Life of a Lab Rat

When I get to the bottom

I go back to the top of the slide

Where I stop and turn

and I go for a ride

A bit of a frustrating week.

The thermal cycler broke down just before it had completed a crucial experiment (but I think it went far enough to get some useful data), someone put agar plates with no antibiotic into the ampicillin plate bag (screwing up my cloning), a Western blot is tantalizingly inconclusive and a beautiful hypothesis appears to have been brutally slain.

Camperdown,™ n
Proprietary name for a broad spectrum anti-fungal agent

e.g.Camperdown brought last week's campsie infection under control.

Henry talks about some typical journalistic scare-mongering.

Now I'm not a developmental biologist, so I'm just basing my opinion on what I remember from seminars and distant lectures. Having said that, the article is an an interesting read, especially seeing as the question 'what does it mean to be human?' is closely related to 'what does it mean to be made in God's image?'.

It's dropped off the front page now, so I'd like to bring your attention to Georg's comment, in which she brings my attention to an article written from a journalist's point of view that, to my simple mind at least, is right on the money.

No, not the video place that is taking teh intaweb by storm.

'Eppendorf' tubes. You may remember I was wibbling about sub-standard tools of the trade. The Greiner rep did indeed show, and was appropriately chastened. I got a free replacement box of 8-tube strips (which appear to be all right) and a sample of eppendorf tubes made by Molecular BioProducts.

Nothing to do with science (except maybe some of the doing of it), but I think I'm in love.

Non-biologists look away for a couple of lines.

For some reason I got distracted by left-handed DNA earlier. It's a bit of a science geek joke, with a serious point.

Okay, you can look back now.

I then wanted to see what else Tom had to say and came across his Errata & Corrigenda page. And he makes the point very nicely that scientific research progresses through the identification of mistakes and falsification of hypotheses. Additionally, most research claims are false and are corrected by further experiment. There is nothing wrong with this; the observation-hypothesis-experiment cycle is how we do science, and some of those hypotheses will be wrong.

I know we've got some hot scientists in this place but one of them ('V') actually caught fire this afternoon.

She lit a match, after noting the head was 'spiky', and some of the sulphur somehow flew backwards and next thing she knew her jumper was burning. V patted it out herself and is unharmed, if a little shaken. There's a burn mark on her clothing, which will be an interesting souvenir from her honours project.

I should have written this up on Friday evening, but seeing as I was driving to Canberra it would have been inconvenient. I did pack the Queen's laptop, but it wouldn't have worked very well in the sauna. So, this post is a tad late. Apologies.

Friday is meeting day in our department. In the morning I set up a PCR reaction, helped a grad student next door with a cell culture problem, grabbed a coffee and went to our regular two-group lab meeting.

I've mentioned before the misconception that scientists deal with facts. There's an interesting debate — rather a scandal — going on over the synthesis of a chemical originally isolated from a Siberian fungus.

Fine, encourage us to submit tax returns online.

I have a perfectly adequate computer system at home (and at work) that suits my needs, except that I can not use it to file my tax return. I seriously doubt that the Feds want to influence my choice of computing platform (because that would be anti-competitive, right?), so the only conclusion that makes any sense to me is that the Australian Federal Government encourages software piracy.

There's a misconception around that research — especially scientific research — is performed with a specific aim in mind. Ghassan makes this mistake:

Research is any project undertaken to reveal new knowledge. Research can be scientific; such as, testing to find cures for illnesses or improve medical treatments.

campsie, n
Non-specific fungal infection.

e.g.We had to sterilize the incubator because everyone was getting campsie in their cultures.

I heard on the radio a couple of minutes ago that Australia faces a severe scientist drought.

Julie Bishop is saying that Australia will be short of about 15,000 science and engineering professionals in six years' time. Tellingly, she has implied that the current (University, I presume) courses and career paths are not good enough. This in itself is progress, I feel; but although the government has admitted there is a problem, we have to ask what are they going to do about it?

The pledge of an extra 50 positions at CSIRO is a small step in the right direction, but there has to be a major rethink in the way science is supported if a real difference is to be made.

All right you life-long Sydney-siders, tell me this:

Why, at the busiest time of day (home time), do they only put six-car trains on the Inner West lines? It was like a bloody cattle-truck! And in the opposite direction ran virtually empty eight-car trains.

Of course, in the morning, it's the other way around: The short trains are running into town and the long trains are coming back, empty. Something, somewhere, isn't quite right.

Aw mate. I read the paper and I must say I'm disappointed.

Oooh. This is a tough one.

I'm torn between

• Flexible working hours and a lot of job variety


• Open-minded yet skeptical approach useful for other aspects of life

After last week's little rant about the portrayal of science in the meeja, I thought it might be interesting to show you a couple of photographs.

This is the view from the lab door.

Thought I'd better include a glossary.

Please email or leave a comment if you want to see anything here.

In one of my previous lives I pretended to be a crystallographer.

In other words, I would attempt to persuade concentrated protein solutions to get together and form ordered three-dimensional arrays - crystals - so that I could then shoot X-rays at them. The purpose of this was to determine their structure.

One of the things I was taught when I learned crystallography was to be very, very clean. No dust, human hair, bits of glass or other muck were allowed into the experiment. The most frustrating thing about crystallography is that all proteins are different, and will crystallize (if they crystallize) under different conditions, and there doesn't seem to be any pattern to this at all. The lab's insistence on cleanliness was an attempt to factor out one of the variables in the process. But I soon discovered that this may have been counter-productive. As with a lot of things in research, people disagreed with each other and there was a lot of intuition and opinion without a great deal of solid evidence. I realize that this might come as a surprise to some of you, to those who, perhaps, believe that 'scientists deal with facts'. The truth is that at the frontiers of science we don't know what's going on and we're trying to find out - that's why it's called 'research'. If you want facts, look in a text book (and they all contain mistakes, too).

So as I went on and got more experienced, I began to welcome small amounts of crud in my crystallization experiments. In fact, one recalcitrant protein only ever crystallized once, along what looked like an insect leg. I was never able to repeat that experiment; although I did have gothic fantasies about breeding every different sort of insect I could find and using various bodily insect parts as nucleants. A little too Shelley, perhaps.

EMBOSS (the freeborn son of GCG) hits version 4. Download site is here.

Lots of goodies in the new version, here are some highlights:

Seriously, Sydney radio is crap, isn't it?

artarmon, n
Pleated or frilly dress shirt, usually worn on formal occasions. Poss. a corruption of d'Artagnan.

e.g.Donald looked quite the swash-buckling pirate in his artarmon. Everyone thought Wil had a job interview, but the bow-tie and artarmon were for a concert that evening.

I keep reminding myself of Sturgeon's Revelation (beware, that article is pretty tedious) that 90% of everything is crud. Nevertheless, I should point out some other weblogs that might be interesting to readers of this site.

I revisited the gel-eating tube question yesterday. I did the experiment in the suspect tube strips and in another brand in parallel.

Guess what? The other brand's reactions were fine, the original strips again ate the gel. How's that for science in action?

Dear Reader, this entry is a bit of a rant. I started writing about one thing, and finished up on a different road. But I think the final destination is the same. There are more things I want to say than I've said below, but I shall save them for another time. love, Black Knight

Something the more socially-aware scientists (ouch! Industrialists can look away now) sometimes think about is our responsibility to the society that pays our salaries and funds our research. When I used to work at the Council for Biomedical Research (names have been changed to protect the guilty) I got involved with one of these 'Communicating with the Public' initiatives. They had a guy with an office and training days and stuff and people started taking it seriously, which was good.

We had a fire alarm earlier in the week (a case of 'provocative maintenance'; we had 'them' in to do some work on the fire alarm system and naturally, it went off) and we all looked at the ceilings, muttered under our collective breath, and prepared to evacuate.

As a good citizen I did a recce of our labs to make sure everyone was out and to close the doors. I came across two honours students in two different rooms.

"It's a fire alarm, out you go," I said.

"But my PCR!" said Student #1, pointing forlornly at his icebucket.

"Leave it. Out now!"

Second lab;

"Fire alarm! Outside!"

"But —" began Student #2, pointing forlornly at the centrifuge.

You get the picture.

The word alone chills the hearts of experienced cell biologists. And when, a couple of months back, someone upstairs was getting strange results from their cell-based assays, the Boss came to me and asked,
'What do you know about mycoplasma?'. The icy black hand of dread gripped me and I spent the rest of the day trying to find a supplier for a mycoplasma detection kit in Australia.

I spent the next two days arguing with various suppliers and AQIS about what I could or could not import and for how much. It seemed that AQIS were upset about the presence of mycoplasma DNA; in effect the small amount of positive control included in the kits I was looking at.

Technorati Profile

I had 96 PCR samples to run on gels today. It was a big experiment; a transfection time course with four different conditions and three different primer pairs.

Hot from Nature, we have Nature Protocols: Recipes for Researchers.

It's in beta, I'm getting a few 404s and the registration/sign in was weird (stealth login, anyone?) but it could be useful. One of those 'wait and see' projects I feel, and probably in direct competition with the protocols section of the OpenWetWare thing I wrote about last week.

What's interesting to me is that these are peer-reviewed methods, with user comments. So it's almost a Wiki-meets-journal type of thing. Hmm.

Bledisloe Cup. Go Toeava!

When it's a management failure.

They've spent the last two weeks replacing the doors to our refurbished offices. I must admit that they look like any other doors to me, and the new one nearest my desk creaks as much as the old one. But it still opens and closes, like doors are supposed to. Apparently the original new doors were too light, or too small, or the wrong kind of wood, or something. So we have improved new doors, which I guess is a good thing.

It turns out that the project was were badly managed and the firm responsible 'lacked local knowledge' (I don't know, I just eavesdrop in corridors) which is why we ended up with sub-standard doors — not that those of us who use them on a daily basis had actually noticed. Ultimately someone has had to pay for the reworking of the doors, whether it's the department (I sincerely hope not) or the firm that was so poorly managed in the first place.

croydon, ppl. a.

Crushed, broken or otherwise dysfunctional.

e.g.This station is croydon. My PCR failed; the Pfu is croydon. I took my car to the garage but the mechanic said it was completely croydon.

It's probably not a good idea to sneeze over your ice bucket while prepping RNA.

OpenWetWare is, and I quote, an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.

Essentially, it's a wiki for biological labs to share information. Think about it: An editable database of all your reagents, projects and protocols and all you need is a web browser.

The aims of the project are certainly laudable: OpenWetWare represents an initial effort to decentralize and lower the barriers to information exchange among all researchers, be they professors, students or research scientists.

This could be worthwhile, or it could be a tremendous waste of time. I'm not sure which at the moment, and it boils down to if it would take too much effort to convert everything we have in (e.g.) Filemaker databases and administer the thing.

I like weekends. Unfortunately science doesn't, and often just half an hour on a Sunday can save a whole day in the week. And that's before you take account of things like cells, which have this habit of growing all day and all of the night.

So it was last weekend, after a pleasant day out with the Queen and Pawns, that I found myself wondering how my transfections were getting on. Now the trains out to Black Castle are pretty good during the week, but a little unpredictable (if not replaced by busses) at other times. The remains of a bottle of wine was also tempting me, and I really didn't think that driving was a good idea. At the same time I was beginning to fret about my cells; were the little blighters growing, was the new batch of FCS good, had I really contaminated a flask. . .?