Life of a Lab Rat

I reckon I should retrain.

The average salary (average!) for a radiologist appears to be Au$600k. Yes you read that right, six hundred thousand (~quarter million, Sterling).

Or maybe mining.

A north Queensland recruitment agency said there was huge pay growth across the whole spectrum of professions in the region, not just the mining and engineering sectors.

When PAs are recruited at substantially more than I earn, fourteen years after completing my doctorate, you might understand why we scientists are a little sensitive about money.

My comments on sexism have obviously been taken to heart. There have been witterings from certain male students about 'roosters' and 'hen pens'. One of the female students has hit back, with a commentary on a Far Side cartoon that went up on the whiteboard:

And while I have your attention. . .

FSP has an interesting piece on "Sexism-driven science",
and this email (about indoor football soccer made me laugh (emphasis mine):

We need more girls so everyone is welcome.

You can spot a protein chemist/molecular biologist who is also a parent by his or her reaction to the smell of bugs grown in minimal media.

Your non-parent will probably say "Ew, stinky" with a side-order of an attempt at description. The parent, on the other hand, will immediately file the smell alongside breast-fed baby's nappy. The nappies that look like they have mustard or sesame seeds in them.

Aren't you glad this weblog isn't scratch 'n' sniff?

Those of you not in this business possibly do not realize how outrageously expensive is the actual doing of science. In the same way that medicine is (artificially) expensive, suppliers of chemicals and equipment to scientists are ripping us off. And it's worse in Australia — there is a stupendous markup that is not accounted for by the obvious extra expense of shipping and storage.

The Black Queen last week discovered that by the simple expedient of sourcing certain not uncommon (and certainly not patented!) chemicals directly from a supplier in the US rather than a multinational distributor of exorbitantly-priced gear with a warehouse in Australia (mentioning no names, but think non-amateur times ten to the sixth), we can save about 12,000 dollars over six months to a year. Including shipping. Twelve grand! And we're not exactly a process lab — nor a manufacturing one.

It's good news for the lab, not least because I'm about to blow another 4 grand on these blasted microarrays. I'm also going to a conference in Maine at the end of June, the plane tickets for which — for some unfathomable reason — are going to cost more than the tickets I've just bought for London.

So every penny helps. Swings, roundabouts, etc.

Anyway. I have, he declared grandiloquently, A Plan.

You see, as the globe, because of the internets, keeps getting smaller, the price of actually oil keeps going up, making travel more expensive. Then there's global warming, fossil fuels are running out, omigodwereallgoingtodie etc., which is only going to make conferences and collaborations more difficult, especially stuck out here on the A E of N. So I'm going to do over a bank apply for money to construct a small fleet of tall ships on which there will be ultra modern labs and a helipad for emergency supplies. We'll cruise the world, working hard, collaborating with anyone who has money but a green conscience, immediately and imminently in touch with everyone via our satellite uplink.

Oh, and a couple of these in case PromegaQiagen pirates show up.

For reasons that may or may not be important, memorable, or even strictly adhered to, I'm going to try to divide the types of posts that I write here and at the other place (my anonymity was always pretty precarious, yeah?).

Here I'll concentrate more on the doing of the science, funny things that happen on the way to the forum and basically 'outreach' — talking to you folks who do other things than tinker with the very fabric of the created order for a living.

If you're a scientist then you've probably heard of Nature Precedings,

a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by our professional curation team for relevance and quality, but are not subjected to peer review. We welcome high-quality contributions from biology, medicine (except clinical trials), chemistry and the earth sciences.

Turns out, from a comment made by Hilary Spencer over at Jennifer Rohn's weblog, that pre-publication research includes stuff that didn't work.

I am eyeing my thesis, curiously and thoughtfully.

One of the great things to come out of the internet phenomenon is RSS. If you don't know what RSS is by now, you've probably got someone to print this off for you so I'm not going to bother explaining.

As I've mentioned previously, RSS makes it ever so simple to keep up to date with my favourite journals.

I realized that Trends in Biochemical Sciences, a review journal that I remember fondly from my graduate days, is not in my feed. So I tootle off to Google, find the website (spit, Elsevier) at ScienceDirect and click on the Article feed button:

Which leads directly to a custom 404 page saying Feed? What feed?

Come on people. It's two thousand and bloody eight. This isn't, never was, rocket science.

Thank goodness for BaRf.

Henry is on the lookout for short stories to be published in the Futures series in Nature. If you have a personal or institutional subscription to Nature you can read them all: if not, there are some freebies here.

There are also Instructions for Authors if you're interested.

The arrangement of chemical stocks on shelves is important. But what causes arguments is whether it should be alphabetical by common name, or alphabetical by chemical symbol.

Obviously for some things — amino acids, or Tris and MES perhaps — the common names should win. However, and the first labmate who could immediately recall the mass of sodium chloride agrees with me, sodium chloride should be under 'N'.

We both automatically look for potassium salts under 'K'. Et cetera.

Wars have been fought over less.

Maxine asks an interesting question in her comment on my previous post:

Do you see women behaving in a sexist manner, also? Flirting, basically, with the powerful males in senior roles, when they happen to be around. Or exaggerated over-friendliness when they spot a "more powerful than them" female?

I'm not entirely sure that I have, but then I might not be sensitive to that behaviour. Usually I'm too buffeted by the Westerns of outrageous fortune to notice what's going on 'above stairs'. Joking aside, it's something to look out for.

And in related news, Chall points out that sexism hurts men, too. This is something I've noticed, especially the bit about it not being 'done' for men to take time off to look after sick children (while their partners, you know, actually work.

I'm not going to whinge about this 'reverse-sexism'. It's not the battle that concerns me most. I am very fortunate here in that I feel I can work at home some days and look after sick Pawns. My day is much more flexible than the Black Queen's, who has chosen to work school hours so that she can be with them in the afternoons.

I also remember a previous (male) boss ranting to a female post-doc in one of my past lives, "Why doesn't your husband take time off when your kids are sick?". Enlightened self-interest? Quite possibly, but hey, if that's what it takes.

One of the advantages of working in a lab with a healthy gender balance is that sexist behaviour does not really get a chance. I can't vouch for the echelons of management, but at least here on the ground anyone attempting to discriminate, put down or otherwise disrespect on the basis of gender is likely to get walloped severely.

I should like to think that visiting speakers would be subject to similar scrutiny.

The problem is that this casual sexism is institutionalized. People, even 'ordinary', 'decent' people think it's normal. And it isn't. The test is to ask yourself,

"If this person was male, would I treat her the same way?"

And if the answer's "No", reconsider. Because I might be standing behind you with a cluebat.

The true molecular biologist/protein chemist will recall instantly the molecular mass of sodium chloride to two decimal places. This may easily be verified in the lab.

That one d.p. is sufficient for the sensitivity of our instruments and applications has no bearing on the matter.

The auto chip-holder.

And people get paid to (a) design (b) manufacture (c) market
these things.

We're doomed, DOOMED I tell thee.

(HT to CK.)

A common technique in a structural lab is to grow up a protein in bacteria and purify it. It's pretty much essential to all structural work (NMR of packed bacterial cell pellets is a different matter, and We Don't Do That). To make things easier for ourselves, some people like to grow 'their' protein fused to something else that makes purification easier.

For example, a protein that we'll call GST binds to a chemical known as glutathione. If you can immobilize glutathione on some sort of supporting matrix, then you can use this to pull GST out of a complex mixture of cellular protein (pretty specifically, in a lot of cases). So if you make a 'fusion protein', consisting of your protein linked to GST, you get a quick and simple way of purifying the thing you're after.

A complication arises if you then, as we often do, need to separate the GST from your protein. We do this by using specific proteases, that you can think of as a pair of molecular scissors which 'cut' the fusion protein at a certain place. In this example we have engineered (yes: "genetic engineering". It's What We Do) the fusion to contain this 'certain place' between the GST and your protein. So in theory you can bind the fusion to the supporting matrix/glutathione, treat with the relevant protease, and obtain just your protein.

There are, as ever, technical issues and nothing's ever that straightforward, but this is what goes on all the time in my lab.

Now, one of the proteases we use has the name human rhinovirus 3C protease. A certain company sells it to us under a tradename, let's call it "Scissors"™. Buying "Scissors"™ is expensive - it works out at around Aus$60 per prep. So the Black Queen finagled a plasmid from someone, worked out a method, and now makes our own "Scissors"™, for about a tenth of the price. Thing is of course that Certain Company gets really upset if we say "Scissors"™ — in a publication or whatever — and didn't actually buy it from them. BQ has been telling everyone that we can't call it "Scissors"™.

"Human rhinovirus 3C protease" is rather a mouthful, though: It's a lot easier to ask "Where's the "Scissors"™" than "Where's the human rhinovirus 3C protease?". To keep everyone happy, we've come up with a new name for it. We're now referring to human rhinovirus 3C protease as K-Zyme, which is easy to remember, say and type, and isn't a tradename. So anyone can use it.

And if you would like some K-Zyme, and instructions on how to make it, then apply to the usual place.

From The Australian:

ALL students at [Macquarie University] will have to undertake volunteer work

Well, it made me laugh.

The hot water in the Cage was turned off for what I'm guessing was the Annual Flow Test.

I must have been the first person to use the gents after the water came back on, because when I turned on the taps to wash my hands there was an airlock: the water hit the handbasin with tremendous force and splashed all over my trousers.

Two hours later I went to thaw some cells. I washed my hands with Hibiscrub. When I turned the water on there was an airlock: the water hit the handbasin with tremendous force and splashed all over my trousers.

(Never mind that I know other people had used the hood since the water came back on...)

And why was I thawing cells on a Friday? Because the bloody RNA prep from the KO experiment failed, and I need more cells:

Fortunately it's the lab advance starting this evening. And breathe two three four...

Dear Black Knight

I'm writing to invite you to Science Blogging 2008, to be held at the
Royal Institution, London on 30 August 2008. The conference, organised
by Nature Publishing Group, will unite over 100 of the world's top
scientific bloggers to discuss common issues.

As one of the most popular bloggers on Nature Network, and a prominent
blogger at the University of Sydney, your participation at the
conference would be greatly valued.
...

Full details of the conference, such as they are at the moment, can be
found on Nature Network.

I look forward to your reply and, hopefully, welcoming you to London in
late August.

It ties in rather nicely with my father's birthday back in the UK, so all I need to do is raise some cash for a ticket. Anyone feeling generous?