Life of a Lab Rat

Email to the Cage, this morning:

I found a specimen jar [...] in front of the -80 freezers with a label of "frontal cortex" dated from 2006.

Its still there if it is yours.

Obviously then, the frontal cortex is not necessary for email, as has long been suspected:
[T]he damage to Gage’s frontal cortex had resulted in a complete loss of social inhibitions.

As promised, my really rather simple miniprep method.

I should again point out that the GTE, NaOH/SDS and KOAc are functionally the same as the lysis reagents that you get in the commercial kits. So you can substitute in either direction.

From a circulatory email this morning:

Last night we had a significant weather event across Camperdown/Darlington campuses. As a result we suffered lightening[sic] strikes and some water damage across the campuses due to the torrential downpour.

[. . .]

We believe that we got to most damage but anticipate that today will bring some additional issues that we will need to address.

If you have any issues please advise Campus Infrastructure Services [. . .]

Translation:

Last night it pissed down. We got flooded and hit by lightning.
We tried to fix things but if your office/lab/classroom is wet, or something is buggered, please give us a call.

Went down to a seminar this afternoon, and saw my young apprentice helping the speaker set up the projector. I had just seen a reasonably interesting result fall out of my microarray data.

So I nicked a piece of paper from another postdoc, went back and stole her pen, and scribbled this:

My young apprentice was appropriately interested.

Now, after another couple of hours looking at more species, I'm seeing definite patterns. I still don't know what they mean, but at least there seems to be the possibility of an answer, and I'm beginning to be excited in my ignorance, rather than frustrated at it.

Ian York is approaching the 1.0 release of XPlasMap (which I have written about previously). He's actively soliciting bug reports and feature requests.

Go to it, team.

Dr Chou, erstwhile partner in crime and padawan, leaves us today.

I played him Taps. It was very moving.

Pub this arvo, anyone?

Elsewhere on the internets I've been reading about what sort of music people listen to in the lab.

Back in Cambridge we used to have about 8 solid days' worth of music in iTunes, as well as access to everyone else's shared music and a (rather crappy, admittedly) radio. We had a lot to choose from, and the only fights occurred when a certain grad student got in early and played nothing but Coldplay and The Whitlams. I still shudder when I hear certain intro riffs. Oh, and when Trevor brought in jazz CDs. Ugh.

Here, music is banned from the main lab area and the offices. I have no problem with that; it does solve all sorts of arguments, even if sometimes you feel the need for Paint it Black when the RT-PCR fails yet again. We have a (clockwork!) radio in the gel room, which provides background hum (but the state of Sydney's radio stations is abysmal, even if some of the adverts crack me up).

This does mean that people tend to wear iPods a lot. I know that some consider this to be antisocial and insular, but I've never really been bothered by this. Having received an iPod for Christmas, I've been able to appreciate the privacy that it gives you, and I wonder if there is a generally accepted etiquette for wearing them.

Let me explain. It's probably obvious that a cove sitting in front of a culture hood is wearing an iPod because it's better than the droning of the fans and putputputput of the suction. This means it is all right to talk to him, although don't expect him to take an earbud out to listen to you (because his hands are aseptic).

I suspect that if someone is working at a bench in the wet lab then you have to look at how many earbuds are being worn. One means "Yup, I'm listening". Two probably means "Do not disturb: I've already made a mistake setting up this PCR and if you talk I shall ignore you. If you persist, I shall stab you with my Gilson". Whether the hands are gloved or not might have some bearing on the situation.

Of course, if someone is bopping along and singing "She never drinks the water and makes you order French Champagne" they're fair game and you are allowed, indeed obliged, to interrupt before it's too late.

In an office, someone with both earbuds in is also probably trying to concentrate and does not want to be disturbed, unless it is really urgent. Try sending him an email instead. Either that or he's trying to drown out the power drill that's been going outside the window all bloody morning.

superlative, a. and n.

A. adj.
2. Raised above or surpassing all others; extremely high, great, or excellent; supereminent, supreme.

dismal, n.¹ and n.² and a.

B. adj. [orig. attributive use of A.]

4. Causing dismay; terrible, dreadful, dire. Now in weakened sense (associated with 5): Causing gloom or dejection, depressing, wretched, miserable.

. . .

5. a. Of a character or aspect that causes gloom and depression; depressingly dark, sombre, gloomy, dreary, or cheerless.

When advertising a trade display, with the company in question providing afternoon tea, it is essential not to confuse these two words. The lack of the promised one might result in the other being descriptive of your sales.

My babies! My poor, starved, over-crowded babies!

I got in this morning, went to Stores, saw the stack of autoclave bags and realized that in the heat of microarray analysis and genomic mining yesterday I'd forgotten to look after my cell culture.

They think I don't love them anymore. Sniff

"Will you show me your miniprep protocol?"

As promised, this is the method I currently use for making maxiprep DNA.

I learned this method from an American in the lab where I did my DPhil. At the time, if I wanted to transfect eukaryotic cells I had to perform a double caesium chloride prep based on isopycnic ultracentrifugation.

That was as completely horrible as it sounds.

Marc introduced me to this method. It uses phenol, which is a bit scary (if you know what you're doing the risk is minimal), but produces superb quality plasmid DNA that can be transfected into cells with no further purification. And naturally you can use it for digests, transformation of bacteria, etc. It's cheaper than any commercial kit, probably faster, and certainly more robust. For the multi-tasking (or just plain lazy. . .) scientist, it is full of breakpoints where you can leave the prep and go and do something else, rather than being tied to the bench watching a column drip.

I couldn't do my job without it. Thanks, Marc.

I have been meaning to have a whinge about the scientific kit culture for more than a little while now.

Last year some time, I used a Qiagen miniprep kit (what can I say? I was in a hurry) and found that some noddy had added the blue dye to one of the reagents. Now, some of you will know what I'm talking about, and require no further explanation. The rest of you; seriously, you're better off not knowing.

The point is. . . well, no. Let's step back a bit.

Just over eight years ago I left a DNA extraction technologies company for reasons that do not concern us here. Eighteen months before that I had completed my first project at that company, which was to revamp a range of DNA extraction kits — minipreps, gel extraction, that sort of thing. I compared my efforts with those of the market leader, Qiagen (Promega and the rest, sorry, but even if your stuff is better it's not the benchmark). And even if I do say so myself, I did a pretty good job. My miniprep kit was faster, gave better yield, as good if not better quality, and was cheaper to produce.

It was, naturally (like the rest of the company down the line), torpedoed by a worse than useless sales and marketing department, and intellectually challenged management.

But I realized, last year as I used the Qiagen kit, that in more than eight years the market leader had failed to innovate at all. Minipreps are pretty critical to molecular biology research, and they still charge a 500% markup for something that, frankly, is crap.

Qiagen's idea of innovation is to add a blue dye, so that people can tell that something is mixed thoroughly. Which is bizarre to say the least; doing minipreps is one of the first things you will learn in a mol biol lab, and if you can't get that right first go you're going to have much more fundamental problems. Qiagen did nick one of my ideas, which was to add a collection tube to the kit. Now, I persuaded management that such a tube in the kit would be a good thing, and moreover, it should have a lid with an extended hinge so that it would actually fasten over the spin column while in the microfuge. Such a tube exists (and existed back then), so we just bought a job lot and packaged them with our stuff.

So Qiagen can't even get that right: Their collection tube is un-lidded, so you still have to fart around with different tubes at the end of the prep. To be fair, they did drop the five minutes on ice thing from the protocol, so I guess someone must be awake there.

Now, you might think I'm being hard on Qiagen, and you'd be right, but over the weekend I received the following (edited) email from my mate Tiddles:

Qiagen Maxi-Kit. first run = 1.3µg DNA/µl = ace. 4 times since ~0.3µg DNA/µl = a fornicating waste of my time. Fornicate. Fornicate. Fornicate. Fornicating fornicating kits. I fornicating hate fornicating kits. I have changed kit, changed solution, re-transformed my plasmid and still bollocks. Do you know what they think it is? I actually agree. . . It's growing too fornicating well and thus clogging their miracle fornicating filter system. What the fornication? Growing too well? What am I supposed to do? Put fornicating bleach in my media?

It's expensive, time-consuming, uses an imperial shedload of plastics, doesn't actually yield all that much DNA and, as m'friend Tiddles points out, can not cope with rich media. So to prep a lot of DNA for, say, multiple transfections, you need to do multiple preps. And if you try to use a decent amount of culture (like 101 ml instead of 100 ml) or rich media (2xTY) instead of that anæmic LB muck, the (bloody expensive) column throws up its beads in despair and fails miserably. Just like the Qiagen miniprep, in fact.

Y'see, back in '98, my miniprep kit could cope with buckets of rich media and still spew out loads of top-quality DNA, so I am very down on Qiagen for not coming up with something better.

But so that you know that I can do so much more than just whinge, my very next post will contain a link to the protocol that I currently use for maxiprep DNA. It makes loads, uses phenol, and gives you the feeling that you're doing some real chemistry. Great stuff.

I did not write about this earlier, and I should have. How remiss of me.

Anyway, the 'Best Science Writing on Blogs 2007' is now available, here, and your humble chronicler, once famously described as the Herodotus of the scientific age, is in it.

A couple of minutes ago in my office, a colleague said to me,

"I think senescence explains all my problems."

It's sad when they finally realize this.

I do most of my literature reading via the built-in RSS aggregator in Safari. It looks something like this:

I find it convenient and useful. However, I have noticed a disturbing trend.

Whenever I see the word 'Retraction' in that list, I have an almost irresistible urge to click on it. I don't care about the scientific field or the content, nor even the authors or institute:

Retraction — click.

It's almost Freudian. Help me, please.