my main point: in some important respects PLoS is indeed failing. However, I'm not sure that Declan's article made it sufficiently clear why, so let me try.

PLoS's original goal wasn't to show that author-pays publishing can be made to work for low-end journals. (By "low-end" I mean relatively low rejection rate and low editorial input. I don't intend it to mean "beneath contempt" or anything similarly pejorative – these journals have an important place in the overall mix.) At the point PLoS came into existence as a publisher in 2002, BioMed Central had already been working on this for three years – and without shedloads of charitable funding. Instead, PLoS's goal was to show that something similar could work for high-end journals (again, defined by high rejection rates and high levels of editorial input). As Helen Doyle, a PLoS director, put it in 2003:

PLoS Biology must be more than a solid scientific journal; it must prove that a new open-access journal can generate top-notch papers, be supported by excellent reviewers, develop a following among diverse and discerning readers, and [Helen's emphasis] become a sustainable business.

This was a much more ambitious goal because at this end of the market the economics are, to put it mildly, challenging. PLoS's own expectations in 2004 that it would break even by 2006 were not fulfilled [764K PDF]. What Declan's article (and an earlier, equally controversial piece by him) shows is that PLoS hasn't even come close, at least with respect to its high-end journals.

This doesn't matter, argue some open-access fans, because PLoS doesn't exist to make money. And in any case, PLoS ONE is making money and taking PLoS as a whole towards break-even. Actually it matters a lot, mainly because of effects beyond PLoS. To understand this, consider its aims. Here is the mission statement from PLoS's 2003 accounts (available from GuideStar.org):

To realize [the potential of unrestricted online access to scientific information], a new business model for scientific publication is required that treats the costs of publication as the final integral step of the funding of a research project. To demonstrate that this publishing model will be successful for the publication of the very best research, PLoS has published its own journal, beginning with PLoS Biology in [sic] October 13, 2003 and PLoS Medicine in October 2004.
PLoS is working with scientists, their societies, funding agencies, and other publishers to pursue our broader goal of ensuring an open-access home for every published article and to develop tools to make the literature useful to scientists and the public.

And in case any of this is unclear, here is a snippet for PLoS's current FAQ:

PLoS is launching journals to demonstrate the enormous benefits of open access publishing. Our goal is to make the scientific and medical literature a freely accessible resource, but the literature is huge, and we cannot (nor do we want to) do it all by ourselves. Using the success of our own journals as a template, we hope to encourage other publishers to adopt the open access model. This has always been our goal.

That's a great goal, and with millions of dollars from the Gordon & Betty Moore Foundation to cover the costs of making this transition, maybe even an achievable one. But it hasn't been achieved, and in some ways quite the opposite has happened.

The situation back in 2002 was that existing publishers (Nature Publishing Group among them) were very skeptical that author-pays economics could ever work for high-end journals. Fast-forward to 2008 and far from bringing other publishers along with them, PLoS has helped to confirm these suspicions. Moreover, it has created heavily and perpetually subsidised journals that act as a strong disincentive for anyone else to try a similar publishing model. Which other publisher will enter the high-end author-pays segment now that there is an incumbent with 'private income' that will always be able undercut any competitor who needs to be economically self-sustaining? In short, the effect has been to reduce competition in an industry that, for the good of science as a whole, ought to have more competition.

Since the economics for high-end author-pays journals may never be workable, it's legitimate to argue that PLoS has merely put some barbed wire and a big "Keep Out!" sign on top of a barrier that was already insurmountable. But that hardly makes it a catalyst for positive change in publishing. And although this outcome was never the intention, that doesn't make it any less unfortunate.

I'm not trying to criticise the principle of open access (on the contrary, I'm a fan), or diss a competing publisher (in my opinion organisations such as BioMed Central are doing genuinely good things), or even pick a fight with PLoS (which has noble aspirations and some employees whom I consider friends). But we need to be able to discuss these things openly because anyone who doesn't care about the economics of open access doesn't care about making it a reality. And it has to be possible to be critical without the risk of knee-jerk counterattacks. (Right now I don't think this is possible, but I guess we'll find out.)

Certainly some 'traditional' publishers have created barriers to progress, and it's right to criticise those. But we also need to be alert to the Law of Unintended Consequences among organisations with good intentions. To me, this is just such an example.

Consider for a moment what you'd do if you really wanted to hinder the spread of author-pays, open-access journals. A few publishers tried PRISM, which was understandably described as "evil" (and the Dr. Evil pose is pretty funny). But that word (even when unaccompanied by its frequent companion, "genius") conjures up the image of someone with an IQ score that's, well, at least into double figures. For reasons I've covered before, PRISM is just too dumb to be classed as evil; "brain-dead" would be closer to the mark.

No, if you really were Dr. Evil, Science Publisher, and intent on imposing limits to the spread of all this open access nonsense then you'd have a much more cunning plan up your grey flannel sleeve. For example, you might imagine setting up a small series of loss-making open-access journals, thus killing off any chance of a competitive market emerging in that segment. You'd fund them through donations for as long as possible, but such income is vulnerable to the vagaries of donors so eventually you'd have to cross-subsidise them from a profitable business line. And all the while you'd explain that you're doing the world a favour. At this point in your imaginings you'd stroke your hairless cat and laugh uproariously, content in the knowledge that you need not lift even your little finger to implement any of this because PLoS has already done the work.

Of course, I'm not saying that this was PLoS's intent, only that it's the result so far. Just as PRISM – an initiative designed to reinforce the importance of publishers and undermine open access – succeeded only in making the participating organisations look like fools while at the same time emboldening the open-access camp, so PLoS is creating effects that run directly against its stated aims of spreading the open access model across all of science publishing. Personally I find this very sad: since I work for a high-end science publisher I'd like there to be a workable economic model that we could adopt too. Unfortunately we're further away from that than ever.

To look on the bright side, none of this may matter very much in the longer run since truly widespread open access to scientific content is coming about through funder-mandated archiving, not open-access publishing. Nevertheless, the ironies and misunderstandings are just too stark to pass them by without comment.

July 02, 2008

Science Blogging 2008: London

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We at Nature Network are putting on a science blogging conference in London on 30 August 2008. More than 100 bloggers, scientists and science communicators will gather at the Royal Institution to discuss topics such as how science blogging can change (improve?) the public’s perception of science, how blogging can boost your creativity and be used as a teaching tool, how scientists can be more open with their primary research data, and what the future holds for online scientific communication.

Click here for the programme. A few sessions have been set aside to be ‘unconference’ sessions, meaning that the topic and the speakers will be proposed and decided on the day of the event.

Click here for more details about the conference. There’s already been quite a bit of discussion about the event in the conference’s forum on Nature Network.

Registration is free. Just email us (network at nature.com) with your name, affiliation, and a link to your blog if you have one.

"Nascent Web publishing efforts have their genesis in a burning need to say something, but their ultimate success comes from people wanting to listen, needing to hear each other’s voices, and answering in kind."
Rick Levine
The Cluetrain Manifesto

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