Life of a Lab Rat

From Alex, probably inspired by 'Australian' cuisine:

Here is the hypothetical situation: It's the end of the world. You are barricaded in your lab. You have unlimited access to water. What lab supplies can you eat? What order should you consume them in?

DMEM comes out a clear winner. Yum.

minto, ?

Come off it, you're having a laugh.

This imposter is not really a structural biologist; he's one of our IT support trolls testing the 3D capabilities of Coot:

Here is the microscope that was used to take those pictures:

The difference between an experienced scientist and a novice in the art is not necessarily that the student makes mistakes where the experienced does not. Rather, the experienced anticipates those mistakes and plans for them; s/he knows when they will occur and how to design an experiment such that the mistake does not matter.

So, to illustrate, I always run asymmetric protein and nucleic acid gels; if I drop them I can tell which way around they are supposed to be. Or, to take a completely random example, when running western blots of multiple samples from two experimental cell types I will make one of the gels subtly different, just in case - oh I don't know - maybe I absent-mindedly ignore cough the labels cough on the soaking trays cough or something like that, then I will, tomorrow, still be able to interpret the experiment.

You know you've been here too long when your RSS aggregator displays

and your first thought is not 'FLICE-associated huge protein, what a cool name for a protein and I wish I worked on apoptosis', but 'What the hell is Flash doing in PNAS?'

This entry is mainly for the benefit of my niece.

Nicole, this is the kind of thing we can see through our really cool microscopes. If you like, I can tell you all about it at Christmas, and when you come and visit us I'll take you to see one for real. Click on the small picture for a bigger version.

mawson, adj
Bitter-sweet sadness or regret

e.g. Although he was excited about going to Australia, Mark was mawson about leaving Cambridge. Black Knight became mawson when he realized that eventually he would run out of Sydney suburbs.

We have had a 'water' audit (yes, we have mainly aqueous solutions) and yesterday had an 'energy' audit (yes, we have to turn things on to use them). I wonder if we are going to have a 'tree-hugging sandal-wearing clipboard-holding hippy' audit, or maybe even a 'is this the best use of public money?' audit.

Talking of hippies, we have had an epidemic of students handing out random pieces of paper this week on campus (which begs for a 'how many rainforests the size of (New South) Wales do students account for?' audit). Especially noteworthy was the juxtaposition of the 'clean energy on campus' sandal-wearing etc. coves with the 'student power' activists.

Wooaah!! I said I wasn't joking:

The moon might be a good place for a massive storehouse of digital information, sort of a Lunar Library of Alexandria (that hopefully won't burn down). That's the idea proposed by NASA scientist David McKay

(from BoingBoing, thanks to Georg).

The New Scientist says
Hollow lava tubes on the Moon could be used as a giant digital library. That's one commercial possibility for the Moon put forth in a white paper by a NASA scientist.

I know there's one or two professional wordsmiths read this 'blog, and I've been having a great time over at Pavlov's Cat just recently. I am going to try to get that part of my readership to consider something.

Alex links to a piece in the NY Times, that raises an interesting point;

Molecular biology is the science of this century. We should be able to build some great clichés on it. But the language of this science doesn’t even give us a toehold. It’s like trying to climb a beaver slide after you’ve been walking through a bog. Perhaps scientists can understand each other when they speak of mRNA’s[sic], and sequencing, and so on. Genomic science needs better words.

There's been some good reasonable suggestions about the name of Ratty, up there.

Yersinia was favourite for a couple of minutes, before I wondered if there were suitable Norwegian names (Rattus norvegicus). I briefly considered Sprague or Dawley, or even SPF, but then I heard on good authority (hello, Wodger) that s/he is is a desert rat. So I toyed with the idea of Ararat, or Shimon, before almost settling on Dot, short for Herodotus.

But late last night it struck me.

Ladles and gentlespoons, I present Monty.

One of my fellow Rats commented that she liked doing cell culture, because what with the laminar flow hood and everything it felt like she was doing Real Science. I know what she means, so here's another photograph of lab furniture; the cell culture, or laminar flow, hood.

There is an arrangement of fans and filters with the general idea that any nasty stuff inside the hood stays there and does not infect the operator, and everything on the outside stays there and does not infect whatever it is that the operator is working on. Obviously this theory breaks down a little bit because you have to put your hands and flasks of cells, solutions, pipettes and whatnot inside in order to actually do anything. We get around the problems this causes by liberally spraying 70% ethanol over the surface and anything that gets put inside (including hands, which are usually also washed with Hibiscrub first). There is also a reasonably high intensity ultraviolet lamp inside that gets turned on when the hood is not in use, to make life unpleasant for any nasties that do manage to find a way in.

And yes, you do get to feel like a real scientist doing real science, and most of us doing cell culture form an irrational emotional attachment to the cell line(s) we happen to be working with at the moment. We care for, feed and nuture our cells and it can be quite distressing (not just because of the time wasted) when, not if, you go to the incubator one morning and find your precious cultures swarming with bacteria, or fungi, or strange beings from the Planet Claire.

I want to make up some RNA loading buffer, right? And I'm googling (yes, Virginia, 'google' is a verb) for a recipe, and I find that a certain company not only makes the stuff but publishes the recipe, too. And then I see the advisory symbols for the product:

.

Now, I get the '4°' symbol — that means store in the 'fridge. But what the hell does the cup and saucer mean? 'Go and have a nice cup of tea while you run the gel'?

If you have a better idea, please post your suggestions here.

ashfield, n
Thick wool weave used for carpets, with a peculiar abstract motif.

e.g. Please remove your shoes before walking on the ashfield.

It's lab talk day today.

And in a quite possibly doomed to utter failure attempt at spreading some reason and clarity in this troubled world, I would like all students to BAN COMIC SANS from their overheads.

We do not deal well with grief.

Hysterical women of Middle-Eastern origin can be seen on news bulletins, throwing their hands in the air and dignity to the wind. In the (political) 'West' we are expected to grieve in private, to take time off for the funeral and affairs of estate, then back to work, to bury ourselves rather than the deceased. Our friends and colleagues are embarrassed. They do not know how to cope with our grief, they do know not if we want an arm around the shoulder or someone just to cry with.

And in the relentless, cutting world we, especially we scientists, inhabit any extra sick or vacation time is weakness; 'You have had your compassionate leave - what is your problem?' Worse, maybe; 'Do the experiment! Write the paper! The French/italians/British/Americans are coming!'.

It's not just bereavement. A spousal argument in the morning can destroy a day's work. Rushing to get back to pick up the children will cause mistakes that if you are lucky you will notice there and then and note in your lab book so that the next day when you look at the PCR gel you do not have to ask, 'what the hell happened there?'.

It might be great science, but it's ruining me as a human being.

This is what happens when you start the autoclave without checking that the water level is above the element.

"Dear Dr Fleming,

Your lab is a mess."

Cells never behave how you want or expect. Except when you least expect it.

Some constants: Transfections are variable. Mountant is messy. Immersion oil is messy. Data are never unequivocal.

Overheard at coffee:

Oh, we (certain technique-people) are far from physiological, despite what we say in papers and on grant applications.

Which is a refreshingly honest thing for a scientist to admit.

For those of you using RSS aggregators to read this (hello Jonathan) there is a new header graphic. And a NameThatRat competition.

That is all.

1. Working out primers that would distinguish between two splice variants.

2.

(a) A sketch to help me explain something to P
(b) Various 5' splicing sites
(c) The molecular mass of something or other and a random note
(d) A couple of names jotted down after a conversation with my ex-boss when he visited.

When I'm famous I will auction off these memorabilia; or you can make me an offer now and beat the rush.

The video I mentioned yesterday reminded me of what I really want to see come out of all this sciencey stuff. There are vast quantities of data coming out of labs around the world, both 'big science' and 'little science'. The trick is to tie it all together, so that it makes some kind of sense. The second trick is to present it.

It is going to take a while, and some serious thinking about interdisciplinary communication, but I hope that within the next twenty five years or so we will have a working in silico cell. A program that models in exquisite detail the complete (OK, maybe 90% — 'first draft') secret life of any given cell type. Computing power will not be a problem, we will in all likelihood have something smaller than a handheld that can cope with it. But imagine, taking a computer model of a leucocyte, giving it some P-selectin and letting the program run. Or changing random proteins to see if they behave as oncogenes. In time we would catalogue all this information but being able to predict cellular behaviour from a rigorous theoretical background would be incredible.

Imagine it as a teaching tool, too. Build — or use holographic technology to project — a 10 metre spheroid, crowded and swarming with life; walk inside it and follow individual pathways and processes. (Take Australia. Scale it down until it fits across the length of your hand. That scale — inverted of course — is the same order of magnitude as your typical animal cell blown up to 10 metres across).

By 2030? Possibly. I'm not making a prediction, I'm trying to inspire. I think we could do it by then, given the phenomenal increases in both biological knowledge and computing power over recent years.

elanora, int.
expressing surprise or dismay.

e.g. Elanora! It's Friday already and I need another silly-sounding suburb!

If you're as old as me, you might remember sometime in the early '90s being completely blown away by Tim Springer's wonderful videos of leucocyte extravasation. For some reason I seem to have a lot of non-science types reading these ramblings and I reckon I've probably just lost half my readership, so I'll step back a bit and put things into plain(er) English.

If you happened to pick up, say Jandl's Blood: Pathophysiology, you might find an opening paragraph that reads something like

Blood is a complex suspension in plasma of nondividing differentiated cells which continuously perfuses the vasculature. It contains a mixture of several very different kinds of cells, all of which stem from an oligarchy of progenitors that originate in marrow or lymph follicles.

Which is a rather complicated way of describing the red stuff that leaks out when you get a real bad paper cut. Essentially, blood is made up of red cells, white cells and little bitty things called platelets, all floating round in a kind of white wine sauce. And it gets everywhere. The red cells are the little fellas that carry oxygen and nutrients around, platelets help stop the red stuff leaking out, and white cells, like knights of old on armour'd chargers, fight infection. Depending on the sort of white cell you are, you can throw chemicals or antibodies at nasties, or actually muscle up and eat invading bacteria and other bits and pieces. Yummy.

You know, if I was the mischievous sort (be quiet, Paula), then I could have great fun in the next couple of days:

Hi all, Just as a reminder to look after the guys who are currently checking the safety of all our electrical equipment. As they are not scientists they don’t realise that they should be wearing gloves to handle certain equipment in places like an ethidium bromide room. So keep an eye out that they don’t handle any contaminated equipment (chemical, radioactive etc) without suitable precautions.

I am out for revenge after my screen and keyboard were covered in paint dust:
"Oooh, no, you can't go in there. That's where we breed the radioactive gorillas. And that's where we keep the failed cloning experiments. It's probably safe but I just need you to sign this indemnity form". . .

As the regular reader of this weblog (both of you) may have picked up, I arrived in Sydney and therefore started work at the Maze not so very long ago. I did go through the very useful "Oh, you must be new here, I'm XXX, who are you?" phase — useful because I had an excuse for not knowing who anyone was — but that honeymoon period was brought to an abrupt end when I gave a departmental seminar just a couple of short months into the job.

Because my name was all over the department on seminar notices everyone learned who I was. And I was lucky enough be able to put importantsenior names to faces because my host kindly said the names of those who asked questions (and my thoughts were along the lines of "Ah! The assistant head. Right. I'll make sure I remember him"). Problem is, I never forget a face, but have a lousy memory for names. So when I was introduced to a group of ten or a dozen people I'd count myself lucky if I could remember the names of two of them. Usually I can bluff my way through the first couple of meetings with someone new to me until I get their name into the rather disorganized filing system that is my memory, so people don't often see the turmoil I'm actually going through.

But aside from that, one rather ego-stroking upshot of giving a seminar early on is that the senior staff know me, and always say "Hello Black" when we pass in the corridor or on the stairs. That is nice because it makes me feel like someone (I'm not sure who, exactly, but anyway). The problem of course is that non-senior people also know me, people who do not have their photos on the name board downstairs. And these are the people I actually might want to work with, or steal reagents from, or — heaven forbid — take out for a beer.

it suddenly struck me that next week is Honours Awareness Week. Our lab tends to take on a fair share of Honours students.

But it can all be very daunting, and if there are any prospective Honours students who would like a quiet word about the lab and stuff then feel free to leave a note here, or drop me a line at blackasknight@gmail.com. I'll now go and try and persuade the boys and girls at Sydney Life that they should direct people here.

Perhaps it's obvious, but I should add that my field is biological research. So if you're an arts or humanities student, then chances are I won't be able to help you. But you can treat me to a coffee anyway.

The thing that makes a weblogger's cockles warm is feedback. We might know that people are reading us — I can look at the webserver stats and see all those lovely unique hits, you might bump into me on the stairs and say something nice — but what really gets the pulse going is comments. That someone has taken the time to prestidigitate the keycaps and share their ineffable thoughts on my humble weblog . . . it's better than drugs.

Trackbacks are good, but I'm not going to be greedy.

But throwing it open to all comers can cause problems. And, in theory at least, this particular weblog is under the auspices of the University of Sydney, which might inhibit some of you. And you have no idea what I think about comments or how I might decide what is suitable, because I haven't told you yet.

So, having read Georg's little spiel this evening I'm going to iterate my comments policy in the hope that maybe more people will feel able to natter away, and maybe we can get some good dialogue going.

Most of what follows is shamelessly nicked from the templatedata, and is aimed at protecting me as well as your rights to free speech (do we have such a thing in Australia? Or am I being seditious again?).

Outside the Maze there are some trees. I first noticed them late last summer when the green-leaved trees mysteriously vanished overnight, and were replaced by morning with trees bearing red and gold and yellow leaves. And the trees were now in boxes.

Time passed. As winter took hold, the trees suddenly had no leaves. More time passed, and this morning I noticed that the trees had small, green leaves.

I have a theory that explains what is happening. Some might say that it is all part of the natural cycle of life, that these trees change the colour of the leaves in autumn, and then they fall off in winter, to be replaced with new buds and leaves in spring.

I scoff, I laugh at such fanciful notions. Ha ha ha ha!

No. It is obvious that the trees are being replaced in the night by new trees that have the appropiate foliage for the time of year. I have not yet seen anyone doing this, but then I am not around the campus at oh dark hundred so it is not surprising that I can not corroborate my theory with evidence. I am also convinced that if the person (or persons, or Person) changing the trees knew I was watching, then he would wait until I fell asleep, or something.

Why else would the trees be in boxes?

Proof that HAL ran Windows?


dbowman% HAL opendoors podbay
/bin/HAL: I'm sorry I can't do that Dave (Permission denied)

dbowman% sudo HAL opendoors podbay
Password:
Opening doors. . .
Done


It might have worked.

If you've enjoyed reading this weblog, then perhaps you'd like to show your appreciation. Say, for example, by making me a gift of this photographic poster of the periodic table.

Geeky as all get-out, but damn' it's cool.

"Nice talk. I understood some words," said the structural chemist to the cell biologist.

It's usually the other way around.

I mentioned that the junior staff in the Maze were to be consulted in the matter of the new Head. I went along to the third of the three meetings that the junior staff representative organized, and I suspect that she was getting a little tired of the affair by then. Oddly enough, most people in this time slot did not bother to show, so it was a reasonably cosy meeting.

We talked about the three self-nominated candidates (and I have to be careful here because one of them passed favourable comment on this weblog as he saw me swearing at the printer this morning, which revealed that (a) he reads this drivel and (b) I am, to one person in the Maze at least, fully nonymous) and their relative merits. As two of us in that meeting are still relatively new to the Maze it was a good opportunity to fill in some juicy background details. My lips, naturally, are sealed and I am very much afraid that you will have to wait for my memoirs before saying anything about that (if, on the other hand, you're authorized by a tabloid editor to offer me, say, half a million Euros I might reconsider).

The chair then asked if we could think of anyone other than the nominated candidates who might be suitable. Unanimously we agreed on one person, who it turned out was also the choice of the previous two meetings. Had this person nominated themself there can be little doubt he'd meet with major approval. The way this works, the Dean can ignore the nominated candidates and ask this Fourth Man if he'd consider doing it. So we shall see.

gymea, Path
A non-specific disease caused by campsie-like fungi and communicated by sexual connexion or accidental contact.

e.g. I had a touch of gymea but some Camperdown™ cleared it up.