Faculty of 1000

Post-publication peer review

Archive for December, 2009

Merry Christmas Everybody

Posted by rpg on 25 December, 2009

To you all… Have a good one!

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Seasons Greetings, Feliz Navidad, Joyeux Noël, Frohe Weihnachten, 圣诞快乐

Posted by stevepog on 24 December, 2009

*instead of bombarding your inboxes, we thought it better to host our Christmas card here and send you best wishes, safe travels and happy searching (for Christmas presents, f1000 evaluations, whatever takes your fancy).

Posted in f1000 | Comments Off on Seasons Greetings, Feliz Navidad, Joyeux Noël, Frohe Weihnachten, 圣诞快乐

Citizen Science campaign ramps up

Posted by stevepog on 22 December, 2009

I’ve mentioned before about the superb efforts of our friend Darlene Cavalier in encouraging non-scientists (and some influential members of US Congress) to actively engage in science, which we gladly endorse.

Darlene is working hard on the ScienceforCitizens website, which will be launched next month, but she also found time to be interviewed recently by Florida radio show Weekend Workout on science policy, cheerleading and other topics.

Take a listen here (her interview starts at 20:50 on the Soundcloud player below or about a third of the way through if you use the basic web player at this link):

Weekend Workout podcast featuring Darlene Cavalier

Darlene, myself and other web 2.0-savvy bloggers, science press, educators and developers will be attending Science Online next month in North Carolina, where we will (as the conference notes promise) “discuss, demonstrate and debate online strategies and tools for doing science, publishing science, teaching science, and promoting the public understanding of science.” Sounds like a hoot doesn’t it.

I’ll report on those happenings in mid January, for now it’s off to cold and snowy Belgium and Germany for the Christmas/New Year break. Keep an eye on our Twitter account for regular updates on f1000 and enjoy the festive season.

Posted in Communication, Conferences, Journalism, Science | Tagged: , , | Comments Off on Citizen Science campaign ramps up

Eighty five thousand

Posted by rpg on 16 December, 2009

It doesn’t seem so long ago we celebrated our 80,000th evaluation here at f1000. Today we hit 85k, with an article by David Borsook of Harvard Medical School, talking about changes in the brain on chronic brain pain treatment—no less than an increase in grey matter!

The evaluation is free at the f1000 website. Enjoy!

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“What about the oceans?” Climate change reversal scheme has its doubters

Posted by stevepog on 16 December, 2009

With most of the science media, green movement and world leader attention focused on Copenhagen and climate change right now, it would be remiss of us not to mention a new evaluation which looks at one of numerous papers promising new ways to tackle the greenhouse effect.

The reviewer, Robie Macdonald, from the Institute of Ocean Sciences in Canada, looked at a paper in Geophysical Research Letters that discussed stratospheric geoengineering as a way to curtail greenhouse gas emissions.

MacDonald said:

This paper estimates the costs of putting sufficient aerosols into the stratosphere to slow down or reverse global warming. For possibly as little as several billions of dollars per year, one might cool the planet, stall or reverse ice melting, thwart sea-level rise, and increase the terrigenous sink for CO2 through enhanced primary production.

MacDonald quite rightly has issues with this proposed technique, as it may on one hand help produce planet-cooling sulfate aerosols but on the negative, as Ars technica also reported, “it would also produce more droughts and worsen ozone depletion. And, crucially, it would do nothing to reverse ocean acidification”.

In a time when the media is not quite sure which side of the climate change `debate’ to be on and newspapers are running unchecked stories which deny climate change exists, alongside comment pieces from an unqualified former vice-Presidential candidate (Sarah Palin) to anti-skeptics (George Monbiot), stratospheric geoengineering could take off as the next big thing in climate change reversal (if there could ever be such a beast).

*By the way, the suggested methods of using military aircraft and artillery shells to save the planet sound a little too Armageddon for my liking.

Posted in Communication, f1000, Journals, Random, Science | Tagged: , , , | 3 Comments »

On making stuff up

Posted by rpg on 15 December, 2009

Benoit’s comment on Jenny’s blog reminds me of the time that I was scooped, but not because my boss was carefree with data. I’ll tell you about that some other time, though, because there’s an another issue he mentions that’s recently become very pertinent.

One of the issues that crops up occasionally at the day job is retractions. Because we highlight the ‘best’ in the biological and medical literature it’s critical that we do something whenever a paper is retracted, for whatever reason. These can be very good reasons, such as conclusions becoming untenable in the light of new evidence, or irreproducible results; or because of deliberate or accidental fraud or misconduct.

There’s nothing inherently wrong with retractions: it’s part of science’s self-correcting mechanism (although we could all use a little more openness). Either way, when a paper is retracted it doesn’t just disappear: the paper itself and the retraction text remain part of the scientific record. As, indeed, do the evaluations we publish. We (i.e. f1000) need to maintain our records for the sake of posterity; we don’t simply delete evaluations of retracted papers.

Now that’s out of the way, Benoit’s comment about PIs:

the PI’s job in those cases is to talk to the competition, figure out where everyone is at […] and make arrangements for co-publication, for example. It is no accident that a recent issue of Nature had 5 papers on the same iPS cell result, or that the cover of Nature was shared years ago by two articles on the role of lunatic fringe in chick limb development

reminds me of a story that started—at least in public—three years ago and is only just nearing closure.

Not being particularly interested in immunology, my response to the publication in Nature of three papers (by Janssen, Wiesmann and Abdul Ajees et als) reporting the structural basis for the activation of complement C3b elicited little more from me than an “ooh, that’s pretty” together with a raised eyebrow at an 80 Å shift in conformation. (I should add, here, that it’s not surprising to see three such major pieces of work published simultaneously in the same journal. As Benoit says, PIs talk—with each other and with journal editors—and publication can be delayed a little, or hurried. Which I suspect has not a little bearing on the current story.)

I would have paid it no further attention were it not for our soon-to-be departmental head, sometime in the waning of 2007, highlighting a rather intriguing Communication in Nature. Two of the authors on one of those three C3b papers, together with a couple of big guns in protein crystallography (one of whom was responsible for the gazumping I mentioned earlier), put their collective hand in the air and said, “Hang on, there’s something fishy with this third paper”:

We have reanalysed the data deposited by et al. and have discovered features that are inconsistent with the known physical properties of macromolecular structures and their diffraction data. Our findings therefore call into question the crystal structure for C3b reported by Ajees et al.

Them’s fighting words. The Communication gets a little technical (this is protein crystallography, after all), but I’ll try to explain it.
These guys decided, as you might expect, to compare the three structures. A sensible move, especially seeing as the published structures are somewhat dissimilar. Indeed, the Ajees structure is missing a huge chunk of molecule!

The coordinates do not form a connected network of molecules in the crystal lattice. The crystal structure forms layers that are separated by a large void in the c-direction (a slab of about 30–40 Å thick that spans the entire unit cell).

Sometimes it’s actually difficult to ‘find’ molecules in large, complex protein structures—if the software you use doesn’t assign electron density correctly for some reason, or the phases aren’t complete, you can fail to join the dots properly, and in the rush to publication this can be missed. So these guys took the deposited data and tried to solve the structure again, looking for the putative missing protein molecule. And they didn’t find it.

Furthermore, they noticed other physically implausible features such as no data indicating that the crystals contained water. In other words, this protein was in a vacuum; which might make theoretical physicists happy but isn’t really consistent with anything we know about biology (and Henry, you can stop the Nature abhors a vacuum joke right now).


_Killer figure_

They also found that the R factor, essentially a measure of the ‘goodness’ of a protein structure, doesn’t behave you would expect if no water was present in the calculation. Another measure of structure goodness, the B factor, looked odd too. This is a measure of how much any given atom might be expected to move; you might predict that atoms on the outside of a protein have more freedom than those inside: so the B factor should vary along the sequence. Right?

Eh. Right. In the Ajees structure, the B factors are pretty much the same across the entire length of the protein, which when you consider that the structure has vast swathes exposed to solvent (or vacuum, perhaps) is somewhat puzzling.


_somewhat puzzling_

In brief, the structure is just too good:

We think that these physically implausible features undermine the validity of the model presented by Ajees et al. and the deposited diffraction data from which it derives. Only when the experimental diffraction images are made available can the deviating C3b model be either verified or falsified.

There’s a bit of a pathetic response from Ajees and co., but basically we (as in the crystallography) waited to see what would happen next.

<eats popcorn>

What did happen next was a veritable storm on the CCP4bb mailing list, kicked off by Eleanor Dodson and titled The importance of USING our validation tools. That’s all it took for Randy Read (one of the Big Four) to weigh in with

Originally I expected that the publication of our Brief Communication in Nature would stimulate a lot of discussion on the bulletin board, but clearly it hasn’t. One reason is probably that we couldn’t be as forthright as we wished to be. For its own good reasons, Nature did not allow us to use the word “fabricated”.

That, and the necessity of waiting for Ajees et al. to respond, is probably why it took eight months for the Communication to be published. Anyway, rather than clutter up this space, I commend to you this zip archive of the CCP4bb discussion, kindly collated by Hari Jayaram.

Why am I talking about this now? Because, as reported by Iddo Friedberg, the University of Alabama at Birmingham has (finally) requested that no fewer than eleven structures, represented in nine papers, from the lab that published the apparently dodgy structure be expunged from the Protein Data Bank:

After a thorough examination of the available data, which included a re-analysis of each structure alleged to have been fabricated, the committee found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not falsified and/or fabricated and recommended that they be removed from the public record.

My spy in Sydney tells me that the Journal of Biological Chemistry has retracted one paper, and that the Journal of Molecular Biology and Acta Crystallography. He also says that Birmingham (Alabama) were slow in informing all the parties, which has delayed final actions. I also understand that journals are moving towards requesting that raw diffraction images (even if they’re as bad as Stephen’s) rather than just structure factors be deposited somewhere, so that we can all keep a big, brotherly eye on each other. And finally, “it is interesting that [the head of the lab] still claims he is innocent”.

It’s funny, that two years ago I suspected that Nature received manuscripts from Janssen and Wiesmann in reasonably quick succession, and knowing that the Ajees lab was working on the same thing poked them with a “Have you got that structure yet?”-type call. Alternatively, I thought, perhaps the Ajees group had seen presentations by the other two and realized they were about to be pipped. In either case, I reasoned, they might have had a structure almost ready, or poor crystals, and maybe they made something up.

Not good, not ethical; but possibly, just possibly, understandable. But to apparently fabricate eleven structures? That’s seriously bad, and implies a level of collusion and—well, let’s be frank here—organized conspiracy unthought of outside certain labs in South Korea.

In the meantime, as soon as the news from Alabama hit my screen, I pulled up the f1000 website and searched for the implicated articles. I’m pleased to say that we now reflect the current state of the scientific record (as you
may verify for yourself at this free link).
Read the rest of this entry »

Posted in Literature, Science | Tagged: , , , , , | Comments Off on On making stuff up

Black night

Posted by rpg on 9 December, 2009

Oh joy. What I missed this morning was Alistair Darling’s pledge to reduce HE and science and research budgets by £600 million. As Roger Highfield says, a dark day for British science.

In a new analysis, Dusic reports that that the UK is spending less on research today than in 1986, when Margaret Thatcher was prime minister, when CASE was first launched as Save British Science (SBS).

This has happened, despite a steadily rising science budget under Labour, because of cutbacks in research spending by Government departments, which have more than offset spending in research councils and universities.

Science needs PR more than ever, today.

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Is it follow the leader, a heads-down mentality or something more obscure?

Posted by stevepog on 7 December, 2009

Reproduction of an artwork by Andrzej Krauze

Vitek Tracz, chairman of the Science Navigation Group (of which f1000 is a member), is a fan of compatriot Polish artist Andrzej Krauze, who is known for his humorous calendars and cartoons in the New York Times,  New Scientist and Sunday Telegraph.

Krauze amused our leader with this cartoon, which Vitek has had reproduced in the f1000 reception area for all to view as they enter.

Much speculation has already been thrown around about what it means: follow the leader, keep your head down, look beneath the surface, stick your head in the sand (bit obvious that one). The man in charge is keeping his view to himself. Any suggestions are welcome.

Posted in f1000, Random | Tagged: , , | Comments Off on Is it follow the leader, a heads-down mentality or something more obscure?

No definite link between cannabis use and suicide: our review

Posted by stevepog on 7 December, 2009

We’ve published an interesting review (aren’t they all though?) on a study that discussed the lack of association between marijuana and suicide risk, in what our reviewer Wayne Hall from the University of Queensland, Australia, described as “the largest and best controlled prospective study of the relationship to date“.

It’s a tough topic to tackle, especially in a time when celebrity deaths, marijuana usage and suicide are so closely linked by tabloid media (Marilyn Monroe being the newest revelation) and when fears that teenage brains getting destroyed by cannabis are high on the news agenda. But on the other hand, when a highly-respected scientist such as Professor David Nutt gets vilified by the government for his outspoken views on drugs policy, the media generally showed support for the sacked Professor while still being skeptical of his evidence-based comments (such as cannabis use being safer than horse riding).

Hall looked at the paper, Cannabis and suicide: longitudinal study, by Allebeck and Price at al. from Cardiff University UK, published in the British Journal of Psychiatry, which went beyond previous small cross-sectional studies to look at whether the cannabis/suicide attempt relationship took into account pre-existing suicide risk between young people who become regular cannabis users and their peers who do not.

In the study, more than 50,000 Swedish men aged 18-20 were followed up for 33 years using death registers to identify those who had died from suicide.

Hall says:

As in previous studies, self-reported cannabis use at conscription was positively related to suicide (odds ratio [OR]=1.62, 95% confidence interval [CI] 0.65-2.07) but this association was no longer significant when plausible potential confounders, such as problematic behavior during childhood, intelligence, alcohol abuse, parental psychiatric disorder, other drug use, and psychiatric diagnosis at conscription were statistically controlled for by logistic regression (OR=0.88, 95% CI 0.65-1.20).
The selection of confounders to control for did not affect the finding that the OR was no longer significant after adjustment for confounders. This study strongly suggests that the modest association observed between regular cannabis use and suicide in cross sectional studies reflects the fact that young people who are at marginally higher risk of suicide are more likely to become regular cannabis users than their peers.

And it’s the last point that is most pressing: those at a slightly higher suicide risk are more likely to become regular pot smokers, not the other way round. If you look at the citation rates on Google Scholar for “cannabis and suicide”, many academics seem to support the view that the two are  strongly linked.

Allebeck and Price’s earlier paper, published in 1990 at this study’s 15-year mark, even stated “the proportion of suicides increased sharply with the level of cannabis consumption“: their new study clarified that the “association was eliminated after adjustment for confounding” and the link was better explained by markers of psychological and behavioural problems.

No doubt long-term studies such as this will lend more weight to the Nutt debate and, if they are given adequate publicity, hopefully help to cut down on biased anti-drug journalism.

Posted in f1000, Journalism, Statistics | Tagged: , , , , | Comments Off on No definite link between cannabis use and suicide: our review

More to Online than just Information

Posted by stevepog on 2 December, 2009

I visited the cavernous confines of Olympia Grand Hall in west London yesterday, totally unprepared for the mammoth event that is the  Online Information Conference (#online09 on Twitter).

Not sure what I was expecting: maybe a few stands with bored sales reps handing out flyers on data management and XML development (they had some of those) but the last thing I thought I’d see was an actual Formula One car and an F1 driving simulator, thanks to the big-spending crew at Thomson Reuters. The simulator was a tricky beast with very light handling but of course I didn’t try it as I was there to work hard (but somehow scored a top six placing anyway).

Simulator similar to the one at Online Information conference

Apparently the heavily-branded car relates to their sponsorship of the AT&T Williams team, though beyond that it was anyone’s guess what it had to do with the conference itself. Apparently even Williams F1 driver Kazuki Nakajima was dropping in today for a visit. No, that’s not him in the car.

Apart from the overly large TR presence, it was great to meet up with my American counterparts from science conferences and library journals to discuss whatever people like us talk about (i.e. telling everyone how amazing f1000 is and encouraging them to write and talk about us to their colleagues and audience).

Many of the free seminars at the rear of the building filled up quickly but one I did catch from start to finish was an admirable effort on social media by iCrossing‘s Mark Higginson.

Mark had stepped in at the last minute due to a sick colleague, which had some of us expecting a dull diatribe on how Twitter and Youtube work. And given that everyone who’s ever used Facebook thinks they can give a talk or write a book on the magical world of social media, I wasn’t feeling too enthusiastic.

But thankfully Mark actually provided some useful statistics and went into detail on what kind of web traffic is important. As he said, it’s all very well for  Facebook to say they account for 1 in 7 web page views in the UK but it’s what visitors do after they hit the homepage that’s important. So it goes that constantly updating and improving content on your landing page is a big key to a website’s (and hopefully company’s) success.

For those who are starting out in science blogging, his points were adaptable to our area: look to see who the most influential and interesting bloggers are, where they are (the obvious scienceblogging.com, researchblogging.com or more specific sites) and what media they are using (straight-up long form blogs, micro-blogs, video sharing etc). Get involved in the conversations they are having and create your own unique content. For those who are experts on a subject such as nanotechnology, commenting on a piece on the Wired website and referring back to your own blog is one way to drive more traffic to your site.

Overall very interesting afternoon out and for anyone who scored better than a 1.57 on the simulator (and I’m sure by now there will be quite a few), I hope you take away more from the conference than a mousemat or free pen.

Posted in Communication, f1000, Random, Website | Tagged: , , , | Comments Off on More to Online than just Information