Life of a Lab Rat

Hal has had a revelation.

Stratagene’s QuikChange Mutagenesis Kit:

Contains: PfuUltra™ High Fidelity DNA polymerase, 10X reaction buffer, dNTP mix, Dpn I restriction enzyme, QuikChange control plasmid and control primers, XL-1 supercompetent cells, pUC18 control plasmid.

I'm wondering what took him so long. I first used that method in, oh, 1996, 1997? Stratagene (patent filed in 1995) had brought out the kit, and I looked at the method and thought what is stopping me doing that with standalone reagents?

So I talked to my then-boss, ordered the kit and the individual reagents from different suppliers, and did the side-by-side comparison. Since then, I think I've ordered the kit precisely once and that was to get hold of the instruction manual, which is now available online. And made countless mutants with DpnI from NEB and bog-standard Pfu.

You can even use Taq with high fidelity if you use dNTPs near the K_{m . . .}

Hello? This is a technical approach to a social problem!

It's bad enough that 'comfortable' middle class parents in the West waste taxpayer's money (oh yes they do - certain treatment is available in some NHS Trust regions) on IVF, but in a region where unplanned pregnancies and STDs are rife, do we really want to treat a sociological failing by diverting money and scientists' time from more pressing needs?

Changing age-old prejudice is going to take a while.

Indeed, but does anyone really think that attitudes will change once IVF/ART is freely available? Of course not — you've just removed one of the environmental pressures that might help bring that change about.

Bah. I need a walk in the fresh air, and it's raining.

There's an interesting phenomenon that occurs in labs.

In normal life we find it convenient to label things. It helps us organize our lives, recognize authority, and in some cases limit concepts and people so that we can deal with them; Takei is Japanese, Samantha is an arts graduate, Larvatus Prodeo is a whiny leftist blog. There are labels that, even with the best intentions, demean the very thing that is being labelled but in a way that constrains it sufficiently for us to understand, cope, deal with it.

And more prosaically we label the sugar and the salt so that our pavs lov.

Talking of hugs, Alethea could probably do with some TLC. Failing that, leave supportive comments.

This ties in with the 'why do we do it?' meme that's been bugging me recently.

Suz needs a hug, but she's written a very droll piece on scientists as, um, lab rats. Or mice, as she has it. The question is what happens when we apply the same criteria to ourselves as we do to our experimental models.

Her conclusion, that her experimental model (which I think by this stage is herself but I could be losing the plot myself at this point),

either has a learning defect or is masochistic

The University has a revamped website. And there's quite the discussion going on about it over at Georg's place (oh, and Andrew lives there too but he's keeping quiet. Sensible man).

It's bright, it's in yer face, and there's lots of content available directly from the front page. Let's be honest here, the idea of a University website is not primarily to make people go 'Oooh, shiny! Look at the pretties!'; people are visiting because they want information. The quality of the research and teaching is not linked to the whizziness of the web site (and if you are so simple-minded as to believe it is, we don't want you here). I have seen too many corporate websites where there's a Flash landing screen and it's almost impossible to find the farking information I went there for.

Shaun Cronin points to a polemic on the politicization of science by the current Australian administration.

I've got little to add aside from what I've already said in the comments, but you should go and have a read.

After commenting on the enthusiastic scientist at CERN, I thought I should bring your attention to this discussion of dark matter, which tells you just a little bit of why the LHC is going to be useful.

belfield, n
Durable, woven sailcloth popular because of its tear-resistance and low cost.

e.g. Bill was looking for some belfield to patch his wynyard.

I've just watched Beyond Tomorrow on Channel 7 — essentially the Australian version of Tomorrow's World. It's a light, frothy show with the weekly high point being an extract from Mythbusters.

But tonight they interviewed a scientist at CERN, and what was remarkable was the lady's obvious thrill she got from doing science for the sheer fun of it.

When asked if there were any practical benefits that might arise out of smashing protons together at near-lightspeeds, she said basically said no, we just want to see what happens. Mad props.

An interesting piece in the Grauniad last week (I know, I know, I'm sorry - I go to work, see an interesting article, try to remember it and the witticisms that spring to mind, finally come home on the mind-numbingly over-crowded Inner West line, have some dinner, the Younger Pawn is running around with a duvet cover on her head and making 'woo woo' noises and by then I've completely forgotten what I wanted to say) about the whole 'we're all doomed' thing.

(One reason I'm linking to it now is because I'm honestly not sure if any of my Australian readership read the Grauniard, possibly the last bastion of halfway decent professional reporting in the UK.)

Jonathan was talking about tactics versus strategy, and what those words mean for project management. Just to recap, 'strategy' is General Patton planning to turn the Third Army around to relieve Bastogne and 'tactics' is what you do when you see a ruddy great 5th Army Panzer cresting a ridge before you.

So the well-paid Generals and staff get to sit safe in Verdun talking about strategies while the poorly-paid, under-equipped and generally knackered grunts get to do tactics. You can probably already see where I'm going with this.

The Generals do their thing, and the grunts do theirs. And you know what? The grunts get really ratty when a General tries to tell them how to do their job. If the Vice-Chancellor were to come into my lab and tell me how to do minipreps I'd either send him away with a burning earhole or give him the Gilson, say "get on with it, then" and nick off to the pub for a pint or three. The Vice-Chancellor is good at Vice-Chancelloring (I hope) and I'm good at minipreps (among other things, he adds modestly). Which is Good and Right and How Things Should Be.

So why have I been asked three times in a week to do a General's job?

The most effective countermeasure against zombie outbreaks has previously been shown to be aerial bombardment. Troops on the ground are not favoured because they are ineffective at the dismemberment – a prerequisite for zombie inactivation. However, carefully targeted high explosives successfully achieve this. A regrettable corollary is collateral damage, as nearby human life is inevitably destroyed. However, these innocent bystanders would, in the absence of intervention, would likely have become zombies – and a threat to their neighbours. This contingency is introduced into the model as a ‘user-directed interaction’ which destroys humans and zombies, making them functionally equivalent: in other words, non-infectious.

wynyard, n
1 Small, two-sailed fishing boat. 2 Aft sail of same.

e.g.The wynyard capsized in the unseasonal storm. "Splice the main brace, square the futtock-ring and tally the wynyard!"

I do not normally do the 'content-free' link-blogging thing, but this is so damn' cool I just had to share it. Mouse neurons and galaxies. Can you tell the difference?

Via Eastern Blot.

You may have seen the report that schools in the UK are 'producing too few scientists',a conclusion reached by the Confederation of British Industry (CBI). It is worth remembering that the CBI has an agenda, and that is to make money. Presumably they think that more scientists means more money for their member businesses country.

A little thought will show then that the CBI is not interested in science at all, rather technology; the appliance of science. The thing is that you do not get that technology unless you have first done basic research. And you need a hell of a lot of basic research to get a single money-spinning technology (if it were otherwise, research scientists would get richer a lot quicker).

Aside: There's a nice example of how politicians lie in that article. The CBI claims that the number of students taking 'A' Levels - the UK's 18+ exam/university entrance exam - in 'hard' sciences has decreased drastically in the last 20 years. One might think that this woould have an obvious knock-on effect on the number of hard science graduates. However, the Schools Minister says that school funding for physics and chemistry has increased, along with the number of science graduates, since 1997 - when the current mob got in. But if we take a look at the numbers it appears that most of that increase is accounted for by computer science and medical graduates, neither of which are famed for basic research (and computer science barely existed as a degree in 1994. No wonder there is such a large percentage increase.). The 110% increase for students taking 'biological sciences' seems hopeful, until you start to ask exactly what that means (I have no idea. I do know that there has not been a doubling in the number of biochemistry graduates). Lord Sainsbury keeps suspiciously quiet about social 'scientists', I note. I wonder if they are included in the statistics?

Five months' work:

In the photograph above, 'a' is the control experiment and 'b' shows the effect of Protein de Jour. That 'SF' band (i.e. the white bit) is stronger than the 'LF' band in 'b'. That is telling me that PdJ is changing the levels of splicing (for this particular protein) in the cells I'm working with. The arrowhead in 'c' is pointing out a third band that I can never see in the control, which tells me that something else might be going on, too. That's somewhat exciting.

What biologists get up to when they think no one is watching.

Email received by the entire department just now:

I've put a stack of Woman's Day (current issue) in the tea room. Please feel free to take home a copy. Enjoy!

Ah, the headiness of cutting-edge research.

Conversation overheard at tea:

"Latin should still be taught in schools."

(in all seriousness) "That's the wisest thing you've ever said!"

Misguided?
Misunderstood?

Unravel the truth . . .

. . . But my heart's not in it.

It is quite a change for me to be in a university setting. The Council for Biomedical Research, although avowedly academic in nature, actually had very little to do with the local tertiary education institute. We had on average one graduate student per group, their stipends usually funded by the Council's fiercely contested fellowships. Local students were not advantaged, and the only time we got to see an undergraduate was when one was poached for the summer, via personal contacts.

So being in a full-on teaching department is a bit of a culture shock. I'm surrounded by students. It's not a problem, it is just different. Being old enough (legally, even) to be the father of some of them has not freaked me out; in fact I find it quite invigorating. Not just in a 'I shall mould these youthful, malleable minds to do my bidding mwah hah hah ahem' way, but more in a 'gosh these guys are keen' sense.

pymble, v. & n.
—n. The gentle, ambling gait of one slightly inebriated.
—v. intr. To stagger unalarmingly, usually after a few drinks.

e.g."That's a nice pymble you've got going there, Dave". Vic pymbled home from the pub.

I am sure that most people in my lab could pass as perfectly normal members of society. I know that some of them even have real lives, and seem to be able to maintain relationships outside the lab.

Therefore I have been somewhat taken aback by the response to the Axygen 'eppendorf' tubes. A fair proportion of the lab rats have come up to me in the last week and raved - there is no other word for it - about these tubes. All right, they are good, but I never expected such an emotional excess.

The old joke (via Alex) about the doctoral rabbit sums up what I was whinging about very well.

Hal's post reminds me: I bumped into Dan from PLP (see this post) in the corridor yesterday. Apparently the poor bloke had been losing sleep because he thought he had promised to bring in some more samples and could not remember bringing them, or indeed what they were.

Curse my honest nature; I failed to seize the opportunity to turn a fast buck and told him I had everything he had promised. But this customer-focus is exactly the kind of thing that means I'm more inclined to consider PLP for other products. They don't do culture plasticware but I did managed to extract a 96-well PCR plate from him.

Which reminds me, as our thermal cycler is broken I had better run and book the other lab's one . . .

According to Derek, we're likely to have gainful employ for quite some time.

The book hiding within that link is exactly the sort of thing that the meeja is likely to jump all over, and the actual analysis of Kurzweil's futurology is just going to pass them by. I had a cartoon in my head when the first draft of the human genome was published, which had all these guys (and gals) sitting around wondering what to to do now they'd sequenced it. And of course the work was only just beginning. Sequence is not everything, not by a long banana.

The dangers of malnutrition in the unborn child, often leading to chronic disease in adult life, are well documented and the subject of much study. For example, searching Pubmed for Barker DJ turns up some 378 citations. However, it seems that over-nutrition can be just as bad, as the abstract below indicates.

Dorota Pawlak, Harvard Medical School and Children's Hospital Boston, is scheduled to give a seminar on Fetal over-nutrition and the risk for chronic diseases in childhood in the Human Nutrition Unit. If you want to come along, be in the School of Molecular & Microbial Biosciences Room 471 (Building G08, Maze Crescent) by 13:00 on Wednesday 30th August.

The younger pawn gets a rollicking because she has not got dressed yet; she's reading the dictionary. Up to 'K' so far.

The elder pawn turns to me, mouth full of foaming toothpaste.

"Dad! I've got rabies!"

I'm sure I'd recognize normality if ever I saw it.

It is quite easy in this business to get disillusioned when you look around and see that, for example, the NIH only funds about 10% of RO1 grants and there is no career structure to speak of for postdocs. You begin to wonder if you are any good at all, especially when you reach a certain age and find that you are really enjoying the bench work but seem to have no luck at finding a real job.

After filling in my tax return form last night (and there is a rant to let brew for maximal flavour) tonight I will be filling in the census form online.

An email just came around our lab (I think someone must be reading this weblog). I heartily endorse the sentiment and hope the meme within gets spread rapidly.

You will recall that we had a problem with doors in our refurbished offices.

Last week the contractors fitted new doors to the internal offices (the 'private' offices off the cube farm arrangement). And then (and only then) painted them. So on Friday it was almost impossible to work in the office due to the fumes. Over the weekend they sanded the doors and are in the process of (hopefully) putting the final coat on.

strathfield, n
Patterned, close-weaved cotton; particularly 1950s-style haberdashery fabric.

e.g.Mary bought five yards of strathfield for some new bedroom curtains.

"Hello, my name is John and I'm a scientist. I haven't been able to clone anything for three months. I'm taking it one day at a time."

The elder pawn (hmm, that sounds vaguely Lovecraftian) wanted to take her bicycle into school today. Turns out they're doing a project on machines. She asked if I had ever taken the back off a washing machine and when I said I had, she said

'Wow! What did it look like?'

I told her why I had taken the machine apart (to find out how it worked so that I could mend it) and from there went on to say actually, that's what I do at work. No, not mend washing machines — I take things apart to see how they work. I did not use the phrase 'the very fabric of Life' (I was tempted; that kind of thing does not faze nine year olds as much as you might think) but we did have an interesting discussion about dissection and atom bombs and all sorts of groovy stuff.

The Western blot became conclusive. The tantalizing band is the potato acid phosphatase, cross-reacting with the secondary antibody. Frustratingly, the phosphatase is represented by two bands, which threw me. Note to self: Sigma are crap.

I said on Friday that 'Z' does not regulate its own splicing, and the gel I ran this morning supports that conclusion. There is one thing that is stopping me drawing a line under that however, which is to do with the way I did the experiment. I performed what we call a 'transient' transfection. What this means is that I made the cells take up the test DNA, and went ahead and did the analysis on a mixed population: Some of the cells took up a lot of DNA and (hopefully) would have made a lot of protein, other cells took up a middling amount; and some cells just laughed and told me to bugger off.

Last chance to get your ionized post-docs! All stock must go!