Faculty of 1000

Post-publication peer review

Archive for September, 2009

From glowing monkeys to glowing cancer cells

Posted by stevepog on 28 September, 2009

One of our recent evaluations looked at an innovative method for labelling cancer cells (see the story here). In the original paper, researchers at Massachusetts General Hospital developed a process to specifically tag cancer cells by using chemically modified antibodies to home in on cancer cells and then cycloaddition to dye the antibody, making the cancer cells glow when viewed through a microscope. Our reviewer saw this is as an amazing techonological advance with potential benefits for early cancer detection.

This reminded me of the buzz earlier this year when  Japanese scientists used marmosets to show how a glowing protein could be passed on to a primate’s offspring through genetic modification. That research created both a misunderstanding of the purpose (one comment I heard was that “scientists are making things glow for fun”) and hysteria over ethical concerns.

Some commentators such as the reliable BBC took an even-handed approach to the monkey research while the UK’s Daily Mail focused as expected on the outrage from a small number of genetic engineering and animal rights activists to fire up their mainly like-minded respondents.

I have no issue with animal rights activists in general, though I question the real need for PETA’s constant nude celebrity ad campaigns, or for people on either side of the genetic modification debate. It’s when a hugely important piece of science gets hijacked by an interest group who have nothing sensible to add that I get frustrated. In my former guise as a journalist, one of the things I hated most was when editors twisted my story to focus on the angst-heavy ranting of a few and ignore the rational views of the majority. It may sell copies but usually science suffers.

Posted in f1000 | Tagged: , , | Comments Off on From glowing monkeys to glowing cancer cells

Take the red poll!

Posted by stevepog on 25 September, 2009

Posted in f1000, Statistics | Tagged: | Comments Off on Take the red poll!

I still haven’t found what I’m looking for

Posted by rpg on 24 September, 2009

My spies over at BioMed Central brought my attention to an Opinion piece in J. Biol by Arthur Lander at UCI, published on Monday. So newsworthy, they press-released it just in time for Stem Cell Awareness Day, which was yesterday. Oh well—we at f1000 have never claimed to bring you the latest research; rather just the best, no matter where it’s hidden.

It’s a very interesting article. Lander argues that just as phlogiston was a useful concept, but one that ultimately proved to be wrong and had to be discarded, so the molecular basis of ‘stemcellness’ might be a red herring. We have a difficult job describing just what defines stem cells, and have had little luck actually pinning down a molecular mechanism (not surprisingly. Defining a problem is pretty crucial to being able to answer it).

‘Stemness’, rather than stemming (ha ha) from a group of defined molecules figuring something out between themselves (like, for example, nuclear trafficking depending on interactions of certain proteins with FG repeats), looks like it’s an emergent property of cell types under feedback control. That’s not to say molecules aren’t involved of course, just that we need to think in terms of systems and networks rather than simple regulatory circuits.

This isn’t simply an interesting philosophical question. There’s been a lot of interest in stem cells as potentially being the little bastards behind certain cancers. The thought goes that if we can find out, at a molecular level, what makes those stem cells make tumours, we could come up with a chemotherapeutic agent, and bang! we’ve cured cancer. But if stemness is non-molecular, then we could be wasting time, money and lives chasing that one.

And the problem arises when we have a 2009 Stem Cell Awareness Day, and then in a couple of years’ time we say, actually, stem cells aren’t all that hot; and then people say ‘you scientists, you’re just making it up, aintcha?’

Because as scientists we’re not that good at explaining that this is how science works. How do we explain to the media (that’s the key, really), that just because last year’s hot model has been disproved we’ve actually advanced our understanding? It’s a mark of progress when  ‘scientists say’ something that contradicts what we thought was true. Ideas are born, they’re tested, and—more often than not— they are discarded as we learn more.

Just like phlogiston.

Posted in Communication | Tagged: , | Comments Off on I still haven’t found what I’m looking for

Just like a woman

Posted by rpg on 22 September, 2009

It’s all in the mind, you know.

ResearchBlogging.org Blame it on my lack of a classical education, but it was only a couple of years ago I realized that the word ‘hysteria’ is a feminist issue. It comes via the Greek for ‘uterus’, hence υστερία. The ancients believed that psychological-based problems (as opposed to physical ailments) only affected women, and therefore had their source in the womb.

…in Greco-Roman medical literature hysteria was believed to develop when the female reproductive system was inactive or ungratified—Bandini et al.

All this had passed me by, and I had never made the connection. I’d quite happily describe certain male colleagues as ‘hysterical’ without implying I thought they were female, or indeed that the quality was particularly feminine. It was quite a surprise to me that certain people felt very strongly about this, and I was saddened at the subsequent reduction of available vocabulary.

Queen Fragg and her mighty state of hysteria

Queen Fragg and her mighty state of hysteria

However, a paper in J Sex Med caught the eye of one of our Faculty just recently, in which the whole basis of hysteria (in the sense of a diagnostic entity of neurosis) has switched sides, so to speak. (Update: evaluation on f1000 Medicine.) By examining testosterone levels and looking for associations with psychopathologies in men seeking treatment for sexual dysfunction, Bandini et al. found that depression and anxiety were negatively correlated with testosterone levels. Of course: real men don’t cry, after all.

But strikingly,

histrionic/hysterical traits were strongly and positively associated with elevated T[estosterone]

(Higher testosterone was also associated, unsurprisingly, with better self-reported sexual function, higher blood flow in the penis and cough bigger balls.)

So what they are saying is that certain supposedly (by the ancients, at least) feminine characteristics, to which men were obviously immune (not having a womb), in fact have their source in uniquely male anatomy, turning the accepted (and vaguely misogynistic) wisdom on its head.  ‘Better’ sexual function (which I assume means ‘more of it’), and higher social dominance and mate-seeking behaviour all correlate with histrionic/hysterical traits. From an evolutionary perspective, the authors speculate that these could all be markers, or signals, of hormonal quality. Hysteria ex orchida.

I’m now envisaging flouncing out of particularly tiresome meetings claiming my hormones are making me do it. More seriously, this possibly means I can go go back to using ‘hysterical’ without my feminist credentials slipping—at least as long as I carry a copy of this paper around with me. Besides, nobody really cares about etymology anymore, do they?

——

Bandini, E., Corona, G., Ricca, V., Fisher, A., Lotti, F., Sforza, A., Faravelli, C., Forti, G., Mannucci, E., & Maggi, M. (2009). Hysterical Traits Are Not from the Uterus but from the Testis: A Study in Men with Sexual Dysfunction Journal of Sexual Medicine, 6 (8), 2321-2331 DOI: 10.1111/j.1743-6109.2009.01322.x

Posted in Literature, Medicine | Tagged: , , , , | 4 Comments »

Award winner to get an Obama audience

Posted by stevepog on 21 September, 2009

Our good friends at The Scientist named those who will receive the National Medal of Science in the US next month and we are happy to report one of our colleagues made the grade.

Biochemist JoAnne Stubbe from the Massachusetts Institute of Technology, who The Scientist recently profiled, is being honored for her work on enzymes involved in DNA replication and repair. Professor Stubbe also happens to be a Head of Section in Chemical Biology at F1000 and is on the Advisory Board at F1000 Reports.

Stubbe told the MIT press office that she is excited to make the trip to the White House and meet President Obama on October 7.

“It’s a little overwhelming, and a great honor,” said Stubbe, the Novartis Professor of Chemistry and a professor of biology. “For the first time, everybody in my family is excited about what I do,” she joked.

According to the award citation, Stubbe was honoured “for her groundbreaking experiments establishing the mechanisms of ribonucleotide reductases, polyester synthases, and natural product DNA cleavers — compelling demonstrations of the power of chemical investigations to solve problems in biology.”

Congratulations to JoAnne and good also to note the gender makeup of the life science winners: three women and three men across genome research, neuroscience and stem cells.

Posted in f1000 | Tagged: , , | Comments Off on Award winner to get an Obama audience

Strange news from a distant star

Posted by rpg on 18 September, 2009

Clive Cookson over at the Financial Times reports on Wednesday night’s têteà-tête between Lord Drayson, the UK’s Science Minister, and writer/broadcaster/medical doctor Ben Goldacre. Goldacre is behind badscience.net and is somewhat outspoken in his opinions. I didn’t sign up to see the debate, seeing as I’d been invited to a movie: which I’m convinced was more fun and better for the soul (I also said I’d review it for LabLit.com). I have to be in the right mood for Goldacre, and that happens rarely.

The subject of the debate was science journalism, which is often said to be in a parlous state, especially by people like Goldacre and his acolytes. Intriguing, then, to read that ‘Drayson had the better of the argument’.

Drayson maintained that the quality of science journalism has improved over the past few years – comparing the reporting of BSE, the MMR vaccine scare and GM crops with the better recent coverage of the Large Hardon Collider, hybrid embryos and swine flu.

Clive says that Drayson also advocated sensationalism in science reporting, which no doubt annoyed the ‘elitist’ (in a surprising reversal of characters) Goldacre. The latter’s comment, ‘Science journalists are very marginal figures in the coverage of science in British newspapers’ would no doubt have pissed off not a few editors and journalists.

I don’t know. Science reporting, in the tabloids at least, is generally wrong (in my experience). But then, much of the other news is also wrong: I have read stories where, from insider knowledge, at least half of the ‘facts’ aren’t. On the other hand, the Telegraph covered a story about money and well-being rather well (we know: we released the story).

And therein lies a tale. The Register got all huffy and sarcastic yesterday because the research was published four months ago, saying things like ‘offering this as an example of its own brilliance in keeping its subscribers bang up to date.’

Which sort of illustrates my more general point about journalism. We (f1000) don’t necessarily claim to be the first with news (although we can be surprisingly quick): rather, we concentrate on the science that is influential, important, and that might otherwise be missed. That’ll be why our Hidden Jewels sections are so popular (and yeah. People pay for this). But perhaps you wouldn’t expect the hacks at the Register to grasp something so subtle.

So there was a vote on Twitter on who ‘won’ the debate. Naturally, all Goldacre’s acolytes voted for him, but I was pleasantly surprised by the number of votes for Drayson. It looks like he did win, after all. That’s not to say science journalism can’t improve, but maybe things aren’t quite as bad as we thought?

And seriously, Clive, your photo scares me.

Update: Could this be the cause of all Ben Goldacre’s woes?

Posted in f1000, Journalism | Tagged: , , , | 4 Comments »

It’s a fine line…

Posted by stevepog on 16 September, 2009

We had a lot of welcome interest this morning on a press release, from the expected (New Scientist, LiveScience.com) to the unusual (Die Welt, Sueddeutsche Zeitung), which showed once again that a sexy title and the combination of money, pain and relationships still make attractive reading.

What we always hope is that the message doesn’t get lost due to over-enthusiasm on a journalist’s part for (what can often seem to them) an academic version of Katie and Peter (front page staples for their relationship, recent divorce and wild partying in the UK, thankfully lesser known across the rest of the globe).

Yes, the story did include a sexy angle: studies showed, in one example, that people with money in one hand will ignore social exclusion such as a lack of friends. The same went for those put under mild pain: a fistful of greenbacks helped take their mind off the fact their hand was submerged in hot water.  Conversely, those reminded of having spent money experienced the breadth of pain and social rejection.

The angle newspapers, blogs, the One Show (ha) will take obviously depends on what they think their audience will respond most to, so there’s no way I could make them follow exactly the same line as the press release. The hope is that reporters don’t try to work a certain celebrity couple into the story to give it an unnecessary tabloid slant.

Posted in f1000 | Comments Off on It’s a fine line…

How do we make sense of peer review?

Posted by stevepog on 15 September, 2009

As a follow-up to yesterday’s  tweet about the Sense About Science’s sensibly titled Peer Review Survey, a few thoughts. Out of the press reports on the Elsevier-funded study I’ve scanned though, a common phrase seemed to “no one has come up with a better method than peer reviewing, so we’re stuck with it”.

My colleague rpg has much more practical knowledge of the peer review process than I do, so as a relatively lay person I firstly wondered what the fuss was about. I know it’s of utmost importance to academics (and their funders) to have their papers appear in peer-reviewed journals.

And scientists who work outside the mainstream can miss out on exposure in their so-called top tier journals. But one of the great things that F1000 does is feature brilliant papers in lesser known publications, so they don’t get forgotten in the global soup of academic research.

Mark Henderson at The Times blogged on the strengths and weaknesses of peer reviewing, particularly the point that reviewers shouldn’t need to have their names known for peer reviewing to be an acceptable practice. Not an idea we subscribe to for business purposes at F1000 but he’s right in suggesting that young researchers may be scared off if they knew their name would appear alongside their reviews. Then again, as a former journalist I took that risk every time my byline appeared next to a contentious news story. If you want the knowledge and experience, you have to take some risks.

Some interesting stats in the survey that many have commented on related to plagiarism and fraud. While 81 per cent say that peer review should detect plagiarism and 79 per cent say that it should prevent fraud, only about 35 per cent say it is capable of doing both. I was discussing this topic with two recently graduated medical communications colleagues last week and they both said it would be an extremely difficult issue to police.

If a reviewer needed to have an in-depth knowledge of all major papers written on a particular topic, including remembering vital chunks of text that are likely to be plagiarised, they would probably also be in the running to replace Ben Pridmore or Brad Williams in the memory stakes.

Posted in Communication, f1000, Literature | Tagged: , | Comments Off on How do we make sense of peer review?

How many more times?

Posted by rpg on 14 September, 2009

…what dreams may come
When we have shuffled off this mortal coil,
Must give us pause

Thomson, in a commentary in the Journal of the American Medical Association, reckon there ain’t nowt wrong with the Journal Impact Factor:

The impact factor has had success and utility as a journal metric due to its concentration on a simple calculation based on data that are fully visible in the Web of Science. These examples based on citable (counted) items indexed in 2000 and 2005 suggest that the current approach for identification of citable items in the impact factor denominator is accurate and consistent.

Well, they would say that.

And they might well be right, and you and I and Thomson Reuters might argue the point endlessly. But there are a number of problems with any citation-based metric, and a pretty fundamental one was highlighted (coincidentally?) in the same issue of JAMA.

Looking at thre general medical journals, Abhaya Kulkarni at the Hospital for Sick Children in Toronto (shout out to my friend Ricardipus) and co. found that three different ways of counting citations come up with three very different numbers.

Cutting to the chase, Web of Science counted about 20% fewer citations than Scopus or Google Scholar. The reasons for this are not totally clear, but are probably due to the latter two being of wider scope (no pun intended). Scopus, for example, looks at ~15,000 journals compared with Web of Science’s ten thousand. Why? The authors say that Web of Science ’emphasized the quality of its content coverage’: which in English means it doesn’t look at non-English publications, or those from outside the US and (possibly) Europe, or other citation sources such as books and conference proceedings. And that’s before we even start thinking about minimal citable units; or non-citable outputs; or whether blogs should count as one-fiftieth of a peer-reviewed paper.

Presumably some of the discrepancy is due to removal of self-cites, which strikes me as being just as unfair: my own output shouldn’t count for less simply because I’m building on it. It’s also difficult to know how to deal with the mobility of sciences: do you only look at the last author? or the first? I don’t know how you make that one work at all, to be honest.

That aside, I think curation of citation metrics is necessary: Kulkarni et al. report that fully two percent of citations in Google Scholar didn’t, actually, cite what they claimed to. That is a worrying statistic when you realize that people’s jobs are on the line. You have to get this right, guys.

But it’d be nice if we could all agree on the numbers to start with.

Read the rest of this entry »

Posted in Indicators, Journals, Literature, Metrics | Tagged: , , , , , | 3 Comments »

Thanks for the intro

Posted by stevepog on 8 September, 2009

As mentioned, I’m the new PR Manager at f1000 and will working on some exciting promotions for the website and the company in general. To give some background, I shifted over from Australia last August and did a short stint in the wilds of local council in Dagenham before a much more interesting senior press officer job at the Medical Research Council.

My  PR history is relatively short, just under three years, owing to finding it difficult to leave my previous  career in journalism (eight years across general news and sports writing in Victoria and the Northern Territory). I occasionally miss the buzz of putting newspapers together but also love the medical research/publishing PR caper as well.

@biggerpills tweeted that PR people should shout, not whisper, which I’m in agreement with when the story warrants. PR often gets a bad rap from those who relate it solely to political spin doctoring or the stereotypical movie/music celebrity publicity reps. Like good journalists, good PROs know the stories that need to be told and do their best to get the message out there. And when it relates to news on medical advances that could save lives, the story seems well worth telling.

Feel free to get in touch if you want more news on f1000, I’m at steve dot pogonowski at f1000 dot com. I’ll be filtering any messages with keywords such as ‘Ashes victory’ straight to junk mailbox (sorry, still in denial).

—SteveP

Posted in f1000, Meta | Comments Off on Thanks for the intro