Faculty of 1000

Post-publication peer review

Archive for the ‘Friday afternoon’ Category

Faculty of a Million?

Posted by rpg on 1 April, 2010

Apparently, the two self-proclaimed ‘top’ scientific journals, Nature and Science, have ended their hundreds of years-old feud and teamed up to launch a new journal, to be called either Scientific Nature or Natural Science, depending on the result of a text-message vote by the scientific community.

Sounds good? Well, not really. We’re a bit upset that they’re also creating a social networking site called ‘Faculty of a Million’, funded by a grant from Facebook, where scientists can vote papers for acceptance by pressing a “Like” thumbs-up button or reject the paper by pressing a “Dislike” button. Our company lawyer has just had an apoplectic fit.

And this seems to be a direct invasion of privacy:

readers will have the option of Skyping authors directly to share their thoughts and feelings about a paper simply by clicking that author’s name. As an added incentive, the first 100 new subscribers will get free genome scans.

It’s a nice cover though:
Easter bunny

Posted in f1000, Friday afternoon, Literature, The Scientist | Comments Off on Faculty of a Million?

Last drinks

Posted by stevepog on 19 March, 2010

Richard has previously mentioned my imminent departure from f1000 and it’s come to the day where I pack up my desk, hand back the security pass and read my last free copy of The Scientist.

It’s been a great experience being involved in a forward-thinking project like f1000 and getting stuck into the social media side of PR (like it or loathe it, PR has a place amongst the Twitter, Youtube, Facebook generation)

But aside from meeting some brilliant people through Twitter (@scicheer, @tallscientist, @boraz, @sciencegoddess, @ritarubin to name a few), this humble blog is where most of the action has happened.

And so allow me to reflect back on some of the inspiring, thought-provoking or just plain amusing posts from my six months here.

Most recently, Callum’s post stirred up controversy on all sides with the Pubmed and PLoS discussion from a few days back, on a day where our usual daily hit count doubled due to the massive interest from the science community.

Richard’s weekly roundups have been getting a lot of interest as he, obviously, looks over the  week’s happening at f1000 and in the broader world of science.

His post on the Faraday Prize Lecture would have excited anyone with multiple passions into maths, music and science while the new competition on scientific mistakes, while not drawing the same enthusiastic responses as his #sci140 comp, has still been kicking along.

For my own part, the most enjoyable pieces I had the chance to write involved anything from the Great Garbage Patch to periodic table-chanting cheerleaders, how music can make us smarter and scientists with fantastic beards.

I’ll leave you with this shot of my Science Online companions and I at the Chapel Hill campus of the University of North Carolina, which we visited during the SciOnline 2010 conference in January.

There’s some historic significance to this well that we are still unsure of but apparently it’s the place where freshmen kiss each other for luck. We declined to participate in the ritual (owing to being neither freshmen nor single) and instead opted for this memento.

It’s one of the good memories I’ll take away from my time at f1000, along with the all-too-regular Friday afternoon cakes and of course the dedication and enthusiasm of work colleagues towards making f1000 a quality database for post-publication peer-reviewed biology and medicine research.

I’m off to travel Europe for five months and then head home to Australia. Thanks to everyone for the support, keep reading the blog and, in the words of my friend Darlene, GO SCIENCE!

**PS I’m on Twitter at @stevepog for anyone wanting to keep in touch and my sports-focused blog is http://stevepog.blogspot.com

Posted in f1000, Friday afternoon, Random | Tagged: , | Comments Off on Last drinks

Music to my ears

Posted by rpg on 5 March, 2010

A few weeks ago I went to the Faraday Prize Lecture at the Royal Society. The lecture, The secret mathematicians, was given by the Charles Simonyi Professor for the Public Understanding of Science Marcus du Sautoy. Du Sautoy talked about five artists, how they were inspired by mathematics, and how their art tells us things about mathematics: a musician (Olivier Messiaen); an author (Luis Jorge Borges); an architect (Le Corbusier); a painter (Salvador Dali) and a choreographer (Rudolf Laban).

Music probably has the most obvious connection to mathematics: rhythm and tonality are based on mathematical relationships, and du Sautoy reminded us of the saying of Gottfried Leibniz,

Music is the pleasure the human mind experiences from counting without being aware that it is counting.

For me, the link between mathematics and music breaks down when composers take the maths and try to base music on it, without reference to several hundred years of music theory. In other words, just because you can use (for example) prime numbers to create a pattern, doesn’t mean you should. Schoenberg’s atonal compositions just sound like noise to me—yes, call me a Philistine if you like—and I reckon you should leave prime numbers to the cicadas. Mathematics can describe all music, sure; but not all maths is musical.

Similarly, the relationship between music and the rest of science has not always been harmonious. I came across the Symphony of Science this week, a musical project

designed to deliver scientific knowledge and philosophy in musical form.

Sounds great, and the website looks nice with embedded videos and links to the lyrics. Unfortunately I’m not convinced it works: some pleasant enough but rather non-descript elevator muzak plays while voices of scientists are processed to sound synthesized (and yes, the pitch and tempo are adjusted to saound vaguely musical but anyone can do that in Garageband) and lip-synced with video. It’s not ground-breaking by any stretch, and is shot through with New Age-style philosophies that I find rather hard to stomach (and check out the strange collection of Google ads on the site!). Richard Dawkins repeatedly saying ‘science is the poetry of reality’ trivializes any meaning he might have been trying to get across. The only thing worth repeating was Jill Tarter’s The story of humans is the story of ideas; to shine light into dark corners but even that isn’t in the same league as Tom Lehrer, whether reciting all the chemical elements or poisoning pigeons in the park; or even Ron Laskey:


Haaaarvard

Back to du Sautoy. In a three-dimensional development of da Vinci’s Vitruvian Man, the choreographer Rudolf Laban claims that Man is inclined to follow the connecting lines of the 12 corner points of an icosahedron with his movements travelling as it were along an invisible network of paths; and indeed his dancers trace out a Platonic shape with the tips of their limbs. But whether the maths drives this, or whether the mathematical description is simply an inevitable consequence of our bodily shape is not clear.

AcropioolisThe Fibonacci series is very familiar to most scientists, and perhaps because it is the result of a simple geometric algorithm it describes many natural relationships: the expanding population of rabbits, for example, or the spiral shape of a snail’s shell. Architects such as Le Corbusier have used it to plan buildings in two and three dimensions, and even the Greeks knew about it: the proportions of the Acropolis follow the Golden Ratio, which is derived from the Fibonacci sequence.

AsteroidsLiterature can also take inspiration from mathematics—not simply in the number of words or letters or syllables (although that is something that has occurred to this writer)—but in the inspiration of Borges’ Library of Babel. Borges, amazingly, uses a literary device to describe one model of the Universe: finite, yet unbounded (as opposed to spatially infinite but ‘flat’). Du Sautoy took the opportunity in his lecture to show how a simple computer game could also model the Universe, which caused not a little hilarity and some reflections on the nature of dimensionality.

Finally, Salvador Dali.

Dali once said

I am a carnivorous fish swimming in two waters, the cold water of art and the hot water of science

and in his art he is actually experimenting with mathematical relationships even as he creates. His art is informed by fractals (‘Visage of War’); by three-dimensional shapes and the Golden Ratio(‘The Sacrament of the Last Supper’); catastrophe theory (‘The Swallow’s Tail’ and ‘Topological Abduction of Europe’); and four-dimensional space:

Dali's Crucifxion on a hypercube
Crucifixion (Corpus Hypercubus)

Christ floats above the exploded tesseract or hypercube (a three dimensional representation of a four dimensional shape); Dali uses a very mathematical and indeed scientific construct to explore how spirituality extends beyond the dimensions and senses normally available to us.

Mathematicians, says Marcus du Sautoy, do it for the beauty, for the art. There is a pleasure in counting, in numbers; and in their relationships to each other. Perhaps then it is not surprising that art and maths do have a great deal to say to each other.

The Michael Faraday Prize Lecture is available from the Royal Society website.

Posted in Friday afternoon, The Scientist | Tagged: , , , , | 3 Comments »

On the run-26Feb10

Posted by rpg on 26 February, 2010

This week, I have mostly been in Philadelphia.

View of Philly

Philadelphia, sometime this week

That was to meet The Scientist team, and sit down with Sarah Greene and figure out exactly how we’re going to run this new beast. The bottom line is that F1000 will now be feeding into The Scientist much more directly, and my job suddenly got a whole lot more interesting (not to mention busy). I’m very much looking forward to it.

We’ve already made a start: our Facebook page is now displaying links from The Scientist (there’s a few glitches that I need to sort out, but it’s there) and I’ll be pitching in with The Scientist’s Twitter feed. And readers should soon notice changes in some of the regular features, as well as additional stuff in print and online. Keep checking back here for updates. Check back here to find out what we’re doing.

Now, I’m totally jet-lagged (the extra two hours on the tarmac waiting to be de-iced didn’t help matters) so I’m going to wish you all a splendid weekend, and I’ll be back Monday.

Dirty snow on the sidewalk

Much as it was a productive week and they’re a great bunch in Philly, I’m glad to be in London again.

Posted in Friday afternoon | Tagged: , , | 2 Comments »

On the run-19Feb10

Posted by rpg on 19 February, 2010

It’s been a short week for me. As I implied elsewhere, I was off sick on Monday, and I’d already booked leave to be out of town Thursday and Friday (which should be today, if this scheduling thing works). And when I got back into the office on Tuesday, I was told that I should take a trip to Philadelphia to say hello to the guys in The Scientist office. The idea is that I can get to know the members of the team, and work out how we’re going to work together to bring even better content to The Scientist magazine. We might also discuss how to use their know-how to build community around F1000 itself.

So on Monday morning I’ll be heading to Heathrow, for a trip to the land of ice and snow. I’ll be back Friday morning London time. News-wise, then, it’s going to be a bit sparse from me, although I hope Steve and Callum will keep the flag flying.

What I can say is that the competition we ran on twitter appears to have been a great success, and some people are already asking when the next one will be. They’re actually asking for the same thing again, but I don’t know whether that has legs. What do you think? Should we limit it to historical papers, or maybe to your own stuff? What else would be fun to do in 140 characters (minus a hashtag)? I’m all ears.

And with that, I have to dash. I’m hoping there will be a new design on the development site when I get back, and I’ll post some screenshots for you to enjoy. Have a nice weekend!

Richard

Posted in Friday afternoon | Comments Off on On the run-19Feb10

On a new publishing model-the winner!

Posted by rpg on 16 February, 2010

Ladles and gentlespoons, the results are in. We had an amazing response, and after sifting through a mass of #sci140-tagged tweets, discarding all the retweets and publicity (and a huge thank-you to everyone who spread the word), we had 197 unique entries (grep saved my life).

Many of you posted very witty ‘historical’ paper summaries, but there were several who managed to squeeze their own papers into 140 133 characters too. This, I think, was far more difficult, even if it did not lend itself so readily to humour.

It turned out to be quite an interesting social experiment, too. There were a number of themes, possibly the most popular being the structure of DNA (not surprising seeing as most of my twitfriends are at least vaguely biochemical). This from @SelectAgent was one of the best:

Salt of DNA structure= double helix. Strands anti-parallel; has implications. (PS Rosie didn’t help)

Physics, especially quantum mechanics, also featured heavily, and @pssalgado deserves a special mention for

Where are you, Heis? “Don’t know exactly, but I can tell you how fast I’m going!”

Galileo was another favourite among physicists, @sciencebase almost scooping the prize with

Dropped heavy and light ball at Pisa; saw landed at same time. Peer review problems now, especially after telescope incident.

Many entries had fun with Mendel; here’s @marymulv:

Peas for tea. Again! (Damn that gardener.) Smooth, wrinkly, smooth… Is that a pattern? Hm. Should I tell that Darwin fellow??

Stanley Milgram was the subject of a couple of tweets, @sciencebase again making me laugh with

Stanley, is this circuit really 450 Volts, those people look like they’re in real pain? Shut up and just push the lever

Some of you are obviously budding behavioural psychologists, as Pavlov’s famous experiment also attracted a lot of attention? My favourite? @enniscath‘s

Rang bell, fed dogs. Rang bell again, dogs drooled. NO FOOD FOR YOU! BAD DOG! (heh heh. Stoopid dogs).

Honorable mentions should also go to silentypewriter and yokofakun for sheer wit and volume dedication.

But there can be only one winner, I’ve decided. For his poetic take on Watson & Crick’s structure of DNA, and for a smart paper of his own, the winner of the #sci140 competition is…

@CameronNeylon (Cameron Neylon)

The winning entries from Cameron are

Take bacterial cell wall chemistry. Replace proteins + wall with any prot + beads. Easy protein labelled beads! (link)

and

2 interwound helices, with handedness right, and a 3.4 pitch, and hydration just right + keto not enol or they don’t zip up right (link)

A bag full of f1000 goodies will be winging its way to him very shortly.

Mad props to Cameron, and a big thank you to everyone who participated. It was such good fun, I rather think we might run something like this again. Keep an eye on @f1000 on Twitter for the next one. The full list of #sci140 entries are below the fold.
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Posted in Competition, Friday afternoon | Tagged: , , , , , , , , , | 6 Comments »

On the run-12Feb10

Posted by rpg on 12 February, 2010

Cancer Causes Cancer!

Well, that was the headline we should have gone with. It is of course a hat tip to the Daily Mail, a tabloid publication that is desperate to tell the UK population that just about everything causes cancer. (I found that website by googling ‘cancer causes daily mail’, which is in itself quite a neat headline. Unfortunately I think we’re closer to curing cancer than curing the Daily Mail. Oh well.)

So, we know that tumours have this nasty habit of sending out malignant cells into the rest of the body. They break off from the primary site and get into the blood and lymphatic systems, occasionally washing up in convenient organs where they can settle down and create new tumours, or metastases. This is partly why cancer is so difficult to cure: you can cut out the original malignant growth, zap it with X-rays and take all sorts of evil drugs (‘evil’ because they are designed to kill cells, and you’re made up of cells; and discrimination between the cancer cells and normal cells is a huge problem); but if one metastatic cell survives, you have to start all over again. And if it’s managed to find a home deep in a bone, or the brain, or somewhere equally inaccessible, it’s game over.

It turns out things are even worse than that. Circulating tumour cells, if they find their way back to their original ‘home’, can actually stimulate growth of the original cancer. Nasty. As the authors say,

Tumor self-seeding could explain the relationships between anaplasia, tumor size, vascularity and prognosis, and local recurrence seeded by disseminated cells following ostensibly complete tumor excision.

‘Ostensibly complete tumor excision’—that’s right, because no matter how good your surgeon is, you can never be sure you’ve cut every last bit out; or that some cells haven’t already gone walkabout.

The good news is that certain cytokines derived from the tumour, IL-6 and IL-8, act to attract the circulating cells, and that they get back in via the matrix metalloproteinase collagenase I (MMP-1) and fascin-1 (it’s the actin cytoskeleton again! These guys get everywhere). If we can find a way to selectively block these pathways we should be able to start thinking about appropriate therapeutic approaches. Gentlemen (and ladies), start your (grant-writing) engines.

Kim, M., Oskarsson, T., Acharyya, S., Nguyen, D., Zhang, X., Norton, L., & Massagué, J. (2009). Tumor Self-Seeding by Circulating Cancer Cells Cell, 139 (7), 1315-1326 DOI: 10.1016/j.cell.2009.11.025

Twitter storm

It’s been pretty hectic on the twittertubes this week. Following a random conversation at the Scholarly Kitchen I suggested writing papers in 140 characters would be a wheeze. I turned it into a competition, and we had an amazing response. Check back on Monday to find out who’s the lucky winner of a bag of f1000 swag.

Badger Wars

vermin shooting verminI don’t have a lot to say about badger culling to prevent/reduce bovine TB (except maybe to say that killing vermin with a high-powered rifle and decent ‘scope is one of the most humane ways of doing this).

I just like the sound of a ‘randomized badger culling trial’. Oh, and when someone ‘explains’

This trial was undertaken in very specific circumstances and it could be misleading to extrapolate the findings to any future control program.

you can be pretty sure there’s a vested interest or extreme prejudice somewhere. Even when the trial shows that there’s no economic benefit.
Jenkins, H., Woodroffe, R., & Donnelly, C. (2010). The Duration of the Effects of Repeated Widespread Badger Culling on Cattle Tuberculosis Following the Cessation of Culling PLoS ONE, 5 (2) DOI: 10.1371/journal.pone.0009090

Valentine’s Day

Just a reminder to all you chaps out there—it can’t hurt to buy some flowers, even if you don’t want to buy into the whole commercialization thing. A nice dinner doesn’t cost you much either, and could pay dividends in the romance stakes. But at the very least, show you really care by getting checked out:

Take a test for #Valentine‘s Day. Sexual health appointments across Lincolnshire within 48 hours. Call 01522 539 145

It gets pretty lonely up there in Lincolnshire. Have a good weekend, and I hope it’s full of lovehearts and kisses. Failing that, a beer or three can have much the same effect.


Posted in Friday afternoon, Literature, Medicine, Random, Science | Tagged: | 1 Comment »

On a new publishing model

Posted by rpg on 9 February, 2010

UPDATE: Entries so far

Twitter, what is it good for? Hunh.

There’s been rather an interesting couple of posts over at the Scholarly Kitchen, recently. What am I saying? They’re all interesting. Anyway, Kent Anderson says that blogs are for fogies and David Crotty talks about ‘talking’ vs ‘doing’. Elsewhere on Nature Network we’re re-visiting the meme of why do we blog anyway? (to which I’m not going to contribute, myself having decided to do rather than talk about). You can look up the links yourself if you can be bothered.

Anyway, in the middle of a rather long and involved conversation, someone made a throwaway comment on David Crotty’s post. Then I thought it might be fun to see if I could write a scientific paper in 140 characters.

“Clned gene _cancer_. KO in Ms. Ms dead. Cure cancer.”

But why stop there? Here’s a challenge for you.

Your task is to re-write a scientific paper, a real, peer-reviewed and published one, in 140 characters. Twitter it with the hashtag #sci140 so we can track them (OK, so that’s 7 characters you’ve just lost but no one said it would be easy). You can do this as many times as you like, as many papers as you like, and it would be nice if they were your own, but they don’t have to be. I’ll see if I can get some f1000 swag for what I deem to be the best entry.

Go for it.
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Posted in Friday afternoon, Literature | Tagged: , , , , , , | 2 Comments »

On the run-04Feb10

Posted by rpg on 5 February, 2010

What was that? I think it was the sound of a week flashing past.

I keep saying things like “We’ve got a brand new website… but you can’t see it yet.” This must be quite frustrating. Truth is, the dev team are working very hard (and specs have changed and changed again—but let’s not go there now) and a lot of stuff has to come together all at once. There’s actually no point showing you what we have at the moment because it’d all “ignore that, we’re changing it” and “the design is going to be different than this” and “oh, yeah, we know about that bug”.

But I can tell you that the new search is very funky and we all like it, and that the new design is very spiffy (hang on, I did that already). On Monday we’re going to work out once and for all what we can deliver and work to that. So far, the ‘definite’ list contains the new design (both what it looks like and functionally), the improved search, comments on evaluated articles and RSS. There are a heap of other behind-the-scenes changes too. Then after we go live we can add on all the other things that are on the backlog, so you will see new things appear as we keep building and tweaking and rolling out new features.

I spent some more time on our journal rankings this week. The critical thing appears to be the timing: as I’ve said before, most of our evaluations are published quite quickly after the original article appears. We get around 90% of all evaluations within about three months of the publication date. So what we want to do, for yearly journal league tables, is capture as many as possible while making our stats as up-to-date and relevant as possible. The issue is that if we took April, say, as the cut-off for the previous year we’d end up giving the journals that publish more stuff towards the beginning of the year an unfair advantage. So we’re going to implement a rolling cut-off, with a provisional ‘current’ ranking and publish the official f1000 stats somewhere around May each year, which gives us four months to collect evaluations for each original article.

However, the big news this week is that we welcomed Sarah Greene into the office. This is part of the move to bring f1000 and The Scientist closer together: f1000 is going to start seeding The Scientist‘s scientific content, and use it to help build a community around the service.

As part of this, my own role is changing. I’m going to move away from web development (although I’ll still have input into the design and user experience), which will free me up to be more editorial/journalistic. I’ll still be running the Twitter feed and Facebook page and wittering about things that catch my eye in f1000 (perhaps even more so). There’ll also be the ‘special projects’, such as the rankings, federated comments and various research collaborations. I guess Eva will still be wanting me to make logos for her too.

And finally

The late pick-up of the disenchantment of a small number of researchers with the peer review process is still making waves this week. Cameron Neylon gives his own take on the matter at his blog. I’m not at all sure that I agree with his analysis, having had my own manuscripts subject to both what I might call ‘good’ and ‘bad’ review. I think that too many people view peer review as a stamp on the ‘rightness’ of the paper, rather than a technical check that the experiments and controls are done correctly and that the literature has been read.

Cameron has also been having a go at Nature Communications. The argument hinges on the Creative Commons licences they ask authors to choose. You can sign up and join the conversation at Nature Network.

With that, have a great weekend. And sorry, no cytoskeletal porn this week. Maybe next time.

Richard

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On the run-29Jan10

Posted by rpg on 29 January, 2010

Vitek quotes a Polish proverb,

If you’re going to fall off a horse, make it a big one.

In that vein, take a look at this graph (don’t look too closely; it’s deliberately a tiny bit obscure):Graph of ffJ and Journal Impact factor

What I’ve been doing this week is mostly hacking away in Perl at some of the information in our database. As you may know, each evaluation in f1000 has a score associated with it, based on the rating given an article by Faculty Members. We’ve redone the scoring and I’ve worked out a way of combining those scores, or ‘article factors’ as we’ve taken to calling them, for each journal that is represented at f1000. This gives us a ‘journal factor’, ffJ. It’s our answer to the journal Impact Factor, in fact; and the graph above is the top 250 journals according to our ratings (in blue) with the appropriate Impact Factor in red.

You’ll notice right away that there isn’t a one-to-one correlation, and of course we’d expect that (the Impact Factor has serious problems, which I’ve talked about previously). I’m currently analysing our data a bit more deeply, and I’ll be writing a paper with that analysis, as well as talking about it at the March ACS conference in San Francisco.

Last Friday evening I went down the Driver with a couple of the dev team and a bunch of people from places as varied as BioMed Central, Nature Publishing Group, Mendeley and Mekentosj. We talked about what we’re variously calling cross- or federate-commenting. On the whole we’ve decided it’s a good idea, and we simply have to figure out how to do it. What this implies of course is that we’re actually going to allow user comments at f1000—and indeed that’s the plan. I’m looking forward to rolling out this functionality to you, not least because when people want to raise questions about articles evaluated on f1000, they’ll be able to.

While we’re on the mythical new site, we asked another web designer what they could come up with for us. And for the first time, all of us who saw the design liked it. So hopefully we’ll be able to get that implemented real soon now and I’ll be able to start showing you what you’re going to get, you lucky people. (Rumours that someone said “It looks like a proper website!” are completely unfounded.)

Interesting reviews

A couple of things you may have missed.

First, the (possible) mechanism behind photophobia in migraines. Turns out that people who are functionally blind, but sensitive to circadian input and pupillary light reflexes are susceptible to photophobia. Work in rats published in Nature Neuroscience implicates a (previously uncharacterized) multisynaptic or heavily networked retinal path.

In Biology, the problem of de novo assembly of DNA sequence reads into sensible contigs from massively parallel sequencing technologies has been addressed. This, if it works, would bring exciting concepts such as personal genomics that little bit closer. The paper is in Genome Research (subscription required) and you can read the evaluation for free.

And finally

Faculty of 1000  is big in Italy—or at least on Facebook. My post on the recycling of integrins drew an excited response from one Grazia Tamma, who was then mocked mercilessly by her brother!

Hang in there, Grazia; science is great and the cytoskeleton rocks.

Posted in Friday afternoon, Indicators, Metrics | Tagged: , , , , | 4 Comments »