Confessions of a (former) Lab Rat

One of the heated discussions I’ve been having at work is about advertising. I’m essentially taking the view that in yer face advertising reduces usability of and traffic to a website, as well as (for reasons I don’t want to go into here) confusing people about who the hell we are. The opposing view is that advertising = $ and £. Not an argument I’m going to review here, but let me just say we’re talking about a top level banner ad and Google context-sensitive ads.

Just now I was writing to a certain person at the Mother Ship about an idea that isn’t a million miles away from the session I’m co-leading on Saturday. And in my research I happened across an entry from Bora’s Snog Blog around the Clock, from 2007. And what made me laugh, given the general tone of the sciencebloggers (ah. Honorable exception, whom I have sadly neglected recently. Apologies) was this Google ad, right at the top:

Bora advertising Bible software

Let’s take a

closer look

Isn’t that brilliant?

Right, back to your scheduled programming.

Jenny’s post last week set me thinking. I have, apparently, a reputation for being a bit down on kits. Can’t imagine how that got started. The truth, as always, is a little more complex than that. Certain people here might be surprised at, for example, my attitude vis-à-vis pre-cast gels.

First, some history.

Back in the pea-soupers of time, when I was but a sprog of a grad student, I learned the secret of what was in the mystical potions A, B, L, M and H. I made 50 ml preparations of these, along with 10 mg ml^-1 BSA and 20 mM spermidine, properly sterile-filtered and everything: and this was such a huge amount that even when Boehringer started supplying buffers with their restriction enzymes I continued using my homemade stuff. Seemed to work, too.

I remember my first ever PCR. I spent a week preparing—under DNA-free conditions—all the buffers, from scratch. I remember being terrified I’d screw up and the experiment wouldn’t work (it did. Work, that is). And then there was the magic of ³⁵S dideoxy sequencing, and the encroaching enkitment of that method, with colour-coded caps and a red dye in the hot stuff. Big sequencing gels, with degassed urea/acrylamide mixes and sealing the bottom of the plate with agarose. Frankly, despite the loss of this skillset, I certainly wouldn’t go back.

The restriction buffers, the magic 10 X PCR buffer (and even the pre-made MgCl₂) stock; yay verily the Sequenase kits: all these supplanted homemade methods and reagents in their time. Overall, a good thing, I say.

And pre-cast protein gels? Anyone who has had to pour a slab of ten gradient gels, complete with stacking and resolving, and then clean up the semi-polymerized gunk all over the desk because one tiny little thing wasn’t nanometer perfect; or who has found bubbles right at the resolving interfaces making half of all the gels unusable— anyone, I say, would gladly spend a few extra quid on the pre-cast gels from Invitrogen. My boss in Cambridge actually instructed us to use pre-cast SDS gels because of the saving in time, reagents and neurotoxins. (Excepting native gels, but that’s another story and I won him over on that one, too.)

But there are—or would be if I went back to the lab—two kits that I baulk at.

The first is the Quikchange mutagenesis kit. I remember reading the paper in which the method was described, and comparing the contents of the kit with what we could put together by buying the reagents individually. I approached the boss with a proposal, we bought one kit and photocopied the instructions—the cycling times and temperatures and advice on choosing primers—and then bought Pfu (which always came with its buffer, natch) and dNTPs and Dpn I separately, at a small fraction of the kit price, for exactly the same reagents. Minus a cardboard box.

Me, not seeing the point.

The other kit I hate (I say ‘kit’, but really it’s the whole industry) is plasmid prep kits.

Take minipreps. Now, I’ve worked in the industry, and I know (a) exactly what goes into these kits and (b) precisely how crap they are. Back in 1999 Qiagen were selling minipreps at £1.09 per. The manufacturing cost was ~17p. That’s one hell of a markup. And they were shit. The standard protocol, if you followed the instructions, would take about 20 minutes. With the kit I made, you could do the same thing in 11. The Qiagen kit, if you followed the instructions, would give you nicked DNA and crapped out if you gave it too many bacterial cells. Mine wouldn’t.

Guess which wouldn’t sell? Betamax versus VHS, anyone? (Marketing, marketing, marketing. It’s so easy, except when it’s done by people who seemingly were lobotomized at birth.)

The thing, the really galling thing, is that you can get DNA good enough for screening colonies (and indeed, with a bit of tweaking, for sequencing) with homemade reagents at fraction of the cost, with the same (if not less) hands-on time, and without those tedious wash steps spewing gunk all over the microfuge that nobody, ever, cleaned up.

So I’m down on miniprep kits. I’m also down on midi- and maxiprep kits because, let’s face it, they are incredibly tedious because they still take half a day if not more and you still have to do a couple of alcohol precipitations and they are fucking expensive.

I say learn about the hazards of phenol, so that you get good and scared when you go into a lab (I made a med student cry once for not treating phenol with respect. But then, you’re talking to someone who before he started his DPhil knew a chap who spilled 500 ml of the stuff all over his legs and spent three months in Stoke Mandeville having skin grafts, and his kidneys pumped) so that when you have to use stuff that is really nasty you aren’t totally unprepared for it (because, for example, I don’t think there is any kit version of paraformaldehyde).

It’s not because you might get asked about the chemistry of these things in your defence. It’s because some things really are a waste of money and time. Other things—like Jenny’s bacmid kit, or those complicated expression systems for insect cells, or (my personal favourite) the rabbit reticulocyte in vitro expression system—are worth every last grant-awarded penny. You have to make the judgement call, and you need to learn how to do that. You have that responsibility.

It’s also because some of the reagents that you get in kits are more dangerous than the stuff you’d use if you did things the traditional way (name the contents of the first wash buffer in the Qiagen miniprep kit…).

And on a lighter note, I used to roll my own weblog. I knew a ‘kit’ existed, but didn’t use it; until it suddenly just got too much and I switched to MT4 WordPress. Talking of which, Bill Hanage is now blogging for LabLit. Go read.

So there I was, trying to figure out exactly what I was supposed to do with over two thousand journal abbreviations (it’s a giddy, hedonistic life I lead), when HD came over to annoy talk about something that I have executive authority over (yay for power. Go me).

HD is a nice enough chap, but he does suffer from that peculiarly English affliction of looking at stuff on your screen, or reading things or your desk, or generally giving into the temptation of nosiness in a totally non-malicious but slightly—once you’ve noticed it—disturbing way that people have.

As we talked his gaze kept flicking over my shoulder. Not, as I initially thought, to the riveting Business Requirements Document displayed on my screen but rather out of the window behind me. This, I thought, was odd even for HD.

Finally, I gave in and turned around.

‘Um, sorry,’ HD said, ‘but I see why you chose this desk. There’s a woman getting undressed down there.’

And indeed, two floors down, in an office behind the building Dennis Publishing was a not unshapely figure in a sheer, silver undergarment. I desperately tried to refocus on HD, who, although not necessarily unpleasant to look at (in a certain light, at least), certainly posed no serious competition to what was going on behind and below me.

I tried, really I did. But after another thirty seconds of talking about stemming and wildcard searches my neck twisted inexorably around and I was rewarded with a vista of bra and panties.

It was pretty difficult to concentrate after that, so in the interests of propriety (although I’m not quite sure whose) we moved away from the window.

A slightly more edifying distraction occurred when I took my lunch break. Waiting at the lights on the corner of Cleveland and Howland, I saw a black car with a pole and camera arrangement on the top. Oh ho, I thought, it’s one of those so-called stealth parking council parking spy cars. But as it drew closer I could read the magic runes on the side.

I turned to the cove next to me and shared a manic grin. The car turned right, and we watched it go up past the Post Office BT tower.

Then I realized that I was grinning like an idiot with an iPhone in his hand.

‘Damn!’

I pelted up Cleveland Street, and nearly caught up with it, but it turned into Maple Street and appeared to be getting away. Then it slowed to turn into Cleveland Mews, and I managed to snap it:

Giggling to myself I continued on to Tottenham Court Road to meet my friend, half hoping the car might make a left, and then—no, because there’s the one-way system. Of course, it might turn around I suppose…

And there it was, stuck at the lights, and I twittered furiously.

I’m hoping that I’ll appear several times on Google Earth. Beverage of choice to the first person to spot me.

When I logged in this morning at work the operating system kindly informed me that my password was to expire in six days, and asked if I wanted to change it. This is the third time it’s done this to me, which means I’ve been at the new gig for nearly four months, so it must be about time for a quick update on what happened when I left the void.

As my profile said until a few minutes ago, I was supposed to be taking up the post of ‘Business Development Manager’ at F1000, the premier site for post-publication peer review (cough). Which was all well and good: I thought I’d be doing the web 2/social media schtick; a bit of writing, that sort of thing.

First day in, chairman takes me into his office and says ‘about your job title…’.

A little while later, I’m in a daze. I’m not merely a BDM with responsibility for a tiny part of the F1000 behemoth. No, I am the information architect (which sounds better than ‘web master’—hey, we even have our own journal, HT Georg). What’s more, F1000 is mine. I mean, mine: cackling, stroking white cats and feeding useless henchmen to sharks mine. (I have to report to the chairman, but it’s still pretty good going for a guy who still has Gilson’s Thumb.)

It was as if I’d gone for a swim in a rock pool and suddenly had the whole Pacific dumped on me. Scary and exciting and breathless all at once.

Four months down the line it’s still like that. I seem to be doing about four jobs: including PR and BDM and social media maven¹ and negotiator to the UN. I keep getting asked to lunch with various luminaries at very short notice. I had the final say-so on the new logo (to the extent of getting the vector files from the real designer and tweaking myself) and interviewed PR manager candidates. I’ve put the new website in front of some very important people and had to decide what will and won’t make it to launch. I’ve got a corporate credit card, I’ve hired two freelancers and have invoice-signing authority. I’ve set up, and provide all the content for, a Facebook page, a Linkedin group, a twitter feed and a blog—all without turning into Bora. I’ve edited and written press releases, been very firm with some people and soothing towards others (sometimes the sets overlap) and still haven’t finished re-writing the ‘About’ pages.

It’s great.

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Once upon a time a callow youth—quite by accident—almost burned down a high school chemistry lab.

This is not that story, but an appreciation of certain details in this one will enhance your enjoyment when I get round to telling you it. This story involves Spencer Hogg, a bunsen burner and the thermite reaction. (Aside: I just googled his name, because I was certain I’d previously written about him on Nature Network. Turns out I’ve written about another exploit of his elsewhere, but as that’s behind a paywall I’ll have to adapt it at a later date.)

So. The thermite reaction.

One fine day in the top chemistry set at Kent School, one Mr Woods mixed together a small amount of Fe₂O₃ and solid aluminum powder in a small, ceramic dish. This was placed on gauze on a tripod (remember them?). Then all 20-odd of us were shooed behind the back bench, and Mr Woods lit the bunsen, turned it down really really low, placed it under the mix and ran like bloody hell to join us at the back of the lab. We waited.

We waited some more.

Eventually, Spencer Hogg spoke up.

‘Sir,’ he said, ‘nothing’s happening. Can I go and turn the bunsen up?’

‘No, give it a bit longer.’

So we waited.

And waited.

And waited some more.

‘Sir,’ Spencer said, ‘can I go and turn it up now?’

‘All right then, but only a bit, and be very careful.’

Now, this might tell you a bit about Sir’s character. One of these days (At SoLo09, perhaps) I might tell you what happened on a school trip to Amsterdam, but I fear that it would only distract you from what happened next:

Spencer duly emerged from the bunker, walked over to the demo, and turned up the flame by the merest amount. He turned away, and there was what I can only describe as a ‘FOOM’.

Actually, that would be wasting a perfect opportunity to use the word ‘pyrotechnics’. Bits of flaming stuff whizzed out of the ceramic dish: sparks, smoke; the works. I think Spencer might have flinched.

One piece of flaming stuff landed in the wastepaper bin by the hand-washing sink. This bin was a wire basket about three feet high with a green (funny the details you remember) plastic liner and full to overflowing with scrunched-up paper towels. Which ignited.

Woods, give him his due, leapt over the bench and dashed to the front of the class, releasing the catches on the red metal box to get at the fire blanket…which happened to be directly over the bin. The fire blanket dropped straight down, still folded, and the flames shot sideways through the wire, the plastic liner giving way almost immediately, while we pissed ourselves laughing.

Not to be deterred, he grabbed the fire extinguisher from the wall and put the awesome power of yeast genetics foam to its God-given purpose.

When the smoke had cleared and we’d filed back to our own seats, Mr Woods called in the teacher from the parallel class next door, and asked for help resetting the safety on the fire extinguisher. This cove placed the extinguisher on the demonstration bench, stood behind it and tried to force the safety; sending foam over most of the front bench and its occupants—fortunately for me my seat was at the very end (nearest the door. I’m not daft) and it missed me.

The extinguisher was left, then, and we thought no more of it, except what a great thing chemistry was and how Spencer Hogg was quite possibly the luckiest boy in the school.

My fun, however, was only just beginning.

If you hear a rustling in the hedgerow, don’t be alarmed now,
it’s just a new kid on the blog.

There must be an easier way.

*All* of Australia is remote and isolated, Shirley?

Filled in my Australian tax return yesterday. Those of you who have never had to fill in a tax return don’t know what you’re missing. For the rest of you, I find that at least half a bottle of wine dulls the pain somewhat.

My relatives are perfectly valid, thankyouverymuch

It helps to have a sense of humour. The Australian Tax Office ‘eTax’ software makes the task a little less painful because if you’ve used it in a previous year you can ‘pre-fill’ a lot of information and you get any refund quite a bit faster than if you submit a paper return. The downside is that it only runs in Windows, which (_pace_ Richard Wintle) is quite a large downside, and results in a great deal of swearing at Black Towers as all the anti-virus software whinges about not being updated and what have you.

photographs, he asked knowingly

So we look around for little things to make us laugh. I am, however, a little disappointed that I can’t claim for going to the pictures. But I did shoot some videos of wildlife: does that count do you think?

Oh well. Glad it’s out of the way. And because I left Australia before the end of the tax year there should be a reasonable refund coming my way.

Yay. Makes it all worthwhile.

Almost.

It’s still Friday. Somewhere.

‘It’s hot like hell. And you smell of death!’ Lieselotte said to Neil one morning, not long before I left that particular lab. This is the girl who uses the English language rather like a cluster bomb: inexpertly, and people get hit by shrapnel.

‘My barbecue cooks like hell!’

Back in Fenland we had a circular dichroism measuring-type instrument. If you don’t know what one of those is it doesn’t really matter, except to say that this particular one appeared to be carved out of solid granite, sat in a scary room in the basement and ate undergraduates for elevenses.

Despite that it was quite fragile, consisting of various antediluvian optics and a mercury lamp that absolutely was not, without exception, under any circumstances to be struck in the presence of oxygen. Not ever.

To help even the most suicidal student with this seemingly simple yet somehow elusive directive, the CD machine was connected to two dirty great nitrogen cylinders with an automatic switching device connecting them: the idea being that one would turn on the tap and flush the machine with nitrogen well in advance of wanting to use it (often overnight)—and if one cylinder were to run empty in the night then the other would without a flicker of a metaphorical eyelid take up the burden. And if one cylinder was empty when one came to use the CD machine one would trog off to Stores to replace it. You could tell that the cylinder was empty because there was a useful little dial on it with a red line and the letters ‘E’, ‘M’, ‘P’, ‘T’ and ‘Y’.

And there were instructions and warning signs all over the room to this effect.

‘BC9 expresses like hell!’ Lieselotte said the next morning. ‘Beta octylglucoside is like hell!’

Uh huh.

Time passed.

‘My CD spectra are like hell!’.

Oops.

Turns out that Lieselotte had stormed into the basement room the previous night, in that inimitable way of hers, switched on all the taps and gone home for the night. In the morning, she’d stormed (like hell? probably) back in, struck the mercury lamp—and yes, you’re a country mile ahead of me—and stormed out again to get her samples.

Not noticing, natch, that the needles on both the nitrogen dials were firmly against the letters ‘E’, ‘M’, ‘P’, ‘T’ and ‘Y’, and probably had been for most of the night.

Was she popular?

Like hell.

Whee. That was a fun weekend.

I, despite my best efforts, completely failed to leave the pawns up a tree near Thetford

so we trundled onwards to Norwich, where they’d laid on a parade and fireworks for us. Which was rather kind, I thought. The Lord Mayor came out and waved to us too, so rather a fun evening.

Sunday morning we got back into the hire car and braved the wilds of deepest Norfolk, rocking up at Chez Gee.

A lovely time was had by all, as were chips and fish and pies, and I found a complete fossil record of Henry Moore’s early works. We also discovered Microsoft’s attempt at an iPhone, and here’s Henry using it:

The ultimate in silicon technology

Seventy million years in development (the iStone, not Henry): proof, if it was needed, against intelligent design.

I did want to write a serious blog post on intermediate fossil forms and the dangers of science, in that it can often show you want you want to see, but (a) Henry has the photos and (b) he’d probably make a better job of it than I, being a palaentologist.

We came home to the blessed safety of the south of the River, checking each other’s hands for the right numbers of fingers and feet for webbing. I’m pleased to report that we remained non-NFN.

Oh, and for those of you who remember the arm-wrestling competition last year, in which Henry cheated by using two arms to my one, you might be interested to learn that despite hours of practicing against his daughters, he was only able to win our table-top football match by 10 goals to nine, and refused a re-match.

Chicken.

I ran a brief and unscientific poll last week, much to Cath’s chagrin. It wasn’t as bad as she would have you believe, because I actually did think about the questions in those couple of teeth-brushing minutes, and figured I could pull out some information: obviously a more sophisticated and less self-selecting poll would be more valuable, but we’re talking about Twitter here, for goodness’ sake.

Anyway, let’s have a look.

Profession of Twitterers (or ‘Scientwists’)

Given the way the question was phrased, and the possibility of an ‘ex-bench scientist’ being also one of the other categories, I was not surprised to find that the numbers from the ‘professions’ category did not match the numbers in ‘disciplines’. However, it’s pretty obvious that of the ~80 respondents, about two thirds self-identified as research scientists. Not many medics—but quite a few people who have left scientific research.

Self-discipline

I’ve always suspected that biologists were pretty web-savvy, even back in the dark days of Gopher and NCSA Mosaic. More twitterers self-identified as ‘bioscience’ than all the other categories combined. These data should be interpreted with caution because those who saw the poll are probably more likely to be biological scientists anyway, simply because my two seed twitterers (rpg7twit and f1000), and hence their followers, are biomedical. Perhaps this result is not, then, that surprising.

Professional vs personal use

This result surprised me a little bit. It seems that most scientwists mix and match business and pleasure. Only nine votes—a bit over 10%—claimed separate work/personal accounts.

If I get a round tuit, I’ll re-do this poll in a more sensible way, and get some non-squishies to seed it. Maybe I could present this at SoLoConf ’09?

All my supplementary information is freely available online.