Nascent

Bora sent us the data too. I got caught up in other stuff and didn't have time to analyze the dataset by the agreed date, but now I'm thinking that was actually a good thing as there's some interesting discussion surrounding the stats happening in the comment threads on BBGM and Science in the Open.

It'll be a couple of weeks before I get round to an analysis (though somebody else in Web Publishing might beat me to it!) but my first impressions were that comments on PLoS One are working out quite well. To be fair the starting point is pretty low - it's not like commenting has really been pushed in many other places - but if comments on papers do more good (by adding some value, say) than harm (by confusing users, fragmenting discussion too much) then IMHO they're a success to some extent, and that's certainly the case here.

I wouldn't go as far as Cameron and suggest that the commenting on PLoS One is in some way like post publication peer review (though I might be misrepresenting his views here?)... the majority of the comments I saw in the PLoS and BMC datasets were nothing to do with reviewing the paper - journal club comments aside - and I'm not convinced that comment threads as they're traditionally implemented would be the best medium for review in any case. Aggregators showing you all the conversation around a DOI (as Deepak, Richard and Cameron have suggested in the FF discussion) though... now we're talking.

Something else worth mentioning quickly, to defend BMC's honour if nothing else: bear in mind they started in 2002. Facebook, MySpace and Firefox didn't yet exist. 'Blog' wasn't in the OED. Commenting wasn't nearly as widespread on mainstream media websites as it is today. You think it's hard to get scientists to leave comments now? PLoS definitely has a much higher comment to paper ratio, but cut BMC's 2% "since the dawn of commenting time" stat some slack. ;)

Posted by Euan Adie at 02:42 PM | Permalink | Comments (0)

The September '08 issue of NRG includes a new paper from bioinformatics hero Lincoln Stein, describing the "cyberinfrastructure" of databases, protocols and services that is becoming more and more necessary for life science research as large scale datasets become common.

We wanted the supplemental information for the paper (which lists different web services, databases, tools and initiatives) to be like a public database so that readers had the ability to add new information, revise out of date descriptions and remove broken links, so with Lincoln's kind permission we put it up on a wiki. Anybody is welcome to contribute, please do check it out!

To ask questions or actually discuss the paper check out this thread on the Bioinformatics group at Nature Network.

Incidentally the paper is free as long as you're logged on to nature.com - if you haven't already registered you may want to do so on the wiki site itself here, as the default registration form is stupidly long.

OK, that was the press release bit.

If you're a regular Nascent reader, though, the idea of throwing some data up onto a wiki may not seem particularly exciting. "Ah", you may be thinking, "Whoop-de-doo, a wiki. What's the big deal? Ever heard of OpenWetWare?".

Yeah. This is an experiment for a whole bunch of reasons: to see if our workflow can handle it, to see if we could get a wiki platform up and running (for technical reasons we couldn't use MediaWiki) and to see if there's an audience for wikified content amongst nature.com readers.

We ran through lots of options at the beginning of this project: working with OpenWetWare or Nodalpoint (Jason gave us some advice early on), wikifying the entire article instead of just the supplemental info, wikifying a selection of articles instead of just Lincoln's, 'freezing' then editing wikis once every couple of years to produce a collaborative review (edited professionally or by the original author, with major contributors listed as co-authors), giving each revision of the wiki a DOI so that it's citable as it evolves, presenting two points of view on a particular topic as an interactive 'debate'... those things are all still on the cards, but for now we're keeping things simple. We're taking things one step at a time.

Are wikified papers a good idea? What would make you as a scientist want to contribute?

Posted by Euan Adie at 08:48 AM | Permalink | Comments (1)

In theory I know these people

Executive summary: we created a new room on FriendFeed which might be a good place to discuss data portability from a scientific networking perspective.

Having the ability to share one network (or a particular subset thereof) of friends and contacts across different social networking sites is a good idea. It has been kicking around for a while and it's a feature Nature definitely wants to support in its social software.

The issue has cropped up before on FriendFeed and in the Network forums, and Cameron has highlighted it in his open letter to the developers of scientific web apps.

We've been thinking quite hard about how we could enable this (as well as debating whether or not we should do anything before a wider standard is developed). Data portability is not a trivial problem. If there was a relatively simple way we could share networks between scientific web apps, though, it might be worth just pushing ahead with something imperfect but workable in the short term.

What is that simple way, though?

Currently we expose a user's social network on Nature Network through XFN (though right now there's a bug that limits it to the first six people in any network, doh). You can use the Google Social Graph API to read this: here's my network.

We use Nature Network identifiers (the 'Uxxxxxx' part). How can you correlate those with identifiers on other social networks?

You could attempt to match on real names, but then you'll hit a wall the first time you make friends with a Mr Smith or Xu.

Should we use plain text email addresses? We can't without access control - or spammers would harvest the user database - and privacy levels - or I could make somebody anonymous (say, Charles Darwin) a contact and then pull their (otherwise hidden) email address out of Network with the portability API.

Could we restrict use of the portability API to 'trusted' apps that promise not to respect user privacy? Probably not. Apart from anything else it would mean no mashups, no Greasemonkey scripts, no fast bedroom coder prototypes.

We could hash email addresses, but we'd need a dynamic salt or they'd be vunerable to being cracked by somebody with a good enough rainbow table. Would rehashing every email address in a user database every time somebody wants to import their social graph be scalable for larger apps?

Could we use Bloom filters somehow? Is the precision good enough? Are there security considerations?

Could we just tell users that if they want to keep their email address private they won't ever be connected automatically to their contacts on other sites?

Could correlations between different usernames be defined by the users themselves? The user could tell each site what their username is on all of the other scientific websites that they use. Alternatively they could create and host a public FOAF file containing this information and just point sites to that (or it could be harvested automatically by a crawler). Is that pure fantasy?

Your thoughts are welcome. We've created a room on FriendFeed to try and help organize any discussion (feel free to share relevant links and blog posts there!).

Posted by Euan Adie at 11:30 AM | Permalink | Comments (8)

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

The recent discovery of water on Mars has flung wide speculation and discussion of the possibility of life on the Red Planet. In a most timely blog post, Joanna Scott features an upcoming seminar, "ExoMars: Europe’s Next Step in the Search for Life on Mars," to take place on Tuesday, 5 August 2008 at 10am PDT, 6pm BST, on Nature’s island in Second Life. The seminar will be given by Jeff Marlow, part of a group developing instrumentation for the ExoMars probe. “Jeff’s specific role in the project is designing the instrument which will look for signs of life on Mars: could water just be the first step?” Check out the talk to hear about Jeff's work on the ExoMars probe and his take on the discovery of water on Mars.

The path of a scientific discovery from bench to patent – and to the real world beyond – is often unclear to scientists, who are not routinely taught the basics of intellectual property law. A new group on Nature Network, Patent Law Primer, addresses this disconnect between the scientific and legal communities. A recent question about the rights and responsibilities of the investigator in a patent held by the institution was addressed by Rahan Uddin from Peer to Patent: "…institutions may work out some sort of royalty agreement with the investigator/scientist, again this really depends on how much of the investigators own time/resources has been invested in development."

An understanding of humanities can make for a better scientist, argues Bob O’Hara. The public backlash to the introduction of genetically modified foods took many scientists by surprise. Study of people’s reactions and behavior patterns could lead to more effective techniques in presenting novel findings and developments. "Because science is done by people, we need to understand how people behave as individuals and in groups. This is the job of the humanities, so we need them if we are to be effective as science practitioners.”"

Miguel Allende discusses pluses and minuses of two divergent approaches to science in Chile – the science that is carried out at large institutions and smaller, independent organizations. The larger institutions can sometimes be encumbered by bureaucracy and politics, while the smaller institutions lack access to students and teams diverse in their skills base. "A balanced view should see the merit in both approaches to research," says Allende.

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.

Posted by Anna Kushnir at 12:05 PM | Permalink | Comments (0)