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The industrious folks at BASE (see their home page or my previous post) have added Nature Precedings and the Signaling Gateway to their search engine, despite the fact that neither provides OAI-PMH metadata. I like BASE -- do a search for "inhibitor" for example and see how many hits you get by data source, document type, free vs not, etc etc.
After two years and 102 shows, we are relaunching the Nature Podcast today. We've got new music, some new presenters (Kerri Smith, and erm, yours truly) and some ace new features on the pod. These include the Podium: a soapbox monologue (so if you've got a campaign to launch, or you simply want to shout about something sciencey that's bugging you then write to us at podcast@nature.com); and Sounds of Science, your chance to record some amazing sounds from your labspace or field, or anything that sounds awesome. This week we've got Nature's top dog Philip Campbell at the Podium, and Sounds of Science is the quite brilliant Genome Dub Collective, who have set the Origin of Species to a reggae beat. Genius. Of course, that's alongside the hottest new research on RNAi, 7000 year old rice paddies, and dinosaurs brought to life on the stage.
The easiest way to listen is of course to subscribe in iTunes. Many thanks of course go to Chris Smith and his Naked Scientists who produced the podcast from its humble beginnings. Thanks also to the Genome Dub Collective for sharing their work with a Creative Commons license.
The third event in the Second Nature speaker series is tomorrow!
Join us with Professor Phil Gibbard, Dept. of Geography, Cambridge University, for a talk and discussion on recent research in the English Channel that has revealed evidence for two catastrophic “megafloods” hundreds of thousands of years ago which led to the creation of Britain as we know it today. Professor Gibbard will talk about how these floods defined Britain’s geographical future, sealed our status as an island and had profound implications for natural life in Britain and the climate of the North Atlantic.
No specialist knowledge required – all welcome!
Title: How Britain became an island
Speaker: Prof Phil Gibbard
Location: Second Nature Island
Date: Thurs 27th Sept
Time: 11am SLT, 2pm EST, 6pm GMT, 7pm BST
Contact: Joanna Wombat
For more info, see Phil's description and Nature Network
Over on Nature’s social networking website, Nature Network, we’ve created a new group called Ask the Nature Editor, where you can get your burning questions about publishing in Nature (or the other Nature journals), peer review, and the scientific publishing process answered by real, live Nature editors! Several editors have agreed to take your questions in the group's forum. We invite you to join the group. Here’s your chance to learn more about what goes on here, straight from the editors themselves. See here for more details.
Over the coming months, we'll be hosting more rounds of Q&A focused on other topics such as careers in scientific publishing and online communications tools. So stay tuned.
The Scientist posted an article last week asking readers to name their favourite life science blogs. They're going to collate the results and draw up something similar to Nature's Top 50 Science Blogs except based on the number of supportive comments rather than Technorati rank, explaining:
"there's really no guide to help inform you about what blogs you should be reading if you are interested in exploring the blogosphere"
*cough* Postgenomic *cough* Chemical Blogspace *cough* ;)
Anyway, it's a good idea and I like the fact that they're encouraging discussion on the comment threads of the blogs themselves.
They got the ball rolling by asking some popular bloggers (Carl Zimmer, PZ Myers & Attila Csordas, amongst others) to nominate their favourite blogs. After some brief controversy over a gender imbalance issue later addressed by the journalist who wrote the piece the suggestions started pouring in.
The comments thread makes for an interesting read. I found lots of interesting new (to me) blogs like Deep Sea News and Tetrapod Zoology.
Every so often, though, you'll see a run of commenters all suggesting the same blog, something that presumably correlates with the blogger in question pointing their readers towards the article and suggesting that they go cast a vote. Hmmm. All part of an open democratic process?
Attila included a few Nature blogs (The Niche, Nautilus and Nascent) on his seed list and I was pleased to see Nascent appear in the comments, too, at least until I noticed that the comment's author was Thomas, who is the editor of an NPG published journal. Not sure that counts.
(I'm not suggesting that anybody go vote for Nascent. Apart from anything else we're not a life sciences blog).
Oh, and for future reference: science blogs on Postgenomic.com, organized by subject area and ordered by popularity.
Photo from GlynnisH's photostream
Moving swiftly on from Ancient DNA to the mysteries of foraging seabirds, this week’s guest in the Second Nature events series will be Professor Graham Martin on the topic of Great Cormorants.
Photo by Sławomir Staszczuk
Graham is Professor for Avian Sensory Science at Birmingham University’s Centre for Ornithology and will be telling us about his work investigating how Great Cormorants have the highest foraging yield of all the marine predators when their underwater vision is as bad as ours.
Title: Through Birds’ Eyes: What does vision tell us about the aquatic foraging of Cormorants?
Speaker: Professor Graham Martin, Birmingham University
Location: Second Nature Island
Date: Wednesday September 19th, 2007
Time: Noon SLT/3pm EST/7pm GMT/8pm BST
SL Contact: Joanna Wombat
For more information and links see full details here. All welcome!
According to reports of a video accidentally leaked from inside Google, the Google Reader developers have interesting plans for the future. While Scintilla works on a different scale from Google Reader (which is said to store "10 terabytes of raw data from 8 million feeds") and also doesn't aim for the same niche of general-purpose feed reader, there are proposals reported that would help aggregation sites like Scintilla, as well as several features that we've already implemented. Here's a selection of the most interesting:
Yesterday saw the first in our series of talks being held on Second Nature. The speaker was Dr Phil Holliger from the Medical Research Council Molecular Biology Lab in Cambridge, and he gave a talk all about Ancient DNA and his work on creating new polymerases to recover it more accurately.
Picture by Troy McLuhan
The turnout was excellent, I reckon about 40 people were there for the whole talk and there were lots of questions at the end for Phil: I've posted the talk, the slides and the full discussion over at Nature Network
Thanks very much to Phil for being such a willing guinea pig in such a new project: after last night, I'm even more convinced that holding these events in Second Life is worthwhile, and I'm absolutely going to keep doing them and trying to make them better. If you were there, I'd love to hear your feeback - if not, don't worry, you can come to the next one!
Attila Csordas (blogger at Partial immortalization and occasional NPG contributor) visited the Nature offices a few days ago. It's always good to meet working scientists but especially when they're as enthusiastic about the web as Attila is.
One of the things he mentioned was that in his opinion social software for scientists tends to focus on individual users rather than groups, which is a fair point. In the life sciences, at least, the lab is the basic organizational unit. Should we be doing more to encourage uptake of sites like Connotea, Scintilla and Network on that level?
There's a clear use case for Connotea within a lab. You're all working on the same thing and want to share references - maybe there's even a student or postdoc who has responsibility for scouring eToCs and PubMed alerts, then forwarding on anything relevant to others in the group. An online reference management package - platform independent, portable, complete with RSS feeds - seems like a good way to organize everything.
Scintilla can also help with disseminating information from sources other than PubMed - news, blogs, events, that sort of thing.
The only problem is that everybody in the lab has to sign up to each site individually then join the same group, sign up for alerts or feeds. This maybe isn't ideal, but it's difficult to think of how we could make it easier.
Even leaving technical barriers aside - who to market to? Where does technical innovation at a lab level come from - supervisors picking up ideas from grad students, lab heads picking up from supervisors?
If you work in a research group that has some sort of interal information sharing infrastructure (there's an acronym in there somewhere) - freezer and sample management LIMS aside - we'd be interested in hearing from you in the comments. How do you share references? Protocols? Experiments? Do you have any sort of messageboards or forums (in bigger institutes)? Any comments on how applicable NPG sites are to your own situation?
(photo from Klass Wynne's excellent photoblog - www.wijnne.com)
For anyone who's interested here is Nature Publishing Group's (NPG's) take on PRISM: Although Nature America is a member of the AAP, we are not involved in PRISM and we have not been consulted about it. NPG has supported self-archiving in various ways (from submitting manuscripts to PubMed Central on behalf of our authors to establishing Nature Precedings), and our policies are already compliant with the proposed NIH mandate.
Those are facts. What follows is just my personal opinion.
PRISM has understandably provoked a great deal of anger among those scientists who care about how the fruits of research are communicated. (In this sense, PRISM has achieved the exact opposite of dog-whistle politics: the only people to sit up and take notice have been those who were outraged by it. Nice work, guys.) My main emotion, however, is closer to bewilderment. Do PRISM's proponents (whoever they are) really think that their approach will do anyone, including themselves, any good? It's tempting to suggest that they are out of touch (e.g., with the ways in which technology is changing science and scientific communication), but it's equally possible that I'm out of touch (e.g., with Beltway politics), so I guess all I can conclude is that they inhabit a different universe to the one I'm in. Time, perhaps, to move on and get back to work.
Except that PRISM — and the reaction to it — is having one particularly insidious consequence.
The things that I find most ill advised about PRISM are the needless belligerence of the message, the crude them-and-us stance, and the distortion of complex issues into unrecognisable caricatures. I wouldn't mind so much if the issues themselves were inconsequential, but they're not. Questions about how scientific communication should be funded, and what roles government should or should not play, are central to scientific progress. If we can't discuss these in a well-informed, grown-up way then science itself will suffer.
It therefore troubled me that the initial counterattacks on PRISM were themselves often lacking in nuance and discrimination. Given the high emotion generated, this was understandable, but that's not the same as saying it was correct or helpful. The most general error has been to lump all publishers together in declaring them "evil", "afraid", "money-grabbing", and so on. True, PRISM seems to have come out of the AAP, which is a publishing industry body, but right from the beginning (when I also didn't have a clue what was going on) it was fairly clear to anyone who cared to make the distinction that PRISM was not the same as the AAP.
To treat the industry as one amorphous lump is a continuation of the kind of misunderstanding that leads people to group together "Nature, Science and Cell" when making comments about scientific publishing. This is a pet hate of mine. If you're wondering where to send your red-hot molecular biology paper then it's OK to talk about those three journals in the same breath. But if you're talking about publishing then you'd better think again: there are hardly three more different organisations on the face of the earth than NPG, the AAAS and Elsevier (the three publishers in question).
All progress is hard, almost by definition. I work on things like journal-database hybrids, social software, and audio-video content for scientists. In my opinion, these will all play big parts in the future of scientific communication, but if the truth be told, most scientists aren't that interested (yet), and a few are even quite hostile (though I'll admit than none of them has gone as far as astroturfing to make their point). So if I were to generalise about scientists with respect to my work, I would say that they are rather conservative, and that they are largely uninterested in new web-enabled ways of conducting and communicating research. As Jim Hendler pointed out, scientists are generally keener on revolutions in scientific publishing than in their own labs. If that were the end of the story then my colleagues and I would need to find other vocations. But fortunately not all scientists are the same, so we try hard to identify the forward thinkers and early adopters, working with them in the belief that others will eventually come around too.
As with scientists, so with publishers: Most are conservative and many are largely clueless about the true impact of the web, but some are genuinely well informed and progressive. Those wishing to promote change need to be able to tell the difference and resist resorting to crude stereotypes. True, scientists don't need publishers as much as publishers need scientists. But why alienate the ones who are already in your side? It'll only slow you down.
A case in point is the criticism that my NPG colleague, Maxine Clarke, faced when talking about "open access" projects at NPG. Not everyone shared her definition of open access and she was accused by some bloggers of using the term as a marketing slogan. (Peter Murray-Rust, who made the original point, later recanted when he understood that Maxine was being genuine, so I don't take issue with him.)
Ignore for a moment the fact that Maxine is not a marketer or publisher but an editor (which means that she works in the interests of our readers, not NPG as a business). Even if that were not the case, her 'offence' was one regularly committed by open-access supporters themselves. For example, Peter Suber has posted a very similar and even longer list of NPG "OA" projects (with some input from me). Jean-Claude Bradley, in a follow-up comment, says that "'Open Access' has had a fairly unambiguous definition" and then proceeds to give one that's at odds, at least to my eyes, with Peter M-R's and Bill's (mainly because it makes no mention of licences).
Intelligent, progressive people in publishing (there are some, believe me) look at this sort of episode and conclude that engaging with open access advocates is always a bad idea because they will never get a fair hearing. (One or two of them even tried to talk me out of posting this, and maybe they were right — let's see.) Some people are just too quick to assume base motives, and employ words like "boycott" as if they were punctuation marks. Also, let's be honest, sometimes open access publishers have stoked these flames to their own PR ends. For me, this cynical and wrongheaded mindset reached its apotheosis (so far) in a comment on this blog post, which suggested that — wait for it — scientists should boycott NPG for having set up the free preprint server and document-sharing site, Nature Precedings:
[G]ood call on Nature preceedings being designed to fail - I totally agree, had the same thought. I think it's Nature's effort to sandbag open publishing. Scientists and open publishing supporters should be crying bloody murder on this. I suggest a boycott of Nature preceedings. Hell maybe even the rest of Nature journals...
Yeah, right, that would be good for open access...
It won't surprise you to hear that I believe NPG to be one of the more progressive publishers around. (And if you think I'm only saying that because I work here then you're mixing up cause and effect.) The working assumption of many open access evangelists is that publishers (including NPG) are congenitally predisposed to reject anything but subscription-based business models. For example, Bora Zivkovic (now at PLoS) says on his blog:
I can bet money that Nature will go Open Access as soon as the forward-looking editors manage to persuade their backward-looking corporate overlords that the data and statistics show that this is the sound business way to go.
Sorry, Bora, but that's about as far from the truth as it's possible to get. Yes, Nature takes an editorial line that is sympathetic to the principles of open access (though that doesn't stop people sticking in the boot when they report inconvenient truths), but it's certainly not the case that publishers are holding back pressure from editors to go open access. The main reason why Nature cannot do so is the absence of a viable economic model for a top-end journal with a high rejection rate and heavy editorial input. Few of the people who criticise Nature for not being open access would also criticise PLoS Biology for losing a lot of money. But the underlying cause of both is the same: current author-side fees don't begin to cover the costs of running such publications. That, not publisher intransigence, is the main barrier.
And just suppose for a moment that Nature decided to become open access anyway, perhaps paid for by grant funding or some kind of cross-subsidy. It's not hard to see the criticisms that would be levelled at NPG. Here's an imaginary blog post, based on things already said about our existing projects:
Nature's open access policy has obviously been built to fail. It's nowhere near covering it's costs, which is obviously a deliberate ploy to discredit open access publishing and provide ammo for those who claim it can never pay its way. More than that, it's anti-competitive: no one else will ever launch a similar journal into this space if prices are being held down artificially by cross-subsidy. Isn't this usually called "dumping" and isn't it illegal? Jeez, we need more competition among publishers, not less. Scientists should be crying bloody murder on this. Boycott!!!
In reinventing scientific communication for the 21st Century we face genuinely difficult challenges. Many of us, in our own different ways, are trying to find solutions. PRISM certainly doesn't help, but nor do some of the more indiscriminate responses. The best antidote to its crude belligerence is not more of the same, but an open, fair and grown-up debate. These issues are too important to be addressed in any other way.
As announced last month, the Second Nature event series is about to begin and the very first event is this Thursday.
Our first guest is Phil Holliger from the Medical Research Council Molecular Biology Lab in Cambridge. Phil works with ancient DNA: DNA samples retrieved from specimens of forensic, paleontological or archaeological interest. DNA naturally degrades over time, making it very difficult to amplify and analyse, and Phil will be talking about a new way to rescue genetic information from damaged DNA, which he recently tried out on a 60,000 year-old cave bear. After the talk will be a discussion on this or anything else you care to ask Phil.
No specialist knowledge is required, and entrance is completely free, so please do come along and see what it's like. To come, you will need a Second Life avatar. Getting one is free: go to www.secondlife.com/join to get started. If you need any help getting started or get lost when you are in Second Life, by all means email me and I will come along and teleport you to the safe haven of Second Nature!
Title: New polymerases for old DNA: molecular breeding of polymerases for damage bypass and amplification of ancient DNA
Speaker: Dr Phil Holliger, MRC, Cambridge, UK
Location: Second Nature Island
Date: Thursday September 13th, 2007
Time: 11am SLT/2pm EST/6pm GMT/7pm BST
SL Contact: Joanna Wombat
In the Neuroscience Gateway this week, read a summary of a recent Nature publication by Welch et al. describing a potential model for obsessive-compulsive disorder (Nature 448, 894–900 (2007)). Genes described in the text of many of the articles in the Neuroscience Gateway are linked to expression data in the Allen Brain Atlas.
This week’s Neuroscience Gateway Update also features new additions to the Research Highlights and Research Library sections. The Neurotechniques section features a new high-throughput knockout technique uses components from retroviruses to disrupt genes at random (Proceedings of the National Academy of Sciences 104, 14406-14411 (2007)). Access to primary research articles from journals in the Nature family is free for three months.
Finally, be sure to visit the Neuroscience Gateway Conference Calendar to see upcoming conferences and events specially selected for the Neuroscience Community!
The Featured Article in Signaling Update this week highlights a Nature article by William Chia, Bingwei Lu and colleagues entitled ‘Polo inhibits progenitor self-renewal and regulates Numb asymmetry by phosphorylating Pon’ (Nature 449, 96-100 (2007)). Visit the Featured Articles section of the Signaling Update for FREE access to the text and PDF of this and several other recent Nature publications.
This week’s Signaling Update also features new additions to the Updates and Research Library sections. Browse the Research Library by date or by subject to stay up-to-date with recent advances in your field.
The Signaling Gateway Molecule Pages database featured pre-computed BLAST searches for homologs and orthologs of nearly 4000 cell signaling proteins. Search or browse the Molecule Pages database to access the extensive collection of automated data available for each page.
"Linking" is one of those things that crops up all the time in science and publishing. This week's Cell Migration Gateway shows typical examples of two of them: links between cells, and links between databases.
An ever-present toil in the life of many database curators is linking between databases. So it's good to report another step forward. The Cell Migration Gateway's Knowledgebase has been supercharged with an array of links to many other databases, including (and please forgive the plug) our very own NCI-Nature Pathway Interaction Database. See www.cellmigration.org/cmcnews/cmcnews.shtml#sep07c.
Finding the right links is a challenge cells face too. Particularly in the developing brain where, in one of the great wonders of the natural world, nerve cells move around to find just their perfect partner cells. It's been known for a long while that so-called gap junctions are the "mouths" that cells use to communicate with each other, but now it seems that the nerve cells somehow use their mouths to move around in the brain. If that seems strange to you ... read a summary of the story.
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