Faculty of 1000

Post-publication peer review

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Moving on

Posted by rpg on 27 April, 2010

Don’t panic!

The F1000 weblog has now been incorporated with Naturally Selected, at F1000 The Scientist.

Please update your bookmarks and use the new RSS feed. You can still find previous entries in our archive.

Posted in f1000 | Comments Off on Moving on

Common people

Posted by rpg on 22 April, 2010

While trolling through the new, shiny beta F1000 site (shh! I’m not supposed to tell you about that yet) I noticed that a paper from way back in September last year is still up there on our top ten lists. This was a commentary in J Neurosci saying, among other things, that the

time has come for the scientific community to make a concerted effort in condemning animal-rights extremism and in reaching out to the public to explain our work, its importance, and our commitment to the strictest ethical guidelines of animal research.

Furthermore, say the authors,

A special effort should be made to emphasize the irreplaceable role for nonhuman primates in neuroscience research to the public.

(10.1523/JNEUROSCI.3738-09.2009)

It obviously touched a nerve because it garnered 17 evaluations (and Steve P blogged it), second only to a controversial paper from 2005 on non-Mendelian inheritance in Arabidopsis (that actually could be wrong—also see this report and editorial in The Scientist.) I get this—most people, I think, have a hard time accepting that animals should be used for scientific or medical research. Especially if they’re cute, fluffy or primates. But we can not maintain the standards of medical care we have come to expect without such testing, despite the protestations of PETA (who refuse to condemn terrorism, by the way) and the rest of them. Despite the problems with animal models (and there are many; the crucial thing is that we do know the limitations and can use other models in addition), animal-based research is the only way to increase quality of life for human beings.

Whether we should treat human beings preferentially in this way is of course another matter and one for philosophers to debate. (Natural selection of course falls over if a species decides not to do the best it can for itself, but let’s not go there.) But I have no time at all for those terrorists who by their actions rate animal life over human life:

we have seen our cars and homes firebombed or flooded, and we have received letters packed with poisoned razors and death threats via e-mail and voicemail. Our families and neighbors have been terrorized by angry mobs of masked protesters who throw rocks, break windows, and chant that “you should stop or be stopped” and that they “know where you sleep at night.” Some of the attacks have been cataloged as attempted murder. Adding insult to injury, misguided animal-rights militants openly incite others to violence on the Internet, brag about the resulting crimes, and go as far as to call plots for our assassination “morally justifiable.”

So I’m pleased to read that the Information Tribunal, that settles Freedom of Information disputes, has ruled in favour of the University of Oxford protecting its staff from potential terrorists: in this case a particularly mischievous request apparently from PETA concerning an individual at Oxford (you can see the decision here: PDF).

It makes interesting reading (from the Understanding Animal research website):

PETA was not satisfied with this decision and appealed again. The case therefore passed to the Tribunal service. In evidence to the Tribunal judge, the University acknowledged that being transparent was good for science and that ‘if there was no special extreme threat here, the exposition of this information would be for the good’.

The Tribunal Judge upheld the previous ruling by the Commissioner, and agreed that the exemption was correctly applied. They also agreed that the public interest in maintaining the exemption outweighed the public interest in disclosure.

[…]

We strongly support the rights of universities not to put individuals at risk.

Common sense prevails. At least in the UK: in the US, PETA tried to pull a similar stunt against the University of South Dakota. There, they also failed, thankfully: but only because they withdrew on a technicality. That’s not good enough—the law should be protecting researchers without question.

Unless you believe that animal ‘rights’ are worth more than those of humans, of course.

Posted in f1000 | Comments Off on Common people

Should I stay or should I go

Posted by rpg on 21 April, 2010

Epigenetic regulation is the new black, or at least charcoal. Modifying chromatin—acetylation or methylation of histone tails, or directly on DNA, in CpG islands for example—can change a number of things in addition to imprinting (turning gene expression on or off depending on parental origin). I’ve just finished one write-up of a F1000 Report discussing histone methylation in meiotic recombination hotspot specification and hybrid sterility, and another one of a paper showing that histone marks regulate alternative splicing patterns (look out for them in June’s The Scientist).

Viruses are getting in on the act too. When Epstein-Barr virus infects a cell it can either hide–latency–or replicate and continue the infection. It uses a single transcription factor to drive these states, depending on the epigenetic status of the host cell; in other words it uses the cellular machinery to wake up when conditions are right. Kind of like a molecular clock, actually. (And you’ve got to love an evaluation that quotes Mick Jones.) We’re also seeing strange but pretty strong effects in certain tumors: hypermethylation of two tumor suppressors in the parathyroid is associated with (and probably leads to) adenoma formation.

Fat’s back in town. Lab rats are obese—morbidly so. But the problem is if you don’t let them feed at will then they get stressed, apparently, which is bad if you’re trying to do experiments on a normal, healthy ‘control’ animal model. Lots to think about there. I’m not going to repeat a comment a colleague made about them being a normal model for certain nationalities, but maybe we could look at knocking out hedgehog, which seems to suppress the generation of white but not brown fat.

Finally (sorry, no room for cytoskeletal porn this week), Faculty of 1000 published its 90,000th evaluation yesterday! David McManus at Weill Cornell Medical College wrote about a paper in the Journal of Clinical Oncology that looked at combination therapy in the treatment of advanced clear cell renal carcinoma.

We’re looking forward to 100k.

Posted in Weekly roundup | Comments Off on Should I stay or should I go

Working for the man

Posted by rpg on 20 April, 2010

I wonder if US President Barack Obama is onto something here.

You may have heard that he’s asked asked for a 6% increase in the NRSA stipend—the National Institutes of Health’s ‘training’ stipend—for postdoc fellows. He’s apparently going to fund this by cutting 0.5% of funded fellowships. (I should add that because of the bizarre way the US funds its post-docs, this is simply an increase in a theoretical baseline. Apparently, most post-docs are paid less than this entry-level, especially if they’re non-US citizens, although some are paid more. The whole thing confuses the hell out of me: in civilized countries each agency sets a national scale so everybody knows what everybody’s being paid.)

Six percent. Sounds nice. Well except some people have realized that this might mean that principle investigators might have to cut the number of staff they employ so that they can afford this 6% increase—and predictably there has been some vociferous reaction. To an outsider (yes, I post-docced in a few labs, but never in the US) this all seems rather confusing. It also misses the point that in general, and especially in the US, post-docs have a pretty raw deal. All right, so short term contracts are no way to live your live, especially if you want to bring up a family and do other normal things that human beings like to do, but at least in the UK and Australia you can get a pension plan, to which your employer will contribute. And the pay, actually, isn’t all that bad: nothing like a physician or a lawyer with an equivalent number of years of training under their belt might get, but certainly a decent wage.

The problem is that there are too many post-docs, and they all want paying. The tragedy is that most of them are eventually going to get so fed up with science that even after two, three post-doc positions they’re going to pack it in and change career. Now, that’s maybe not such a bad thing for the person involved (and I certainly can recommend it) but I wonder if that’s good for science in the long run. I wonder if it’s more cost-effective to have fewer, better paid post-docs and really give them a good run at this thing called science?

Jenny Rohn has already called for revolution along these lines. Nobody here is talking about reducing the science budget (although I have argued that maybe we shouldn’t be so precious about science funding); rather we’re thinking of giving more to the very best and giving them more to do it with. Is that President Obama’s plan, do you think? Is he that far-sighted?

Whatever you think about this, if you’re in the US please remember to take our salary survey and get in with the chance to win $100 Amazon vouchers (direct survey link). And tell us about your worst ever vacation job using the #vacjob hashtag on twitter to win a bag of F1000 goodies.

Posted in Funding | Comments Off on Working for the man

Money

Posted by rpg on 19 April, 2010

One of the things I did as a student to supplement the meagre maintenance grant involved driving tractors around and tying up clematis. Not a wholly unpleasant time, to be honest, although it was the overtime that really made it worthwhile.

Then came the summer when I couldn’t get the gig at the plant nursery, and ended up jobbing for a gang (that’s a work gang, quite common in rural Lincolnshire) for six weeks. One of the things I had to do was clean the floor of a petfood factory (and believe me, if you ever see petfood being made you will never buy it again). That was pretty gross, but not as bad as the mate I was with, who had to handle the whole organs from slaughtered cattle before they went on the conveyor belt–complete with pulsating tumours and the like.

So, here at The Scientist we’re running a survey of pay in the Life Scientists. It’ll be published in November, and we’re giving away three US$100 Amazon gift certificates. (The survey is open to US-based employees only I’m afraid, but read on.) To—I’ll be honest—get a buzz going, I’m running another Twitter comp.

I reckon it’s unrealistic to remember what you got paid for vac jobs at college, so this time, I want you to tweet the grossest or funniest vacation job you ever had. The usual bag of F1000 swag to the winner. Use #vacjob for the hashtag, and have fun! And don’t forget to answer the survey, at http://www.surveymonkey.com/s/H7XZ2MF.

Posted in Competition | Comments Off on Money

Procedural note

Posted by rpg on 15 April, 2010

Just to let our regular readers (both of you) know that this place will be closing shortly (boo!), but all our bloggy-type content will continue to appear at Naturally Selected (yay!).

This’ll happen just as soon as a last few tweaks are made: URL redirects, happy linkage, etc. Nip over to Naturally Selected anyway, as all content is duplicated there and has been for a while. Callum and I promise to keep you entertained as usual, and we’ll also be featuring guest and The Scientist writers.

Posted in Meta | 2 Comments »

Everybody’s Talkin’

Posted by rpg on 15 April, 2010

It’s been a while since I’ve said anything about the F1000 website. You might remember that’s what I was working on when I first arrived at SNG (much to my surprise, it has to be said); since about February I’ve been increasingly full time on The Scientist. I still maintain a professional interest in what’s going on across the office, though, especially when it comes to a couple of my pet projects.

One of those projects is user comments.

We’ve been having a bit of a discussion about comments on evaluation pages. My original plan was to have a separate forum so that people could talk about articles evaluated by Faculty Members. But for various reasons that morphed into comments directly on the evaluation itself, which I think is probably a better way of doing things. This does cause a few headaches, though: we don’t want to ‘dilute’ the impact of what our FMs say, we’re a serious site—by professionals, for professionals—and need to honour the trust our users place in us (so can we allow comments from just anybody, and how are you, as a reader, to judge the worth of those comments?), we want to avoid trivial and inappropriate content but at the same time commenting for the bona fides should be as easy and straightforward as possible.

I’m encouraged that Nature are now allowing commenting across the site, and will be watching what happens with interest. In the meantime, Neil Saunders has some useful advice for publishers who want to encourage comments.

My question to you is, what else would you like?

I should point out that we’ve already decided that only registered users who are in a ‘subscription zone’ can comment (only subscribers can read the content anyway; except for the articles we make free), and that all comments will go live immediately, and there’ll be the ability to flag comments as inappropriate. That’s on the advice of our lawyer, so is unlikely to change! But have at it: what really annoys you/stops you from commenting on other sites?

Posted in f1000, Website | Comments Off on Everybody’s Talkin’

Watching you watching us

Posted by rpg on 13 April, 2010

I was nosing around Google Analytics yesterday, seeing if our Faculty Daily section is attracting any interest to the F1000 main site. [Update: that’s the F1000 Biology site. Medicine is different, but not interestingly so.]

And I saw a very strange thing.

First, look at the browsers hitting http://f1000biology.com. Firefox has 3% more share than Internet Explorer, and Safari comes in third with 16%. Checking the operating systems, we see that nearly 70% of visits are some version of Windows, and 29% of you are using Macs. (This simply proves that F1000 users are more intelligent than the rest of the population, but we knew that anyway). Linux users don’t quite manage 2%, but look at that: fourth in the list is the iPhone, with 0.42%—not much, but more than all other mobile devices and ‘unknown’s combined (data not shown, but trust me. I’m a doctor).

So then I checked all mobile devices. No real surprises initially: the iPhone blows everyone away, and Android is in third place behind the iPod.

(There’s also some mildly interesting usability stats hiding in there: people using any of the Apple devices or Android phones are more likely to visit other pages and spend time on the site than the other users. I don’t know if this reflects a user mindset, ease of use of the device, or usability of the actual site on those platforms.)

But here’s the real funny thing. Some of you are already using the iPad, more, in fact, than use a Blackberry to access the site. (All data are taken from the period 21 March to 13 April; considering the iPad was only launched in the US a couple of weeks ago these data are even more impressive.)

You geeks, you.

Posted in Technology | Tagged: | 5 Comments »

At the movies

Posted by rpg on 7 April, 2010

Busman’s Holiday

Faculty of 1000 published 1472 evaluations last month. This is a world record! And it should help you predict when we’re going to hit 90,000. Remember, we’re running a competition: simply twitter the date and time you think we’ll make 90,000 evaluations with the hashtag #F90K for a chance to win some F1000 goodies.

Easter Hollidays

Image: Richard Wheeler, Wikimedia Commons

Faculty member Fyodor Urnov wants to know if you remember the lecture on homologous recombination (HR) from your genetics class in college. I certainly remember tutorials, and seeing micrographs of Holliday Junctions for the first time. I was fascinated and not a little excited at actually seeing a physical representation of an incredibly important biological process.

Fyodor answers his own question,

For many people, sadly, the answer is “no, and not regretting it.” This is a shame — not only are we the products of HR that took place during gametogenesis in our parents but the repair of double-strand breaks (e.g. after a dental X-ray) keeps our genomes intact.

and recommends you read a recent paper in Nature showing that double Holliday junctions are indeed involved in repair of double-strand DNA breaks. He goes on to bang the drum for traditional biochemistry:

single-locus analysis continues to offer remarkable insight into biology, despite the ubiquity of massively parallel omics. A proper Southern blot — of which this paper has many — is a very, very powerful tool.

Roman Holiday

You probably saw that Nature Reviews suffered its first retraction across its stable recently. In an interesting case of intellectual plagiarism, Mariam Sticklen was accused of writing a paragraph that was “paraphrased without attribution”. This becomes interesting in that the principle of anonymous peer review has been challenged: Sticklen reviewed a paper and allegedly lifted the offending ‘thought’ directly from it. The editor of Plant Science, Jonathan Gressel, said
“When you have done something that’s way beyond the pale, you forfeit your anonymity as a reviewer,” and “I think Nature Reviews Genetics was nice to her in allowing her to say ‘paraphrase’.”

The full story by Bob Grant is available at The Scientist. I only mention it here, really, for the comment thread, in which we see both editors getting involved, as well as Sticklen herself and her ex-husband, who gives her a glowing character reference. If there’s any film makers out there who want to make a blockbuster about science, this has all the ingredients.

And finally

Trees are good for you. At least, if you’re an arboreal—i.e. tree-dwelling—mammal. But not a primate or marsupial. If you’re one of those (what are you doing reading this?), you

should have longer lifespan than terrestrial species of similar body mass, the rationale being that arboreality reduces the risk of predation by terrestrial predators.

As Douglas Adams once said, coming down from the trees was a bad idea.

Posted in Weekly roundup | Tagged: , | Comments Off on At the movies

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?