Confessions of a (former) Lab Rat

bq. just saw AVATAR… long and a bit boring in places but GODDAM AMAZING EFFECTS

says the Elder Pawn on her Facebook profile.

Which is a succinct review, if a little lacking in insight. But she’s right: I took the Pawns to see James Cameron’s latest oeuvre this afternoon, and it is a very long movie (subjectively at least) but made rather special through the clever use of 3-D. We’re not talking about red/green glasses here, either: these are (rather nerdish-looking) specs that I suspect are made of slightly differently polarized lenses, such that each eye sees a slightly different view and the brain interprets this as 3-D.

I spent not a little time taking the glasses on and off and squinting at the screen—the bits that are meant to be given depth are fuzzy when viewed without the glasses, but you can see perfectly normally with them on. Very neat. (And someone said, as we entered the theatre, ‘I wish the cinema itself was in 3-D!”. Um, yeah, we laughed at that.)

Enough technology. And enough of the politics: there are a few points I want to ponder later, but Abigail Nussbaum has already dumped a load of well-informed comment into her excellent blog. Let’s talk about the science (or the biology, anyway) a bit.

So I was reading somewhere else that the complete world that Cameron has built is one that is “intelligently designed” rather than evolved, because of the whole hexa/tetrapod thing they’ve got going on. Now, laying aside the fact that this is a goddammed movie, folks, and once you start talking about consistency of alien species you may as well pick up your Star Trek collection and go home, I’m not convinced by that argument anyway. It seems to me that the land-dwelling beasties could quite happily share a common ancestor; indeed, the sloth-thingies had a joint for the extra pair of legs three-quarters of the way up the front limbs, and it wouldn’t take much of a mutation to give animals an extra set of limbs. Hox genes, anyone?

What is more unbelievable is the presence of bipedal humanoid creatures that (apparently) breathe through their noses; where everything else on the planet breathes through their chests. (A much more sensible arrangement than the Terran, one would have thought). But as we all know this is simply a case of narrative imperative: if the dominant, intelligent aboriginal species was a six-legged herbivore then you’d have no chance of manipulating the sympathy of the audience.

Being able to grow a body and transfer one’s consciousness into it willy-nilly strikes me as a reasonably original concept. This of course isn’t the message of Avatar: that’s the rather naive and insulting one about ecology and nobel savages, which has been pretty much taken apart all over the shop. Even the ability to plug oneself into the brain of another animal has been done (Terry Pratchett, anyone? “I aten’t dead”?), although I did appreciate that this was possibly related to how the ‘avatar’ mechanism was supposed to work in the first place.

What was cool, and what actually flowed naturally from this concept rather than being a stonking great deus ex planeta, was the entire biosphere being some kind of interlinked super-organism. This wasn’t given to the credulous viewer as axiomatic; rather the idea of a mass of communicating nodes giving rise to intelligence—some flavour of deity, in fact—was compared with the fact that billions of synapses make up a functioning and above all conscious brain.

And this is where it was rather neat to see Sigourney Weaver scrabbling around in the lab and saying things like “signal transduction!” in cold blood. That the signals were being transduced between trees rather than neurons is just a matter of scale.

That about wraps it up for science, so I’ll finish with some thoughts about the politics. A braver movie wouldn’t have had the Red Indians Na’vi winning. A thoughtful movie, one that wasn’t simply toeing the party line on ecological messages and being a showpiece for admittedly gorgeous special effects, would not have had a cartoon bad guy talking in clichés; would not have had the industrial-military complex being beaten by guys with sticks: rather we’d have seen the scientists save the day.

The scientists (embodied in the amazingly fit Sigourney Weaver) were treated sympathetically, even if portrayed as a little kooky (and why, 140 years from now on a planet with a hostile atmosphere, would anyone smoke cigarettes?). The scientist, just as in 2012, went up against the baddies (in this case the industrialist rather than the politician). Unfortunately in the movie common sense and compassion didn’t prevail, and Sigourney Weaver karked it at the bottom of a huge, glowing tree (and that had to be a body double, surely?). She did have a brilliant last line, though—Jenny laughed and poked me in the ribs and told me to remember—”We need to take some samples”. That’s biological dedication for you.

And all this is a bit of a shame, really, quite apart from the wasted opportunity to do something interesting with the plot. Because you know what’s going to happen in a dozen years, don’t you?

A private company has managed to build a spaceship; a rather lovely one, actually, that reminded me strongly of the Discovery. They’ve had their mercenaries wiped out and been sent packing, leaving behind vast deposits of some incredibly expensive and above all useful if stupidly-named element (just what do you think was holding those mountains up, hmm?). What’s more, there’s a shedload of technology been left behind in the hands of not-too-bright-but-obviously-quick-learning natives. Natives who are incredibly warlike, too—they only accepted Braveheart Smurf on parole when he said he was a warrior (of the ‘Jarhead’ clan: possibly the best line in the movie). I’d actually be quite jittery if they were my neighbours.

And not just the technology—a scientist and a technician who in all likelihood know how to use it. Can we say ‘accelerated development’? I think we can.

So the company reps get back and go straight to the most powerful government on Earth at the time, and say hey, there’s these guys who just whupped our corporate ass, who’ve got guns as well all sorts of wildlife on their side, and what’s more they’re sitting on these deposits of magical ore. You don’t think they might be a bit sore about this? You don’t think they might be plotting revenge? You don’t think that the traitors might be teaching the natives the secrets of interstellar travel?

Don’t you think that maybe, just maybe, we should build another spaceship and nuke the site from orbit?

It’s the only way to be sure.

bq. I should imagine that most readers of this blog do not seriously think that women are any less able, intrinsically, than men to do science. (Wired readers excepted.)

It all started when I gave a friend a Bosch cordless drill for her birthday.

Something that isn’t pink

She was glad it wasn’t pink: there seems to be a lot of pink going around and I don’t know why. Pink used to be a boy’s colour; the colour of blood, but watered down a little. Sometime in the earlier part of the last century it became a girl’s colour, and in the last couple of decades it has been appropriated by marketeers intent on selling things to girls (or their mothers). You can get pink lego, pink mobiles, and yes, pink roadside tool kits (complete with a ‘Help’ sign).

<img src="http://ecx.images-amazon.com/images/I/519KlQIopgL.SS400.jpg” title=”Sweet Jesus it’s pink” alt=”Sweet Jesus it’s pink” width=”400″ height=”400″ />
Something too pink

It’s now necessary to dress your human offspring in either pink or blue, just so people can tell what sex they are. As if that matters. And let’s not even start about the infantilization of one half the human race, and the trivialization of serious matters by corporate bigwigs who make a profit by pretending to be responsible and caring.

So this drill. I think its non-pinkness was appreciated, and that set me to thinking that anyone who really appreciated power toys tools wouldn’t want them in pink, and that anyone who didn’t know what to do with same probably wouldn’t be in any better a position if it were pink.

I find the whole thing a little distressing, because I’d hoped we’d moved on from attitudes that patronized and repressed women (which, if it’s not clear, I think pinkification does). This contributed to the depression I felt at the sheer masculinity—no, masculinity is good ; this is more patriarchalism—of the Eureka supplement. And of the “cavilling response”:http://network.nature.com/people/UE19877E8/blog/2009/10/14/in-which-i-have-seen-the-future-of-science-–-update from its editor. (I notice there’s another issue of that out, but the web version looks boring, and offering to do a special piece on women scientists completely misses the point, so I’m not really keen to give Rupert Murdoch any more of my money.)

Fortunately, the state of science and technology with respect to sexual equality is not all bleak (and this is where my wireless scanner comes in handy). Jenny was feeling a little homesick last week and went and bought a copy of the New Yorker. We were quite taken by the cover, and indeed podcasted it.

The New Yorker last week

Leaving aside the “scientists=white coat + glasses” thing (and to be fair, they probably should be wearing safety goggles anyway), the representation of the sexes among the ‘scientists’ in the cartoon is pretty good. Similarly, check out the ‘engineers’ (who you can tell are engineers because they’re wearing yellow hats): three male and two female. (The dude with the ponytail has stubble. So either a man or a very testosterone-fuelled woman). Not only is 2/5 equal to 1/2 in biological terms (i.e. the sample size is too small), note that the woman engineer is quite obviously the foreman, that is, in charge. This is brilliant stuff, and The Times would do well to learn from the New Yorker.

Thumbs up there, then.

Kinda related to this directionless ramble is a little shi flurry that blew up on Twitter last week. Via @womenintech I saw that Maggie Philbin said she’d been to the Royal Society, and noted that of 50 paintings on the walls, only two were of women. Shock, and indeed horror.

But wait a minute. The Royal Society elects members according to how good they are, and (unrelated to that statement) it’s only been relatively recently that they admitted women—and I think it’s more than slightly unjust of us to judge the actions and attitudes of long-dead men by contemporary standards. So let’s have a closer look.

According to the RS itself, women comprise 5% of its membership. And 2/50 is four percent, which to a cell biologist is the same number. So that sounds fair. But isn’t that number itself discriminatory in some way? Surely more women than that deserve to elected to the RS?

Well, in the last eight years ten percent of new members have been women, which is a bit ‘better’. According to their website, candidates for election to the Fellowship must have made

“a substantial contribution to the improvement of natural knowledge, including mathematics, engineering science and medical science”.

and seeing as the Society’s place is not to drive recruitment choices, no matter how noble the cause, but rather to recognize outstanding contributions; and given the Higher Education Statistics Agency reports that of full-time and part-time professors in science subjects at UK universities, about 9% are women, we can see that the proportion of female Fellows now elected reflects the small percentage of female professors in university science subjects from which Fellows are elected.

Again, quoting from the RS website (emphasis mine),

In August 2002, the House of Commons Science and Technology Committee published the report of its inquiry into the Government funding of the scientific learned societies. The report concluded: “We do not think that the present low level of female Fellows in the Royal Society and Royal Academy of Engineering represents any discrimination against women.”

Listen up. You’ve got to be good at science to get in the FRS (certain high profile non-FRSes might consider that this is why they didn’t get elected; not because of their sex). It’s nothing at all to do with sexism or positive discrimination.

So there is a related question, the which I don’t know how to go about answering: what percentage of ‘top’ papers are authored—and I suppose we should say, in the biological sciences at least, senior authors—are women? Does it reflect that 10% figure?

And if not, why?

You already know I’m a propeller-head. I heart technology. I’ll love any gadget as long as it’s black. Or has wings. Preferably both.

So there I was, ready to write a serious blog post about sexism and whatnot, and decided that I needed to scan the cover of a certain magazine (that, coincidentally, starts with ‘N‘). So I fired up the new, shiny black wireless HP all-in-one printer|scanner|copier thing; that sits next to the new, shiny black Bose speaker system; that in turn accepts the not-quite-so-new-but-still-shiny, black iPhone (or indeed the rather scratched and tarnished-but-still-black iPod), thinking that I could wirelessly squirt some pixels all of ten feet across the living room to the shiny, aluminium MacBook Pro (it has a black edge to the screen and black keys. Close enough).

And it’s having none of it. I can wirelessly print to the printer, I can copy from the printer; I can even do a preview scan in the embedded web server (you can tell it’s the Twenty First Century: even printers are sodding web servers); but I just can not get it to scan.

I can access the printer—see how I access the printer! </Eddie Izzard>—but I can’t scan.

I’ve prowled around the HP support web shite site [You were right first time—Ed.] and discovered once again what a living hell life must be for Windows users, but to no avail. I’m currently downloading the latest drivers—although because the ‘About’ information of the applications and utilities I already have says I have version 4.4.2, or 2.0.21 (5), or Benny Goodman and the fucking Andrews Sisters; but NOTHING AT ALL that looks remotely like ‘10.3 (Released 10-2009)’ I can’t tell if this is a waste of time or not.

Of course, the smart money would be on traipsing my sorry arse ten feet across the room and plugging in the USB cable, but goshdarnit, that’s not what I just paid a hundred quid for.

Happy New Year.

Benoit’s comment on Jenny’s blog reminds me of the time that I was scooped, but not because my boss was carefree with data. I’ll tell you about that some other time, though, because there’s an another issue he mentions that’s recently become very pertinent.

One of the issues that crops up occasionally at the day job is retractions. Because we highlight the ‘best’ in the biological and medical literature it’s critical that we do something whenever a paper is retracted, for whatever reason. These can be very good reasons, such as conclusions becoming untenable in the light of new evidence, or irreproducible results; or because of deliberate or accidental fraud or misconduct.

There’s nothing inherently wrong with retractions: it’s part of science’s self-correcting mechanism (although we could all use a little more openness). Either way, when a paper is retracted it doesn’t just disappear: the paper itself and the retraction text remain part of the scientific record. As, indeed, do the evaluations we publish. We (i.e. f1000) need to maintain our records for the sake of posterity; we don’t simply delete evaluations of retracted papers.

Now that’s out of the way, Benoit’s comment about PIs:

the PI’s job in those cases is to talk to the competition, figure out where everyone is at […] and make arrangements for co-publication, for example. It is no accident that a recent issue of Nature had 5 papers on the same iPS cell result, or that the cover of Nature was shared years ago by two articles on the role of lunatic fringe in chick limb development

reminds me of a story that started—at least in public—three years ago and is only just nearing closure.

Not being particularly interested in immunology, my response to the publication in Nature of three papers (by Janssen, Wiesmann and Abdul Ajees et als) reporting the structural basis for the activation of complement C3b elicited little more from me than an “ooh, that’s pretty” together with a raised eyebrow at an 80 Å shift in conformation. (I should add, here, that it’s not surprising to see three such major pieces of work published simultaneously in the same journal. As Benoit says, PIs talk—with each other and with journal editors—and publication can be delayed a little, or hurried. Which I suspect has not a little bearing on the current story.)

I would have paid it no further attention were it not for our soon-to-be departmental head, sometime in the waning of 2007, highlighting a rather intriguing Communication in Nature. Two of the authors on one of those three C3b papers, together with a couple of big guns in protein crystallography (one of whom was responsible for the gazumping I mentioned earlier), put their collective hand in the air and said, “Hang on, there’s something fishy with this third paper”:

We have reanalysed the data deposited by et al. and have discovered features that are inconsistent with the known physical properties of macromolecular structures and their diffraction data. Our findings therefore call into question the crystal structure for C3b reported by Ajees et al.

Them’s fighting words. The Communication gets a little technical (this is protein crystallography, after all), but I’ll try to explain it.
These guys decided, as you might expect, to compare the three structures. A sensible move, especially seeing as the published structures are somewhat dissimilar. Indeed, the Ajees structure is missing a huge chunk of molecule!

The coordinates do not form a connected network of molecules in the crystal lattice. The crystal structure forms layers that are separated by a large void in the c-direction (a slab of about 30–40 Å thick that spans the entire unit cell).

Sometimes it’s actually difficult to ‘find’ molecules in large, complex protein structures—if the software you use doesn’t assign electron density correctly for some reason, or the phases aren’t complete, you can fail to join the dots properly, and in the rush to publication this can be missed. So these guys took the deposited data and tried to solve the structure again, looking for the putative missing protein molecule. And they didn’t find it.

Furthermore, they

noticed other physically implausible features

such as no data indicating that the crystals contained water. In other words, this protein was in a vacuum; which might make theoretical physicists happy but isn’t really consistent with anything we know about biology (and Henry, you can stop the Nature abhors a vacuum joke right now).

Killer figure

They also found that the R factor, essentially a measure of the ‘goodness’ of a protein structure, doesn’t behave you would expect if no water was present in the calculation. Another measure of structure goodness, the B factor, looked odd too. This is a measure of how much any given atom might be expected to move; you might predict that atoms on the outside of a protein have more freedom than those inside: so the B factor should vary along the sequence. Right?

Eh. Right. In the Ajees structure, the B factors are pretty much the same across the entire length of the protein, which when you consider that the structure has vast swathes exposed to solvent (or vacuum, perhaps) is somewhat puzzling.

somewhat puzzling

In brief, the structure is just too good:

We think that these physically implausible features undermine the validity of the model presented by Ajees et al. and the deposited diffraction data from which it derives. Only when the experimental diffraction images are made available can the deviating C3b model be either verified or falsified.

There’s a bit of a pathetic response from Ajees and co., but basically we (as in the crystallography) waited to see what would happen next.

<eats popcorn>

What did happen next was a veritable storm on the CCP4bb mailing list, kicked off by Eleanor Dodson and titled The importance of USING our validation tools. That’s all it took for Randy Read (one of the Big Four) to weigh in with

Originally I expected that the publication of our Brief Communication in Nature would stimulate a lot of discussion on the bulletin board, but clearly it hasn’t. One reason is probably that we couldn’t be as forthright as we wished to be. For its own good reasons, Nature did not allow us to use the word “fabricated”.

That, and the necessity of waiting for Ajees et al. to respond, is probably why it took eight months for the Communication to be published. Anyway, rather than clutter up this space, I commend to you this zip archive of the CCP4bb discussion, kindly collated by Hari Jayaram.

Why am I talking about this now? Because, as reported by Iddo Friedberg, the University of Alabama at Birmingham has (finally) requested that no fewer than eleven structures, represented in nine papers, from the lab that published the apparently dodgy structure be expunged from the Protein Data Bank:

After a thorough examination of the available data, which included a re-analysis of each structure alleged to have been fabricated, the committee found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not falsified and/or fabricated and recommended that they be removed from the public record.

My spy in Sydney tells me that the Journal of Biological Chemistry has retracted one paper, and that the Journal of Molecular Biology and Acta Crystallography. He also says that Birmingham (Alabama) were slow in informing all the parties, which has delayed final actions. I also understand that journals are moving towards requesting that raw diffraction images (even if they’re as bad as Stephen’s) rather than just structure factors be deposited somewhere, so that we can all keep a big, brotherly eye on each other. And finally, “it is interesting that [the head of the lab] still claims he is innocent”.

It’s funny, that two years ago I suspected that Nature received manuscripts from Janssen and Wiesmann in reasonably quick succession, and knowing that the Ajees lab was working on the same thing poked them with a “Have you got that structure yet?”-type call. Alternatively, I thought, perhaps the Ajees group had seen presentations by the other two and realized they were about to be pipped. In either case, I reasoned, they might have had a structure almost ready, or poor crystals, and maybe they made something up.

Not good, not ethical; but possibly, just possibly, understandable. But to apparently fabricate eleven structures? That’s seriously bad, and implies a level of collusion and—well, let’s be frank here—organized conspiracy unthought of outside certain labs in South Korea.

In the meantime, as soon as the news from Alabama hit my screen, I pulled up the f1000 website and searched for the implicated articles. I’m pleased to say that we now reflect the current state of the scientific record (as you
may verify for yourself at this free link).

Continue reading →

Some Friday cell porn for you.

Among other things, I used to be a cell biologist (which reminds me: I need to blog about Jenny’s mis-classification of me). I used to be able to spend hours simply peering down microscopes (more recently, swearing at confocal software) because it was so damned pretty. I miss that a little bit, and take any chance I can to nip over to UCL and get me some red/green fix.

GE Healthcare are running (yet another) competition where you can vote for your favourite picture and get a calendar. It’s a marketing exercise for their Cell Analyzer [sic] but hey, it’s Friday and the cells really are very pretty.

Regular listeners will remember the Science Online London gathering back in August. The day before, Mendeley hosted a pre-conference ‘fringe’ event, organized by Jenny. It turned out to be quite a wild evening, and there is video evidence of shenanigans.

One thing I remember clearly (some of you might be surprised I remember anything from that evening, but anyway) is David Colquhoun getting a tad rabid about PR. The gist was that science doesn’t need PR, it’s a waste of time and money; I don’t remember him saying explicitly PR people are professional liars but that was the impression I came away with.

I thought that was bollocks, and I still do.

PR is necessary not simply because scientists like to eat, and therefore need to be funded, and therefore need to convince various bodies (and by extension the people who influence those bodies) to give them money (and I want to talk a little about about ‘justification’ of research in another post) but also because there are crucial social and public health aspects of what we do. We don’t just have to convince the wider community that a particular piece of research is ‘correct’, but we need to demonstrate–somehow–that it directly affects their health (or their wallet, or whatever).

I’m reminded of this because a friend of mine sent me a link via Facebook last week, saying

Some (including me) would argue that the greatest battles against illness and suffering should be fought on the PR/HR front, rather than purely in the arena of science. You, O Great Stream Feeder in the Gyre of Science Publication, may well have already seen this: RT David McCandless RT @GreatDismal: Emotional Epidemiology Of H1N1

The article is from a medical doctor (or possibly here), and describes the reactions, preconceptions and attitudes of visitors to her clinic in the face of the H1N1 epidemic; or, as she describes it, Emotional Epidemiology. In brief, her patients at first demanded a vaccine against H1N1 (despite not wanting the seasonal jab…) and then, when the vaccine became available, refused it.

It certainly isn’t related to logic or facts, since few new medical data became available during this period. It seems to reflect a sort of psychological contagion of myth and suspicion.

Another report last week backs up my claim. The Daily Express reported that taking aspirin could “significantly reduce” age-related macular degeneration. Sounds great. But let’s see what the NHS has to say:

This is a well-designed and well-conducted study, the results of which have been incorrectly reported in the press. This study found that low-dose aspirin had no effect in preventing age-related macular degeneration, a common cause of sight loss in the elderly.

Far from being a significant reduction, the authors of the reported (large, double-blind) randomized controlled trial took pains to stress that there is no benefit. Indeed,

There are risks associated with taking daily or alternate-day aspirin, which should be weighed against the benefits. Elderly people, to whom this research will be most relevant, are most at risk of gastric irritation if they regularly use aspirin.

What’s going on, here?

In both cases, it’s a failure of PR. It’s not simply a matter of education. It’s a matter of getting things right, and getting that information out there, to the public–via the newspapers or schools or physicians in surgeries. Just as with anthropogenic global warming there is no (serious) debate about the science; it’s a matter of PR. And I know it’s difficult. I have no idea who Jo Willey is (apart from Health Correspondent for the Daily Trainwreck), but I would love to see the press release that she read. Because I also know that they are difficult to get right. On Monday I had to completely re-write a release that we were about to publish because the person who produced the copy got the message of the research completely wrong.

PR is necessary. And it’s hard; perhaps even harder than the science.

Continue reading →

Who gets custody of the Gilsons?

I’ve left a few labs in my time. It’s part of the nature of science: we’re all at least a little bit itinerant, needing or wanting to move on every few years (except for the lucky few who get tenure and who can then reabsorb their own brainstem). First degree; graduate degree; first, second, nth postdoc—we’ve been there.

We’ve hastily indexed freezer boxes and photocopied notebooks, fought over items of equipment, snuck into the lab in the dead of night to make surreptitious aliquots of treasured plasmid stocks. Taken chemicals and dissection kits that we took into that lab, and that nobody else would use anyway. We’ve said our goodbyes, got pissed on cheap lager, woken vowing never to do it again; at least until the next time.

My own series of farewells started earlier than most: my father was in the RAF, which meant that every two to three years I’d have to move on, say goodbye, make new friends—and this has continued into my adult life. Longest time in one place? Six years, leaving for reasons that turned out not to be very good after all.

It is tempting to paint previous engagements with a brush that does not reflect the truth. This will often depend on your current situation: if you’re having a good time you’ll tend to think more poorly of your previous job, or boss, than the reality would warrant. Similarly, if you’re struggling a little bit, you’ll wonder why you left that cushy number. The psychopath you couldn’t wait to away from was simply encouraging you to do your best; the mentor who let you find your own way lacked discipline and leadership skills.

When I finished my thesis I had to find a job pretty quickly: my boss’ programme grant wasn’t renewed and he got offered his dream job on an entirely different continent. I had no time to finish up the experiments and write papers, and took up an offer that had been kicking around a while. No time for lengthy goodbyes or second thoughts (although I did receive a dressing down for not asking if I could take various plasmid stocks). Leaving my first postdoc was soured by the boss having a complete benny on discovering I was going into industry—and then screwing me over on paper authorship. Again.

I’ve talked previously about the next episode in my professional life, but didn’t say that it led directly into the best six years I’ve spent in science. When I left the MRC-LMB (in the process turning down the offer of a permanent contract) it was for all the wrong reasons, even if the split was on the best of terms (despite having no leaving party, and working right up till midday on Christmas Eve solving a structure by NMR). As you might know, that’s also when I left the UK, seriously expecting never to see certain places —or even certain people—ever again.

I did better that time round, and kept the contacts, kept the collaborations alive; in spite of the seeming impossibility of it all made a serious attempt at not burning bridges. I never seriously thought I would need anything else—professionally or otherwise—from my colleagues in Cambridge, but I stayed in touch, stayed friends; moved on but with gratitude and friendship.

Then it all changed, and I came back to the UK, back home; and began rebuilding those friendships (that had never, really, gone away; they’d just been put on hold). Made new friendships too, of course; and I have never felt so alive or fulfilled as I have these last few months in London. They say that you spend the rest of your life trying to unmake friendships formed in the first week of college, but while that may be true (and I have felt some of it myself), some friendships, made long ago, can survive drought and famine and are just waiting to be picked up again when time and circumstance are right.

And this evening I am very pleased that I did pick up and rekindle one of those in particular.

Rob was my best mate. I knew him at Oxford (not during the first week though: maybe that makes a difference?) and attended his wedding. I went to his ordination (despite my theological uncomfortableness) and supported him as best I could. I loved him like a brother. When his marriage collapsed, despite feeling utterly betrayed I was there for him as much as I knew how. I helped him move house. When no one else wanted to know, we were there for him (and his wife and children). Just three weeks ago I was hoping he’d do the same for me. We spent a warm night in August making matchstick rockets, and exchanged jubilant text messages over this summer’s cricketing successes.

But that dark and rainy Friday night, a vehicle coming down a hill lost control and crossed onto his side of the road. It took the fire brigade two hours to cut him out, and he never regained consciousness.

I’ve been to Gloucester and back today for the final goodbye. Took a Streetcar, Kate and the girls. Stood during the first song of the service unable to make a noise above a sob. Held the girls: gave and received comfort. Hugged his wife for what seemed the longest time, but that could never be long enough. Hoped he knew that I loved him.

Vale, Rob.

Following on from a number of posts about mentors or mentorship, I got thinking about my own experience of being on the receiving end of leadership. I should think that most of us who have had the fortune to work in academentia are familiar with Alexander Dent’s ‘Nine types’ series.

Nine different leadership styles is probably pushing it a bit, to be honest. According to Forbes publisher Rich Karlgaard there are four different successful types (H/T Noelle Chun):

• Visionary
• Empathetic
• Humble servitude

• Moral/ethical

Steve Jobs is probably the most obvious example of a ‘visionary’ leader. This is the chap who took a somewhat cultish computing platform and turned it into a–well, a cultish computing platform that was not just suddenly incredibly sexy but also successful. Karlgaard gives a submarine captain as an example of an empathetic leader, as well as the cofounder of Hewlett-Packard. In the military, the function of the team is paramount, so it makes sense that you understand your charges. The heir to Wal-Mart, S. Robson Walton, is apparently a humble servant (in contrast to his father), and Starbucks is held up as an ethically-led company.

All very interesting, and in stark contrast to my own list of scientific leadership styles (some, none, or all of which I have experienced):

• Micromanaging control freak
• Psychotic bitch queen from hell
• Incredibly bright but otherworldly professor

• Waste of oxygen who mucks around on internet all day

Can you think of any of your own mentors or PIs who have displayed any or all of these traits? Does this assessment hold true for science as well as business?

“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.

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