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.

It was nearly a month ago that David Attenborough and I went to see a preview of the Jon Amiel film Creation.

Well, I say that, but there were 398 other people there too. And I didn’t actually get to meet Attenborough. Or even see him. But we were in the same room. I say ‘room’, but I mean the Science Museum. He touched Karen James’ shoulder! And she’s my friend, so that counts. Doesn’t it?

Where was I? Oh yes. Heroes. David Attenborough is a hero to many. On the other hand, Charles Darwin has been turned into a saint. I’ve reviewed the movie elsewhere. These are some thoughts that didn’t quite make it there.

Philip Campbell welcomed us to the IMAX theatre at the Science Museum, telling us that Nature is a magazine as well as a journal; the narrative is as important as the science. (There may have been a small cheer from the LabLit representatives at this point.) After welcoming various luminaries (the producer Jeremy Thomas, screenwriter John Collee and Toby Jones—who played Thomas Huxley), he introduced the director John Amiel.

“This place is so cool!” Amiel said, before apologizing that the film was in 35 mm and not IMAX. He played on the narrative theme again, explaining but not apologizing for the liberties taken with objective reality: He made the point that a ‘true’ dramatization would have to spend eight years studying barnacles: ’I’m not going to say, guys it’s only a movie: get a life.’

The film we were about to see was an imaginative rather than a literal truth, dealing with the spirit of Charles Darwin: man and scientist, because his ‘life and science were one piece’. I don’t know if it was intended, but I saw him drawing direct parallels with the Biblical account of creation. Truth in spirit if not in literal fact.

Nature selects for survival; man for appearance

The film was a feast of visual elements and hidden meaning. The (fictionalized) account of Jemmy Button and the del Fuegians; the bad science (or medicine, rather) juxtaposed with the bad theology; Jenny the orangutan; the process of decay, Huxley’s bullying and the balance of nature with a fox and a stunt rabbit. The opening scene of the movie, with the finger of Charles reminding us forcefully of the finger of Michelangelo’s God. (And I would have cheerfully held Darwin’s coat while he thumped the vicar—or performed harm bodily and grievous myself.)

We would do well not to idolize our scientific heroes. Darwin himself tells the doctor that ‘logic isn’t everything’—and tries to make a childish bargain with God for the life of Annie. All great scientific advances are made by human beings, heir to the same heartache and thousand natural shocks as all flesh: and the message of Creation is that this, not our idealized notions, is true cause for celebration.

So there I was, desperately trying to get on top of my nuclear inbox (i.e. it had exceeded critical mass) when the head developer came up to me and says ‘Do we really need an evaluation of an 1866 paper, classed as a ’New Finding’?’

I knew immediately which paper he was talking about, because I’d blogged about it previously. But this conversation was in the context of our hush rankings, and we decided that a paper in an obscure journal from a century and a half ago really wasn’t going to affect matters that much.

When I got home I checked the f1000 blog to see if there’d been any activity. And there, in the referrer list, was the search term “ber verh königl-sächs ges wiss, lovén c”. The first hit for that phrase on google is the f1000 Biology entry for the paper in question, by Wilfrid Jänig of the Christian Albrechts University in Kiel. The second hit is my blog entry.

The paper by Christian Lovén, written in German, is exciting since it formulated for the first time, based on experiments conducted on rabbits, that blood vessels involved in regulation of arterial blood pressure (that is peripheral resistance) and cutaneous arteries are differentially regulated and, therefore, also innervated by different types of efferent neurons. This important conclusion anticipated that the sympathetic nervous system is differentially organized according to the target organs.

Now, it’s possible that Phil searched for the journal, which means it’s not coincidence at all. And if I were Ben Goldacre I’d now swear a lot and say how this is an example of something or other that leads to bad reporting or death in baby rats, you bastards, but I’m sure you’re all smart enough to figure it out yourself.

I’ll instead close by saying that my flickr account also gets some strange referrer search strings. My current favourite is Gee spot, which finds two of my Flickr pictures, here on NN.

You might be forgiven for thinking that Hogg was the only character in my high school chemistry class. Indeed, sometimes I was forced to make my own entertainment: such as the time I poured a glass of water over the housemistress’ head. From two floors up. Or set fire—but no. I’ll leave that one for later.

High school physics experiment

There was, in fact, a whole regiment of patsies that could be relied upon to relieve the routine of studying for ‘O’ Level. And some of them managed to do it from behind a wall or two…

One fine day we traipsed into the chemistry lab to be given a list of instructions, complete with boxes for us to write down our observations. It was meant to be some sort of test; and just so that there could be no cheating, the other top chemistry set was sitting it simultaneously.

The first task was to take a set amount of chalk, and heat it over a bunsen. Then we were to let the powder cool, weigh that, then transfer it to a watchglass and add water. Finally we had to measure the pH of the suspension and figure out what just happened. Something like that, anyway.

We had instructions. Clear and and detailed instructions. We heated up the chalk. We (eventually) transferred the resulting powder to watch glass. We read the bit where the instructions said ‘holding it in your hand, add three drops of water’. And because we were doing this (all forty or so of us between two classes) simultaneously, the scream came at the precise moment we were dripping water onto the innocuous-looking powder in a watchglass.

Because some berk next door (and I know who it was was but I’m not going to embarrass him, on the off-chance he might track me down after 25 years) had taken the instructions too literally: tipped the powder directly into his hand and added water to that. The exothermic reaction alone must have hurt; the alkali burning a hole in his hand did the rest.

CaO (s) + H₂O (l) ⇔ Ca(OH)₂ (aq) (ΔH_r = −63.7 kJ mol^-1)

Can you tell what it is, yet?

These mornings, my alarm runs ahead of the Earth turning to bring the sun above the Thames; and the sky is already dark by the time I emerge from the Tube in the evening. There is a smoky, leafy scent to the air; hazelnuts litter the paths and I shoof through the drying leaves of red-haired Autumn.

This weekend is my church’s harvest festival. We’re having a shared lunch after the service: unfortunately I think that my vision of long oaken tables and marrows and carrots and whole roast pigs and raucous singing and lusty young wenches serving foaming mead Ed: does mead foam? Please check from pewter mugs is likely to remain unfulfilled. It does, however, remind me that back in May and June, when the year in bright blues and greens danced to an altogether less sombre tune, I set to my own little garden and tried to defend it against the Axis of Gastropod.

You might remember that I used coffee grounds to keep the slugs and snails at bay, much to Jenny’s amusement. And I remember that I never reported back on the long term effects of that experiment. So, the coffee grounds did keep the little bastards away, although I am not tempted to use that method routinely in future, for two reasons.

First, the power of coffee waned rather quickly, meaning that I had to replenish the Maginot Line every week or so. Although it was tiresome, this wasn’t a major problem because we managed to persuade Kate’s lab to give us all their coffee grounds. More worryingly however, I think the coffee was actually poisoning my runner beans. And as they were the plants I wanted to protect, this was rather self-defeating.

How do I know the coffee was poisoning the beans? I don’t have direct evidence, but my plants were rather pale, spindly things (and one just upped and died), until I stopped giving them coffee (maybe they couldn’t sleep?). Then, from the top down, they started to go a darker green, and indeed flourished (although still behind everyone else I knew who grew runner beans this year). Next year, I’m considering protecting some plants with coffee and others with metaldehyde, to see if it really does make a difference.

Beans

You see? I’m still thinking about experiments.

When I came over from Australia, I spent a bit of time with my parents in Lincoln. There I helped my mother (her of Chilean Potato tree fame) dig the allotment and plant several rows of seed potatoes, aided by my young assistant, Sophie.

Sophie

Much to Sophie’s delight we’ve been eating some of those potatoes for a month, now, and there’s no end in sight (which is good, because the few I planted here won’t keep us in wedgies for very long). But more excitingly, the tomato seedlings my mother gave me did rather well. ‘Excitingly’, because for three bloody years in Sydney I had no luck at all with them.

Tomatoes doing well

I also scored some cucumbers from up North. And this isn’t scientific at all, but I thought it was pretty:

Cucumber