On taking a good look at ourselves

Cross-posted from Naturally Selected for added controversy.

Perhaps the most distinctive and powerful thing about Science is its tendency, or rather proclivity to ask searching, even uncomfortable questions. And unlike belief systems, or ideological and political and movements, or pseudoscience, it asks those questions of itself. There’s been a fair bit of that going on recently.

An article in the New Yorker looked at the puzzling phenomenon, as yet unnamed, of seemingly solid observations becoming less reproducible over time. This article received two evaluations on F1000 (here and here), and sparked a lively discussion over at Naturally Selected (= the day job, for those who don’t know).

The New York Times reported on a paper in the 4 January issue of the Annals of Internal Medicine, which claims published clinical trials don’t cite previous trials. Now, there might be trivial explanations for that, but in the same vein Sir Iain Chalmers, editor of the James Lind Library, has some harsh words for scientists. He says there are fundamental and systemic things wrong with the way research, particularly clinical research, is done today.


It’s certainly misconduct

Among these, he accuses (some) researchers of not addressing questions that are not of interest to patients and clinicians, of failing to contextualize new findings, and being clear about what they’ve actually discovered. He also takes aim at the failure of scientists to publish negative or ‘disappointing’ results. In Ann Intern Med* last year there was a paper, recently evaluated at Faculty of 1000, scrutinizing the reliability of and inherent bias in clinical trials. And today, Nature published a Correspondence arguing that it’s critical to publish negative results.

Interesting times. Are the criticisms Sir Iain makes fair? If so, is this fault of the scientists themselves or the system in which they find themselves working? If the latter, how can it be changed? What about publishing negative results, and reproducibility and publication bias?

Are we questioning Science enough?

Continue reading

Posted in F1000, Politics | Tagged , , , , , | 21 Comments

On peer review and trials by Twitter

(Edited to add: just three seconds after hitting ‘publish’ I saw that Girl, Interrupting, has a very fine post making some of the same points. Please read that, too.)

Towards the end of last year, the day job ran an issue on the subject of peer review, very much taking the line that it’s in crisis, that it’s not the best way to do things, yadda-yadda.

That put me in a bit of an uncomfortable position because I didn’t agree at all with the message coming out. It didn’t help matters that we started getting comments along the lines of “You would say that, because you’re now a shill for Faculty of 1000 and they hate peer review too.” But although that is not necessarily true I couldn’t write about it at Naturally Selected, because it would start to look like the Battle of Marston Moor (for my American cousins, think Gettysburg.)

So I kept my head down.

Until Thursday, when Nature published a News Feature looking at peer review and ‘social media’ in the context some high profile controversial papers, Peer review: Trial by Twitter. Various colleagues emailed the story to me (which isn’t in itself all that exciting) because of the criticisms of F1000 that were contained therein. In return I wrote a typically robust response. In brief, I showed how those criticisms were wide of the mark, and I was fuming at the unattributed ‘critics note that F1000 rankings…’ line. (I think I know where this was sourced now, and the stats in the paper are—according to my own source—crap.)

Anyway. There are two real issues here: first, is peer review really in crisis? Second, is the use of ‘social media’ tools damaging to science? (I don’t really care if individual scientists get upset—more on that in a bit.)

As I hinted above, I really don’t think peer review is in crisis (£: letter from Tim Vines et al.), and neither do I agree with Cameron that we should publish everything and let the market decide. The sheer volume of papers makes such a model unworkable (we’re already looking at around 1 million papers yearly in medicine and biology), and even if you could solve the search/filter problem in terms of identifying what you’re looking for, with no barrier to publication how the hell do you flag the crazies, the lazy and the simply inexperienced? Having experienced the full gamut of peer review, from having a manuscript accepted without revision, through having one improved by review, all the way to chasing around for two years to get something published, I’m approaching this without an axe to grind.

Look at it another way: you can already publish your manuscript, open access, with no peer review (or editing, come to that). It’s as easy as typing a blog post. Why aren’t people flocking to do this, if it’s the way forward? Because peer review is the standard supported by the vast majority of practising scientists, and they recognize the value in it. And don’t say to me that the grant funders won’t stand for it: there are plenty of scientists who don’t depend on competitive grants.

I’m not denying there are problems with the current system. The whole anonymity/open review argument is not settled, not by a long chalk. There will be the vindictive and the inexperienced in any human endeavour. Peer review is often deemed—especially by the media and the loons (coughhomeopathscough)—to be a mark of correctness. And we all know it’s not—it’s not even a quality control stamp. Peer review says (or should say) that the work in question, as far as we can tell, has been done correctly, the appropriate controls/stats/ethical approval have been included, and the right literature has been cited. Anything more than that is an editorial decision (‘is this important/general enough for Nature?’ say).

So at F1000 we actually quite like the peer reviewed literature. I do, anyway. With a very few exceptions everything at F1000 has already been peer reviewed—so in a way F1000 does post-publication peer review lite. I started using the phrase ‘post-publication peer review’ in the context of F1000 a couple of years ago, without in any way meaning to imply we should do away with traditional peer review.

By the way, looking at the two examples of high-profile paperswith problems, you’ll notice that they, along with many, many others, are high-profile simply because they have been pimped shamelessly by various parties—the journal, the media, the press offices or even the scientists themselves. I fail to see how strict post-publication peer review will change that.

Moving on, you’ll notice I’m using scare quotes around ‘social media’. That’s because I thinks it’s a bit of shit phrase, to be honest. The internet has been social from the beginning. It started, for goodness’ sake, as bulletin boards and emails. What can be more ‘social’ than that? (As somebody on Facebook said the other day, asking what’s after social media is a bit like asking ‘what’s after porn?’)

Nothing has changed, really. I’ve stood up at big conferences and had to defend my work. I said in my blog post that getting trashed via twitter and whatnot is scary: well, it’s nothing compared with a couple hundred of the best brains in the field trying to pick holes in what you’ve just said. We’ve always, always taken papers apart in private, at conferences, over coffee: now we have the tools to make it happen even faster, and perhaps more importantly give instant feedback, good and bad, to the author.

Which can only be good, surely? Scientists might have to rethink how they respond (and do it faster), but if you don’t want to fight for your work, you shouldn’t be in the job in the first place.

Of course bad things happen on twitter. There’s a lot of noise, but a lot of really good stuff (and for a well-balanced view I commend to you David Kroll’s meta report on Scienceonline 2001) too. It’s what you make it.

And the bottom line is, none of this is going to affect how most of the lay public view science or its process. Most people aren’t on Twitter, and those that are don’t follow active scientists. They are going to get their information, as they always have done, from the media and from celebrities. More to the point, the vast majority of scientists don’t engage with what we are calling ‘social media’ (a highly unscientific straw poll of ~40 Wellcome Trust Fellows revealed one who used Twitter and four that read blogs).

So. This all makes for exciting news articles and opinionated pieces in blogs and whatnot, but frankly, I think it’s so much guff. Peer review will trundle on much as it has done for years, and whatever replaces Twitter will bring prognostications of doom and death and the end of civilization as we know it™, but nothing will change, not essentially, and scientists will continue doing totally awesome things.

It’ll keep editors happy, though.

Posted in F1000, Literature, Rants | Tagged , , , , | 21 Comments

Albatross

Here’s number two in the penguin series. You’ll note, please, that this was about ten years before Henry’s comment thread.

Let's go to work

Posted in Penguins | Tagged | 5 Comments

Razzmatazz

Hello folks at world!

Greetings from sunny North Carolina (yes, ‘sunny’), where men are real men, women are real women, and science bloggers come to pay homage to the blogfather. Yup, it’s Science Online 2011, where I am but one of a 14-strong British contingent.

The conference is only just underway, and this morning there are some tours of local attractions, so there’s not a lot to report yet. There was a storming keynote yesterday evening though, by Robert Krulwich, NPR’s Science Desk correspondent. He talked mainly about RadioLab, which was moving and inspiring, and as an added bonus Jenny and I chatted with him at breakfast this morning. A little Oberlin connection goes a long ways.

The hug from Henry to Bora has been passed on, and I’ve already caught up with Brian Malow and Joanne Manaster; we have been plotting. But the main business of the conference—for me, at least—is to shoot some video. As I said a couple of days ago, I’m going to be helping Jenny and Karen James interview working women scientists. So, if you’re at Scio11, and you see any of these:

camera and stuff

please nobble me and don’t let me go until you’ve been filmed.

Right, now off to see what’s happening. More later!

Posted in Scio11 | 8 Comments

Songbird

Because I was looking for something else, I was reminded of something very silly that I did in the MRC-LMB in Cambridge. Something that was a hit at the time (and we’re talking the year 2000) but has since disappeared into obscurity (and possibly the Wayback Machine).

A dusty trawl through the darker recesses of my hard drive revealed an archive I thought was lost forever. And why not?—I’m going to share them with you.

The story goes that there was a company that gave out squishy penguins (hello Eva?). The things marketing execs get up to. This was too good an opportunity for me to pass up. Here, then, is the first in a series of penguins in rather strange situations:

In Defence of the Realm

In Defence of the Realm

Posted in Penguins | Tagged | 13 Comments

On Popper

I have to say, I disagree with Jenny’s post, and I’m going to disprove the alternative hypothesis for eight minutes.

Disprove *this*, frat boy

Posted in Friday afternoon | Tagged , , , , | 5 Comments

On lucky breaks

I’ve been somewhat out of things for the last couple of weeks. I took some well-deserved vacation days and generally chilled out (even the presence of 350+ unread emails in my inbox when I got to work this morning didn’t spoil my mood) and even got away for a few days over New Year.

Fossil beach, Kilve

We met up with my parents and stayed in a cottage in Somerset, about a mile from the coast (and about 90 minutes drive from my favourite North Devon beach). We walked a bit, drank a bit, ate a lot. Had a really nice time, in fact.

Bamboo at Kilve

We discovered a bamboo field. I guess it has to grow somewhere, but I envisaged somewhere more tropical—to be fair, after the past few weeks the climate did feel positively balmy.

Jurassic beach

We walked on the beach, a new experience for five month-old Rosie, but one she seemed to enjoy.

Fossil beach

I marvelled at the revealed strata in the cliffs. I hypothesized that the rock underfoot was an ancient lava flow, and that countless long-dead sea creatures made up the layered slate above it, and that there must have been further volcanic flows followed by periods of relative calm (and dying sea creatures) in the 50+ million years of the Jurassic. I wondered what Henry would have made of it.

Lava flow

And, incredibly, just as I got down to the beach, I found a fossil.

Fossil -ve

‘Incredibly’, because I don’t find stuff like that. Not usually. The odd tuppence on the pavement maybe, but never something as awesomely cool as a creature that lived in the Jurassic. I picked it up, saying, “I’m having this.” I traced the outline of the fossil with my finger, realizing that it was rather the negative of a fossil; just an imprint in the rock.

Disappointed? Hardly. But as I looked around, I saw another fossil-bearing rock, lying not eighteen inches from the first. Picked it up. Traced the rock that once swam here. Turned it over and realized it fit the negative perfectly.

Fossil +ve

I thought about how the rock, as it fell from the cliff, had split in just the right place to reveal the fossil and its impression. Pondered that I was (probably) the first living being in 150 million years to see this creature.

Was—most likely—insufferably gobsmacked for the rest of the day.

Posted in Personal, Science, wibbling | Tagged , , , , , | 53 Comments

Merry Christmas

Christmas

All being well, I’ll be at Midnight Communion when this post goes live. It’s the first I’ve been to in a good number of years. It’s been a stressful time recently, what with one thing and another (getting this place live was, in a way, the least of my worries). I’ve barely managed to get cards off to family and my goddaughter. So if you haven’t heard from me, it’s nothing personal and hopefully I’ll get my act together next year.

In the meantime, a very merry Christmas to you all, and every blessing for 2011.

Santa hats

Posted in Personal, you | Tagged | 10 Comments