Life of a Lab Rat

Just a quick one:

Alethea links to a page of linky goodness about gender (in)equality in the sciences. There's a whole heap of stuff there that is relevant to over half the human race.

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We are pleased to inform you that the sequencing price for the reaction,
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Damn. That was our last, best hope.

What's wrong with this picture?

Here's the full text from the University's website, accompanying the single image:

Physicist Laszlo L Kiss last night captured these stunning images of the lunar eclipse.

The eclipse began at 6.51, when the earth's shadow made its way slowly across the moon and reached a climax at 7.52, when the moon was entirely engulfed by the earth's shadow.

During the eclipse, the moon appeared to be red, as light from the earth's atmosphere passed through it.
Lunar eclipses occur twice a year when the moon partially disappears as the earth shadows it.

Sometimes, I despair.

Last week, I asked a PhD candidate in our lab whether she'd got a date for her thesis defence. 'My what?' she asked. We looked at each other in mutual incomprehension before light dawned.

It turns out that there is no viva voce requirement for an Australian PhD.

I was shocked and stunned, and not to say a little amazed. No thesis defence? And no auditing of examiners. Well, well. Just how much do you think that little book is worth, then?

Today I read that there are calls to reinstate the viva voce, which raised a little cheer from me. But the whinging has started already:

Nigel Palmer, president of the Council of Australian Postgraduate Associations, said: "Students are always going to be cautious about anything that looks like a viva.

"Particularly towards the end of their candidature, PhDs are close to exhaustion. It's a very daunting proposition to come out and give a stunning presentation. Also, (a viva) disadvantages international students."

Poor wee grad students! Heaven forbid that an Australian PhD candidate should be daunted by anything. Won't somebody please think of the children?

In civilized countries it is not enough to be able to write something; you are called upon to answer criticism of your work and defend your conclusions, to be able to prove that you can contextualize and think independently, and — importantly — recognize when you've got something wrong and be able to reassess, to think on your feet. It's a public exam — and in some countries the defence really is public, the people who paid for your studentship can verify that you were worth it. International students are no more disadvantaged by a viva than they are when it comes to reading the literature (and writing the damned thesis in the first place). Someone who can not give a talk in the language of the country they do the lab work (I'm ignoring humanities/arts. Sticking to what I know) has a more fundamental problem than being able to defend a thesis. The argument about external examiners does not even get off the ground. Additionally, if someone can not complete a (non-coursework) PhD in three to four years, then serious questions about their ability, and that of their supervisor, need to be asked.

Look, a PhD is not about doing great science. It is about teaching you how to think like a scientist. That's why it is possible to fit it into three years. No one seriously expects a PhD to be your "life's work", or a new PhD to have a great publication record. We know the pressures of a PhD and we're looking to see if you have the nouse and the gumption and the sheer bloodymindedness to cope with real research. You do not actually start to be a scientist until you begin your first post-doc, when you will be expected to think for yourself and not have your hand held all the time, and cope with serious deadlines. In the real world, people are not going to wait for you not to be exhausted and daunted before doing something. And guess what boys and girls? Part of the training is to be able to give a full seminar, not just answer questions about your work.

And yes, a PhD is bloody hard work; exhausting and daunting. That is precisely why they are so valued.

Oh, we like this.

These glasses were designed with wedding gifts in mind, but are equally fit for [...] Nobel prize celebrations.

They only ship to the US, which is a shame. Perhaps you could get me some boxers instead?

(HT to Eva)

I wonder if the art of subtlety is a lost one?

Over at lablit.com we've been talking about courtesy in the lab, specifically the leaving of notes by and for other labrats.

Here, in our gel room, we have three boxes. One for big combs, one for small combs, and one for spacers. This seemingly simple arrangement appears to be too complicated for some people, because I often find myself having to look in the big combs box for small spacers, and I'm sure I'm not the only one because yesterday this message appeared on the whiteboard:

This morning, I was still having to look for small spacers in the big combs box. Maybe the art of subtlety is not dead; it's just that the target audience is too dense to get it.

This is Science.

You try. You push, you fight, you struggle. You take tiny, baby steps, and all the time you feel like you're running to stand still. Everyone else seems to be successful, and your plugging away only draws attention to to the void that waits where your next paper should be.

But still you try, hoping against hope, long ago going through the place where any sane person would have given up because deep in your heart you know that this is the only thing you can do; the only thing worth doing.

And maybe you look at the papers in the field and realize that the experiments that set you off on this wild goose chase were complete crap anyway, and the mechanistic interpretation, if there is one, is deeply, fundamentally flawed. You present a poster with your ideas, which, despite — or maybe because of — your lack of results, is very pretty and even enjoys a brief moment of glory on display alongside the prize-winners of this year.

Others need convincing, so you perform more experiments, and with tragic inevitability any data you generate are variable, standards don't and negative controls aren't. Little hints here and there suggest you might not be completely crazed, but you wonder if you've given your boss any reason at all to believe in you.

Then one afternoon you sit down to look at some very preliminary data: incomplete, waiting on the proper controls and still shy of the experimental nirvana that comes from n = 3; and you really don't know what you should be doing with this program but you fight it because by God it's not in you to give up, and you realize that you're reading the wrong strand of the chromosome but when you finally get the numbers to match six bases SHOUT at you from the Ensemble web site and you echo the shout to the office as you realize that here, indeed, is an Answer.

All your heartache and disappointments are forgotten in that sweetest of brief moments. You are the only person in the entire world to know what you do now.

You savour the exultation while your pulse recovers, then you grab your scribbled notes and a pencil and hotfoot it to the boss's office, where you try to keep the shaking out of your voice while you explain what you've just found. His reaction stuns you, as he leaps from his chair and calls in other members of the lab who have a vested interest in this project and whose own work has just been vindicated. You have to explain the result three times while phrases like "this is the best result" and "this is so fucking cool" are bandied around carelessly. The uninitiated look on, somewhat bemused.

Then comes the inquest, the 'whatifs' and the 'yeahbuts' and you have to explain how your model appears be right, pending further investigations and appeals and peer review. It's dark outside, it's late and you still need to set up a PCR before you can leave.

Nonetheless, they can not take it away from you:

For a Day, you were King.

As Dr Chou and myself walked to Redfern last night we mused about how lucky we were to work with some very smart people; people who (within a rather narrow community, admittedly) are world-famous.

And then this morning I looked at the front page of Nature.com, and read a name that I know is familiar to at least some readers of the Rat. Maybe not fame, but a little notoriety at least:

Oh, the main picture there; I don't think we're related but she may have tried to chat me up at a party once.

Hah! And you guys think I'm a pedant?

Whee. I checked Technorati this evening, as you do (seeing as the bastard spammers have destroyed the usefulness of trackbacks), and discovered that yesterday's post was spreading ripples in the blogospheric pond. It came first to the attention of Peter Murray-Rust, who has a thing (a good thing! — I hasten to add) about open access and open science in general, and thence to the open science community itself, in the shape of Cameron Neylon.

Funnily enough, Neil Saunders then picked it up from the OpenWetWare people, and I do some digging and find that not only did Neil do a DPhil but that he is now in Bostjan Kobe's lab. Bostjan is a long-time collaborator of my previous boss and from meeting him at Lorne he seems to have quite forgiven me for not going to work for him when I had the chance (or forgotten about it).

Brisbane, bleh.

So, anyway, it turns out that I had previously made contact with OpenWetWare, and talked about them over a year ago. Which just goes to show that (a) it's a small world and (b) incest is more fun than you'd think.

This has got to be in the running for the coolest cloning experiment ever.

Last Tuesday a grad student in the reciprocal space cadet lab, let's call him Fu Manchu, asked me if I had any GFP. 'GFP' expands to 'green fluorescent protein', which is a protein that is green, and, um, fluorescent. It's naturally found in a certain jellyfish and glows green when you shine a certain wavelength of blue light at it. This is really useful for studying where proteins go inside cells or whole animals, because you can join the DNA that codes for GFP to the bit of DNA that codes for the protein you're interested in, and put that into your experimental model. Much like I did here, there and elsewhere, in fact.

But Fu Manchu didn't want to localize a protein in a cell (because as I hinted above, he's a scatter-brain and wouldn't recognize a whole cell if it mitosed); he wanted the protein itself to use as a crowding agent in some unspeakable experiment. I had to tell him that no, it wasn't the sort of thing I kept in my fridge, but I did have the DNA that codes for GFP in a plasmid vector and he was quite welcome to take it out and make the protein in a system of his choice. It would take a few days to design and make the primers and do the PCR but it would be simple enough.

I went to have a cup of tea and realized that actually, GFP in a protein expression vector, that is, in plasmid that we use to make vast quantities of purified protein rather than in a different sort of plasmid that we use to make relatively small amounts of protein in situ, might be a useful reagent and I was a damned fool for leaving a very similar reagent in Cambridge and not getting it shipped over with my other useful bits and bobs (and I couldn't get it shipped in the time frame that Fu Manchu wanted it). So I trooped back to the computer and had a look at restriction sites, and realized that if I was only semi-clever I could cut the GFP gene out of the one plasmid and into the other sort.

So on Wednesday I set up a couple of enzyme digests, purified the appropriate bits of linearized DNA and set up the reaction to stick that gene for GFP into this expression vector, where it would, if I did nothing else, make GFP and GFP alone (and left a couple of restriction sites so that I could, at a future date, drop in the gene for some other protein after the gene for GFP and make green some-other-protein).

To retrieve the construct made in this way I had to transform some bacteria — in other words, persuade them to take up this new construct and propagate it. The bacteria can be persuaded to do this because the vector you make has a gene for resistance to some antibiotic on it, and you select only the bugs that contain the plasmid you want by growing the bugs on plates that contain that antibiotic. Thursday morning, then, I hoped to see colonies on my plates; each colony having grown from a single antibiotic-resistant bacterium.

That's the theory: in practice you always get 'background'; bacteria that grow because they have taken up some plasmid that doesn't have the gene you really want, or one of a myriad other excuses. And you then have to make DNA from several of these colonies and cut them up in special ways and all sorts of tedious stuff. Knowing this, I chose the bacteria that I would transform to be the sort that cannot help but make protein, even when you don't want them to. And I reasoned that the bacteria that had the right plasmid, that is with the GFP in it, would be green.

On Thursday morning then, I took my plates upstairs — which indeed had colonies — and asked to borrow Tiffany Case's fluorescent microscope. I told her what the plan was, and we looked at the plates together, and this is what the butler saw:

That's two photographs of the plate. On the left, normal light, and you can see all the colonies. On the right, we've illuminated with blue light and the only colonies you can see are the ones that are making GFP, and are therefore glowing green. Ignore the black pen marks — they're just from when I counted colonies. Here's a closer look:

.

See those two really bright suckers? They're making GFP from the DNA I gave them. That third colony isn't, and therefore glows not. So on Thursday afternoon, forty-eight hours after conceiving the experiment, I was able to hand Fu Manchu a fresh plate containing bugs that make the protein he was after.

The University's main campus telephone system is currently experiencing a large number of faults. This is due a fault in a major cable that feeds many telephone services to buildings across the Camperdown / Darlington Campus.

If your telephone service is faulty please contact the telephone fault
line on ext. 42053 or 9750-1080

Priceless.

Female PI to male group leader, during a post-seminar discussion of a particular method:

Come along and spend three hours in the dark with us

This incident reminded of when I was a fresh-faced young student doing my Part II lab project, and I took the new lab tech upstairs to show her the dark room and X-Omat. We got back to the lab and my supervisor asks her, "How was it for you?".

You could hear me blush.

The major difference between myself, and normal people such as Dr Chou, is that when an email comes round bearing a request for a piece of equipment, say a "magnetic particle separator (or a similar machine)", he will actually puzzle over the request for a couple of minutes wondering if he has missed something obvious; whereas I will witheringly declaim "It's called a magnet" and hit 'delete' without further ado.

What's a 'permierwhip' and should I go to that interesting-looking shop in Newtown to find one?

(from http://www.usyd.edu.au/news/rss/newsSite1.rss)