“Scientific publishing is not primarily about communication. It’s a way of keeping score.”

Discuss.

Over on another planet blog Darren Saunders asks what is an Associate Faculty Member (AFM).

There was some sales training on this subject last week and I sat in, so I should know. I’ve also been re-writing the FAQs for the new f1000 website and have just realized that there isn’t an FAQ relating to AFMs there, either. (Meta: how many times does a question have to be asked before it becomes ‘frequent’?) So, let’s have a stab at explaining it.

As you may or may not know, what Faculty of 1000 does is publish short reviews of the scientific (currently biology and medicine) literature. How this works is through our eponymous Faculty of over 5000 top scientists and medics, all over the world. These people are principle investigator level or higher. When they read a paper that they consider interesting, important, or otherwise worthy of wider recognition they write a review (or ‘evaluation’), assign a score (or rating) to the original article, and submit it to our editorial team (usually via a web interface). The piece is then edited in the usual way, coded to appropriate sections (i.e. sub-disciplines), and published on the website at f1000biology.com or f1000medicine.com, depending on the specialty of the contributing Faculty Member.

This system has been pretty successful for a few years now, and we know that people really like the service (because they tell us!). It lets scientists and medics see very quickly what’s happening in their own field, and rapidly get at what’s considered important in other communities (whether simply out of interest or because they’re moving into unfamiliar territory). Identifying important papers quickly and easily gauging the opinion of a field easily are not trivial tasks: f1000 is intended to help everyone, from students through to vice-chancellors, achieve this.

Critically, choice of articles to review is left entirely to the Faculty, and may come from any journal. Any journal: even the Harvard Business Review. Naturally there are a high proportion of articles from the usual suspects—Nature, Cell, NEJM, etc.—although about 80% come from ‘second tier’ or less popular journals (he says, desparately avoiding the ‘I’ word).You might expect this, seeing as certain journals review editorially before a paper goes anywhere near peer review, and actually are quite successful at it.

In a sense, we don’t care about the providence of the articles reviewed at f1000. If they’re good, we want to know (and ‘good’ means 1-2% of the current eligible literature). However, there are a lot of journals publishing good stuff, and how do we know we’re scanning the right ones if we’re just leaving it to serendipitous reading by the Faculty?

Enter the Associate Faculty. Currently about a thousand Faculty Members have one or more Associates: less senior members of their lab or practice (which can mean anything from a post-doc to a PI in their own right). Once a month we send these Associates a table of contents from two journals: one general, one ‘specific’; both self-nominated. The Associate checks the table against their own reading, and selects articles that they have already read that they will review. They also let us know if there are any articles that they think should be reviewed but that they will not do themselves: these then go into a ‘pot’ which we send (a couple of weeks later) to Associates who haven’t committed to producing a review that month.

When the Associate commits to reviewing an article, it’s pretty much between them and their Faculty Member as to how it’s handled. Sometimes the Associate will do the bulk of the writing, other times the Faculty Member will. In either case, the full Faculty Member has to approve the evaluation and has final say—they are the corresponding author.

We cover, at the last count, about 660 journals in this fashion. We’ve asked the Faculty to tell us what journals they think should be scanned in this scheme, and eventually we’ll be covering over a thousand different journals. This does not mean that we won’t be evaluating articles outwith this ‘core’ of journals: Faculty Members have complete freedom to evaluate papers regardless of where they are published. Our Associate Faculty help them identify the good stuff, and we help them to choose by providing the tables of content with a selection system (somewhat arcane, but we are working on it). The buzzphrase is ‘systematic and comprehensive’: we’re certainly systematic and are working on the comprehensive.

Hope that clears some things up for Darren.

In the day job I am responsible for getting a website relaunched. Part of this involves looking at what other people are doing and stealing ideas. Part of that involves usability testing and making sure stuff just works. Another part, and one I hope to develop once the site is launched, involves taking our information and, well, architecting it.

One of our sales team asked a question this morning, which I thought would be easily answered using the venerable PubMed website and comparing their answers with our own data. So off I toddled, and spent a few minutes getting really frustrated with their new site.

Don’t get me wrong: I love PubMed; I always have, ever since we moved from SilverPlatter. But this is putting a real strain on our relationship: where is the ‘advanced search’?

Spot the difference

I finally tried it in a different browser

Oh, man. The NCBI budget dwarfs ours, and nobody thought to check that?

Does anyone else find it odd, that of all the opportunities the British have to let off fireworks outside the usual New Year shindig, we choose to celebrate the time someone tried (and failed) to blow up Parliament?

The Shackledraggers celebrate Australia Day, the French Bastille Day, and the Americans Independence Day (sensibly, these latter two are in July, far enough away from New Year/Christmas to make it time for a knees-up).

In a bar in Charleston last week, a colleague and myself were discussing this matter with Pete Binfield of PLoS. When should we have a national holiday in the UK? We do, already, celebrate May Day more than the Americans, but maybe we should also declare 4th July a public holiday. It could be argued that both nations started to grow up then. Perhaps 23rd April? But not only is that English, what does some Turkish cove who went around slaughtering harmless wildlife have to do with anything?

We’ve never declared independence from anyone, although 14th October is a good candidate for the English nation, at least. January 1st is already taken up with New Year and is too close to Christmas. September 3rd, perhaps, when we finally woke up and did something? But it seems odd to celebrate the outbreak of a war, and celebrating VE Day might be in bad taste: similarly 18th June or 21st October (while it’s fun to annoy the French, this might be taking it too far). September 3rd also celebrates the end of the English civil war.

Similarly, anything marking a political anniversary is right out. Perhaps we should celebrate Sir Winston Churchill’s birthday? But again, too close to Christmas and New Year.

Maybe the first time the Kingdom was first joined? That would be 1st May, but we already dance around Maypoles and throw tomatoes at men in white shirts and wearing bells that day (as well as get busy with any fair young wenches who happen to be at hand… hmm. Potential). It also excludes Ireland.

The first date we dismissed last Wednesday night is, on reflection, possibly the best candidate of all. It is already the ‘National Day’ in our diplomatic missions, and civil servants (including everyone who is paid by one of our Research Councils!) get a ‘privilege day’. Let’s extend it to everyone else: the Queen’s Birthday. After all, apart from trying to blow up our politicians, there’s nothing more peculiarly British than our monarchy.

Huzzah, and pass the rockets.

oooh

aaah

(Next blog post I might actually consider some science: that behind gunpowder, naturally.)

I’m sitting in a hotel in Charleston SC, in a somewhat uncomfortable armchair, MacBook on lap and cursing the dodgy wireless signal in this place. Looking around, lots of people seem to be having similar problems. I’ve forgotten my adaptor so I’m hoping that my hung-over colleague makes it in with the work laptop.

It’s around 72°F outside and it hurts to look at the pavement sidewalk through the hotel window; my boots and winter trousers are definitely not suitable.

I’ll talk more about the conference some other time, but rather than go through my presentation again (I hate over-rehearsing) I’m going to tell you the long-promised story of how I nearly burned down the chemistry lab at school, assuming I get enough connectivity to upload it.

You might presume I was a keen student. Indeed, my imagination was limited only by limited access to necessary reagents and school safety policy (although when I did my A Levels I managed to—but no, that’s another story). So when Mr Woods performed a demonstration of something that didn’t blow up or burn holes in hands or set fire to massive amounts of paper, I thought this was my chance to have a little play.

Take, if you will, one open-ended glass cylinder about two inches in diameter. Place a square of wire gauze in one end and push it up a little way. Clamp the arrangement over a Bunsen burner. Ignite the Bunsen, allow the gauze to start glowing, then remove the heat. 

Listen

This simple set-up results in an organ-like descending tone, full and rich and reasonably loud. (Why this was in a Chemistry lesson and not Physics yet escapes me.)

I turned to Allan Jones and said, ’Let’s come back at lunchtime and see how loud a sound we can make.’ He agreed, so we approached the teacher after the class ended and put our proposal to him. He readily agreed to find the largest cylinder he could, and have it ready for us.

An hour or two later we had wolfed down our lunch, and hot-footed to the sixth floor of the Science block. Woods was waiting for us, with a cylinder about six feet long and six inches diameter.

Made of cardboard.

‘You are having a laugh. Sir.’ 

‘No,’ he told us, ’it’s compressed cardboard that they ship glassware in. It won’t burn.’

‘Fair enough,’ we said, ‘hand over the kit.’

So he went off for lunch and we were left alone in the Chemistry lab with a huge cardboard tube, clamps, a box of metal gauzes and an endless supply of natural gas. And matches.

We clamped the tube between two retorts on the front bench, stuck the largest piece of gauze we could find up inside the tube, and lit a Bunsen under it. After a minute or two we guessed that the wire might be hot enough by now, and removed the burner.

Nothing.

Not an issue, we said, we’re obviously not getting the gauze hot enough. A problem solved by the application of scientific thought, and a second Bunsen. We repeated the experiment with this minor modification. Again, after a couple of minutes we removed the heat.

There was a rich, deep, loud tone. It went sort of

bwooooPHUMP

As one, we looked up. smoke billowed from the top of the tube. Faster than you could say ‘nucleophilic substitution’ I had vaulted the teacher’s bench, wrested the fire extinguisher from the wall and was climbing on the bench with the chimney, pointing the extinguisher down the hole from the top.

I squeezed the trigger.

Allan screamed.

I squeezed the trigger again, and looked down.

Flames licked round my feet and trouser leg: this was the same extinguisher Woods had used a couple of weeks previously to put out the fire in the wastebasket… and replaced without recharging. The compressed air in the extinguisher was having exactly the opposite effect as I’d intended.

I leapt off the bench, flinging the worse-than-useless extinguisher towards my friend, and sprinted to the next lab. There was no extinguisher there at all. I ran into the third and final lab on that floor, grabbed the extinguisher and pelted back into our room, which was rapidly filling with smoke. I scrambled up onto the bench, pointed the extinguisher into the top of the very flammable indeed cardboard tube, and squeezed the trigger.

The tube broke free of the retorts and tumbled to the floor. I jumped down, squirted again and the tube shot across the lab’s floor like an off-course Saturn V. Through my laughter, I managed to make Allan understand that I needed him to stand on the tube, and we got the fire under control.

‘Open a window, Jones.’

We coughed our way to the exit, just as the end of lunch bell rang. Mr Woods was coming up the stairs.

‘We had a slight fire, Sir,’ I said, ‘but it’s out now. The class is a little bit smoky, though.’

‘Oh, don’t worry about that,’ he said as he pushed open the door.

We ran.

I’ve allegedly been on holiday this week. It was enforced: not only is it half term and the Pawns require a bit of childcare, I also found myself with rather a lot of annual leave that I have to use up, or lose, before the end of the year. Just before we go beta, too. Of course, I haven’t actually been able to treat it as a holiday, what with certain things too boring to go into here, so I think I’ll have to have another holiday real soon now. I have one day in the office next week and then I’m off to Charleston to speak at a conference, and back as soon as I get off the podium so I don’t miss too much of the Younger Pawn’s birthday celebrations.

Karen gets peer-reviewed

Despite various things that I really could have done without, alluded to above, I was able to take the Pawns into the Natural History Museum on Tuesday, there to meet with the incomparable Dr James of Beagle Project fame. Karen took us backstage, to gasps of awe and astonishment.

In a pickle

Sophie enjoyed the Tank Room, and loved the Cocoon, so we went back again today. As it’s half term, and it was totally packed out on Tuesday, we planned to get there just after opening time today. This tactic paid off, and we were able to walk straight into the Cocoon without tickets. (They have this really neat system where you get a card with a bar code and when you get home, you can enter a unique code and access more information about the things you were interested in while you were there, thanks to the awesome power of the internets.)

One big egg

One of the things that is not immediately apparent about the NHM, and something that sets it aside from a lot of other collections of things in London and around the world, is that it is a research museum. Karen told us that there are ~350 scientists working at the NHM, in five departments. With over 70 million specimens, they should be kept busy.

There’s another 69,999,999 to see

Strangely, for the first time since leaving the lab, I got a slight pang about bench science. It must have been the videos of scientists talking about phylogenetics and the pictures of Gilsons. I stood back and watched other people, and was amazed by the number of mothers, in particular (don’t ask me where the dads were) telling their charges about the science being done there. It gave me quite a thrill to hear ordinary people, in a public place, use words like ‘DNA’ in cold blood.

And yet… in the main part of the Museum, the displays are incredibly old-fashioned. Plastic models in the Human Biology section, strangely Victorian exhibits in the Arthropod room. I guess there’s only so much you can do with stuff that doesn’t move, but the Darwin Centre at least is a step along the evolutionary ladder.

What it’s all about

(More photos on Flickr)

Published literature is not free. To be more precise, the process of turning your treasured manuscript from a Word document (LaTeX nerds can shut up right now) through peer review, editing, XML-ification, whatever, to what you hold in your hand or see on your screen costs money.

Even if the peer review process is performed by volunteers, someone has to spend time deciding to whom your manuscript is going to be sent; chasing the reviewers and collating the reports. Not to mention the organization that has to exist, the necessary infrastructure.

Online-only journals obviously have (effectively) zero marginal costs, but the overheads are significant: storage and high speed ‘net access still don’t come cheap, and you probably want to pay a database manager and someone—several someones—to look after the website. And that is in addition to actually making manuscripts readable (have you seen the preprints, or the ‘accepted for publication’ stuff that some journals do? Double-spaced, unformatted references—and don’t even dream of hyperlinks—and all the figures at the end of the document, disparate from the legends).

So. Literature, even stuff that’s only half-usable, costs money—or someone’s time, which boils down to the same thing. I’m banging on about it because in much of the Open Access debate this simple but critical fact is often over-looked. The wild-eyed prophets want it all to be free, without realizing that this can not happen (at least, absenting a Star Trek economy).

Taking that as a given, the whole of Open Access hinges on a simple question: who’s going to pay for it?

The traditional publishing model says that you pay for the literature at point of use. In other words, reader pays. And, you know, that’s really not such a bad thing, is it? I buy milk and I expect to pay for it. You want the literature, you pay for it. But maybe that’s a bad example: milk is a commodity and it perhaps can be argued that scientific knowledge isn’t, or shouldn’t be. For the sake of argument, let us concede that scientific knowledge, for whatever reason, shouldn’t be commoditized.

But even if we do that, even if we don’t take publishers’ moral obligation to their shareholders into account, we still come up against the cost of production. Money has to change hands somewhere. So let’s say that the producers of the literature pay for it. Now, this is a little like saying the farmers should pay (net) to get their milk to us. Isn’t it? Well, maybe it is, maybe it isn’t: let’s assume, again for the sake of argument, that we want milk to be free at the point of use. Maybe we want to get it to poor people, or to somewhere remote (like Birmingham), so we have to subsidize delivery.

Or, just maybe, someone like the government decides that it is good for us to get ‘free’ milk. Except nothing, neither milk nor literature, is free.

In the UK, you don’t pay for healthcare at point of use—unless you really want to. You don’t pay for education (below tertiary level) at point of use—again, unless you really want to. It has not escaped my notice that the Left-Pondians are currently having a debate, largely along party political lines, about State-sponsored healthcare. Some say that you should pay for your own healthcare. Some say that if you get sick you should be able to get treatment without worrying about payment. Some of those in the first group pay for insurance and get really pissy at the thought of subsidizing, through taxes, the layabouts (and Democrat-supporters) who don’t have their own insurance.

Isn’t that the model of ‘author-pays’ Open Access? The Haves, effectively, pay for themselves and the Have-Nots. I pay my taxes, and when you get sick you get cared for. In return, you pay your taxes and I get treatment—and so do those who can’t afford it themselves. I produce the science, I write it up, and I pay for everyone to be able to read it. In return, I get to read what you’ve paid to publish; along with everyone in Birmingham.

It’s socialism, really. But please don’t think any scientific publishing model is going to come at zero monetary cost: we all know how well Communism worked out.

Just how annoying is Luke Skywalker? Man, I’d like to fetch him one across the self-righteous chops. And this whole rebellion schtick? Just what’s going on there? I mean, you’ve got a galaxy with peace and order and what seems to be thriving economies on planets with no apparent means of support or trading advantages; different races, hell, different species seem to be able to mix and get on with each other—and the crime that does occur seems to be various lowlifes working it out between themselves. So a bunch of crazy mixed-up kids decide to start blowing things up, it’s hardly any wonder the government’s going to get a little bit pissed off.

I sat with the Younger Pawn on my knee as we watched yet another ludicrous light-fight, saying things like ‘No Sophie, I am your father’ and ‘it is your den sity’.

We suddenly realized that I am Darth Vader, and you can work out the implications for yourself. Just to help you, here’s a typical day in the office:

SCENE 4 INT SCIENCE NAVIGATION GROUP – RECEPTION

The f1000 Chief Editor, Merkin Jeremy, a tall, confident technocrat,
strides through the assembled coders to the base of the north elevator.
The coders snap to attention; many are uneasy about the new arrival.
But the f1000 editor stands arrogantly tall.

The door of the elevator opens with a WHOOSH, revealing only
darkness. Then, heavy FOOTSTEPS AND MECHANICAL BREATHING. From this
black void appears rpg, Information Architect. rpg looks over the
assemblage as he walks down the ramp.

Merkin Jeremy: rpg, this is an unexpected pleasure. We’re honored by your presence.

Information Architect: You may dispense with the pleasantries, Editor. I’m here to put you back on schedule.

The editor turns ashen and begins to shake.

MJ: I assure you, rpg, the developers are working as fast as they can.

IA: Perhaps I can find new ways to motivate them.

MJ: I tell you, this website will be in beta as planned.

IA: The Chairman does not share your optimistic appraisal of the situation.

MJ: But he asks the impossible. I need more pizza.

IA: Then perhaps you can tell him when he arrives.

MJ (aghast): The Chairman’s coming here?

IA: That is correct, Editor. And he is most displeased with your apparent lack of XML.

MJ: We shall double our efforts.

IA: I hope so, Editor, for your sake. The Chairman is not as forgiving as I am.

LATER

Chairman: As you can see, my young apprentice, Elsevier has failed. Now
witness the XML of this fully beta-tested and operational website.

into comlink
Publish at will, Editor.

It’s going to be a long, hard week.

Not long ago I was talking about Twitter, and how it seems to have grown up. I said that it’s no longer about telling people what you had for breakfast, but has turned into a meaningful communication tool.

Web 3.0, Thursday

In a similar vein, I was at a conference on Thursday and Friday, the Internet Librarian International. Because my company was a sponsor, we got a speaking slot, and I was the one who stepped up to the plate. Now, the organizers had asked us, even though we were sponsors, not to do too much of the corporate hard sell. This was fine by me, and I planned to give a typical rpg ramble.

As it turns out, I got a fair bit of positive reaction from the organizers and other people: the other sponsors did talk about themselves, and I only mentioned what we are doing in passing. I was also far more interesting than the guy I shared a session with (which wouldn’t have been difficult).

So, Twitter. Last year at the blogging conference, we used Friendfeed to comment on the sessions as they were happening (sorry, Eva). This year we used Twitter, and if you’re anything like a regular twit(terer) you’ll notice hashtags from conferences popping up all over the shop. Twitter is the new Friendfeed, at least when it comes to conferences.

ILI 2009 was no different (even if there was a plethora of hashtags —although given our experience of the organization I’m not surprised). The beauty of Twitter is not in the execrable interfaces for it, but in the search mechanisms that exist. It’s easy to twitter, and it’s even easier to stick the search terms for a particular topic into an RSS feed and keep up to date—or even to go back a few days later and see what was said about your own talk.

Almost Web 3.0. Almost.

And then, while I was sat with Tom (our sales bloke) at lunchtime yesterday, merrily twittering on my iPhone*, he asked me whether anyone was paying attention to the talks or if we weren’t all just too busy twittering. Then it struck me, just as that famous study (which I can’t be arsed to go and look up right now) showed that doodlers can recall more of seminars than non-doodlers, so twitterers probably pay more attention than those who don’t (and certainly more than those who are simply checking email). See, if you’re twittering about the talk, you are almost by definition paying attention. Even you you have to multi-task to do so. For me, at least, I have never felt the slow creep of the heavy eyelids while I have been tweeting and reading tweets in a talk.

Maybe we should make it compulsory.

rpg, Thursday

I’d be interested to hear what other people think about this. Do you think that Twitter could actually take the place of conference notes, for example? Do you go back and check tweets post hoc to remind you of what was said? Are hashtags and search the ultimate in conference evolution? Most importantly, does Twitter keep you awake in conferences?

(And I’ll post a link to the YouTube vids once the carrier pigeons have made it from Sarf of the Riva.)

I’ve got to give a talk tomorrow.

In the best traditions of scientific conferencing the abstract submitted a month ago bears little relationship to what I’m actually going to say. (And in that tradition: What am I going to say? It’s only because I had to upload some slides to their server this afternoon that I even have my slides ready.)

But in recognition that I’m now Mr Dr Corporate, and that I’ll be addressing internet librarians internationale, I’ve decided against wearing my Levi’s with the RM Williams. I’ll still wear the boots, but smart trousers instead of jeans. By the way, don’t buy RM Williams boots if you can avoid it. They look good, but the build quality is surprisingly disappointing. I think they’re designed for riding dingoes around all day and shooting kangaroos, rather than walking to walk.

Where was I? Oh yes.

Talks given from the corporate side of the fence are subtly difference from those you might give as an academic, when you describe your research. For starters, unless you’re giving a terribly boring presentation on sales or ROIs or whatever, you can just make shit up have quite a bit of freedom in how you present, and indeed what you’re presenting. Your standard scientific talk takes a problem, gives you some background, describes what you did to answer the problem, shows some data and presents your conclusion (which is usually ‘it didn’t work’ or ‘we need to do more experiments’, or most frequently ‘give me a job. Please’).

I don’t have materials, methods, data or conclusions. I’ve got an interesting problem, sure, but it’s more ‘oh, here’s a fly-infested ointment; what’s being done about it and how might we tackle it?‘. It’s not ‘gizza job’, nor even ‘buy our product’, actually.

I’m looking forward to it. Even if I have to dress a little smarter than usual.

Now, there are principles that apply equally to academic and corporate talks, such as the ‘10-20-30’ rule, the ’don’t talk to the screen’ rule and the ‘my God but Powerpoint is complete crap, isn’t it?’ rule. But I was reminded of one rule in particular a couple of days ago, when I received a really lovely Facebook message from a student back in Sydney.

Nurse Donovan said,

RPG you have left a lasting mark on me:

Once at mmb you came and looked over my shoulder at the slides i was making for my lab talk, and you said “the title of your slide should always be the conclusion of the slide”.

And I have never been able to forget it!

That’s not to say that all my slides now have great punchy all-conclusive titles, but it means that now when i make a slide that has some sort of an airy-fairy title or (slide-god forbid) an ellipsis, i feel this nagging sense of guilt…

Just thought i’d share that with you because i’m making some slides right now and there you were haunting me again!

Hope you’re great!

Isn’t that totally brilliant? I may be gone, but my smell influence lingers on.

And tomorrow, I’m going to totally break my own rule. Rather than show each slide with a conclusion, episodic-like, I’m going to continue something I started experimenting with in Sydney, and managed to pull off in Nantwich. That is, I’m going to stand there and tell a story, and going to use the slides behind me to illustrate what I’m saying, rather than being the focus.

I’m going to tell a story. With pictures.