Life of a Lab Rat

What do the words chthonic, eldritch and preternatural have in common?

Some Lovecraftian opening sentence, perhaps? An obscene mélange of tentacles and Welshmen?

No — but then again, maybe yes. They all occur in a News and Views item in today's Nature, by that Senior Editor and master of purple prose, Henry Gee. What's more, they got there as a result of a bet, upon which was riding a hug and a pint.

From the top, then:

But with [the] publication [...] of the draft genome sequence of Branchiostoma floridae, one of the 25 or so recognized species of amphioxus, this eldritch organism is set to re-enter public life.

The age of genomics has rescued the amphioxus from chthonic obscurity, as new data

Such studies reveal the amphioxus genome to be, in fact, of preternatural importance

A round of applause is called for. You don't get philosophers of science talking about this sort of japing, do you?

San Diablo reminds me of Marc Zimmer's fantastic site about green fluorescent protein. Among other attractions is a beautiful QuickTime movie of Ca²⁺ stimulating aequorin to emit blue light, which is absorbed by GFP and re-emitted as green light (I only realized it was a picture and not a still picture when weird things started happening as I scrolled down using my Mighty Mouse scroll ball).

But the very special thing on that page is right at the bottom: the rap video by Notorious GFP.

yo i just do it like, oh oh, i be the kid with the laminar flow i just go: hey cell its your birthday, lets party like its your birthday, we gonna inject dna cuz its your birthday, so every single day we transform DNA I'm packing two fiddy micros into my Gilson

(lyrics)

Mental. Total Dagenham.

There's been a bit of discussion in the Cage about the bridge-dismantling video. Those who are interested can read all about what's going happening on the University's website.

But in our proud tradition of getting things wrong, we find that the Cage has been renamed:

To which I would like to add a proposal that could only improve the campus:

Not to mention what the byproducts might do for my roses.

sillyDalton , n.

Unit of molecular mass. See mega, giga, zilli etc.

e.g. "How big is a ribosome? Oh I don't know, a few sillyDaltons maybe?"

sarcomere , n.

Smart-alec myofibril. "Oooh, call yourself a muscle? I've seen better fibres on Kate Moss".

What the hell. Another one:

Last week whilst cloning a gene

Question: Why is the sky blue?
Answer: Because that's what it looks like.

Philip has been exercised by this question. It turns out that the standard response, to do with the dependence of scattering intensity on wavelength, actually comes up with the answer "It isn't; it's purple".

But interestingly, our eyes are more sensitive to blue light than purple, and so the sky only appears blue. This fascinates me in much the same way that no two people ever perceive the same rainbow (for certain values of 'same'). Our reality is indeed influenced if not determined by our perception.

It's like fishing. If last week's was the burley sack, then here's a lure that's positively brimming with potential, or barbs, as it were (I should perhaps clarify that the intention is for each commenter to contribute a single line).

With the demise of Word of the Week, I promised to try something else. I have decided to buy into the 'Web 2' philosophy a bit more, and thought it would be a fun experiment to have a limerick contest.

Well, it's not really a contest, but those of you familiar with ISIHAC will get this one straight off. I provide an opening line to a limerick, and then up to for of you (that's probably two goes each, then) write subsequent lines, in the comments.

The form of a limerick (surely you both know this?) is that lines 1, 2 and five rhyme, and are 7 - ten syllables. Lines three and four rhyme with each other, and are shorter, usually only 5 to seven syllables. The length of the lines may, occasionally, be altered for comic effect, but the rhyming (AABBA) is of utmost importance and it's good to try to maintain the beat and scansion.

Try to keep it clean (implication is often far funnier than explicit obscenity), have fun, and if it's successful I'll make it a regular feature. In the case of multiple entries for a single line, I am the sole judge and arbiter, but I'm quite willing to have complete, alternate versions.

This friendly notice on our lab board

resulted in the following silliness:

Finally, a use for VB.

The Black Queen thinks I'm mean for not letting my young apprentice filch her phosphate buffer, but forcing him to make up his own.

I told her that it's a valuable skill. What do y'all think? Am I a harsh task master or one who is rightly concerned that he learns the ways of the craft?

We're starting up a post-doc group in the Cage. We have already had one successful pub meeting, and are planning further events. It is not intended to be a political group, a post-doc union such as you find in the US, but a more of a social/support network. The students have an active social calendar, under the name 'Amoeba'. Nothing similar existed for the backbone of the Cage's research efforts, so we decided to organize ourselves, and decided on the name 'Nematoda' (a tad more advanced and hopefully more organized).

The sentence "A free-swimming roundworm thus looks rather like it is thrashing about aimlessly" also seems depressingly appropriate.

We have a name, so we need a logo. There's a competition running for one. Earlier in the week I came across a lovely picture of a nematode with teeth;

and realized that the mouthparts could easily be modified to reflect the Cage's initials. Here, then, is my entry to the logo competition:

This gentleman:

informs me that a llama's gestation period is 11 to 12 months.

He's correct, as it happens, and I wish him and his offspring all the best.

Because today it was very windy in this harbour city, I thought you might like this:

There was nearly a riot in the tea room last week when we ran out of real milk and only virtually water was left. A debate on the preference for fat milk versus thin milk ensued.

Being a fat milk person myself, I found this quite intriguing as semi-skimmed tends to be favoured in the UK. Here, the majority was definitely in favour of the the whole cow. But then this is a country where allegedly two thirds of men are overweight or obese.

That is something I really do not get, to be honest. That should mean two in three of the blokes in our building are porkers. And they patently are not. So if my sample is skewed, that means there are some real fat so-and-sos in statistical clumps around the place^[0].

On 31st October, 1517, Martin Luther nailed his 95 theses to the door of the church in Wittenberg, accidently jump-starting what became the Protestant Reformation, scaring the bejeezus out of Roman Catholics everywhere.

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.

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

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.

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.

What biologists get up to when they think no one is watching.

Email received by the entire department just now:

I've put a stack of Woman's Day (current issue) in the tea room. Please feel free to take home a copy. Enjoy!

Ah, the headiness of cutting-edge research.

Conversation overheard at tea:

"Latin should still be taught in schools."

(in all seriousness) "That's the wisest thing you've ever said!"

Misguided?
Misunderstood?

Unravel the truth . . .

After filling in my tax return form last night (and there is a rant to let brew for maximal flavour) tonight I will be filling in the census form online.

An email just came around our lab (I think someone must be reading this weblog). I heartily endorse the sentiment and hope the meme within gets spread rapidly.

Last chance to get your ionized post-docs! All stock must go!

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

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

Bledisloe Cup. Go Toeava!