Archive | October, 2011

Bioinformatics Notes: The Second Installment

31 Oct

Also, the second half of the conversations were in someone else’s book. I’m not just a crazy person writing notes to themselves. I’m occasionally much more than that.


I know I’m arriving really late to the Neon Indian party, but gosh darn am I loving this song.





This is legitimately school work

30 Oct

So I don’t feel bad about having spent the last couple of hours on it.

This is an exercise in ‘world-building’. It’s not meant to be particularly nice writing, or have any structure or plot. It’s just me trying to work out a location in which my story can take place. I basically wrote a place I want to be right now, instead of here in my room surrounded by journal articles on carboxylesterases and blowflies and organophosphate resistance.

* * *

Two smooth, stone columns reach skywards, widening, then splaying towards each other overhead to form a perfectly curved archway. This arch opens onto the courtyard, Oxford’s Market Town. The wide, sunlit expanse is bordered by long, stone buildings on all four sides. There are three concentric squares of cobbled pathways, linked at their corners by broader roads, all funnelling in towards the very centre of the Market Town, where the Fountain sits. Between the pathways and streets are lawns, clipped and well-behaved. Bands of light green, then dark green, then light green map the paths the dutiful groundskeepers follow. The morning air, still cool with night-time, carries the wet scent of cut grass. The almost metallic smell of stagnant water is there too, but only near the Fountain.

The Fountain is supposed to be the heart of Oxford; a bronze cylinder, as tall as two men and twice as wide, with water being pushed constantly from inside it, up and over the rim, spilling in a soft curtain to a slightly green pool below. Carved into the metal in a sensible typeface are words like ‘courage’, ‘perseverance’, ‘dedication’ and ‘reverence’. The water fills the grooves of these values the college holds in such regard, and trickles playfully around the plaque stamped with

Transcendence Fountain
Opened by the Rt. Hon. Lord E. Friesland, 1201
Magica Illuminatio Mea.


In each corner of the Market Town there stands an oak tree. The combined age of these trees would certainly be greater than the college itself, maybe even older than Old Oxford. Boughs radiate from the trunks, gnarled and knotted. The canopies sprawl, green fingers reaching higher than the awnings of the shop-fronts, higher than the pub’s many chimneys, almost as high as the steeple of the Halls. Despite the mass of foliage and branches, there is never a stray acorn or leaf to be seen on the Market Town lawns. The groundskeepers and their rakes make sure of that.

Many of the shops are closed, because it is a Friday morning, and traders know that students like to sleep ‘til past midday on Fridays. The glass window of the stationery suppliers’ is bubbled and yellow with age. The wooden frame it’s set in is almost spongy in places, from a few centuries of damp. Further along the cobbled path is the bookshop, its door flung open to the morning. Inside, the floors consist of dull wooden slats, worn down by students pacing back and forth, heads tilted sideways to read the spines of the dusty books. Opposite the bookshop, behind one of the ancient oaks, is the college pub.

The pub has two wide doors that slide into the walls either side of them, opening the bar onto the courtyard lawns. Behind the bar, polished wooden shelves hold bottles and flasks of every colour. On evenings of post-examination merriment, the warm timber grates as bottles are selected, removed, rearranged, and emptied. The glasses sing as they knock into each other, and the dull thud of pint glasses against cork coasters fills any occasional gap in conversation and laughter. As those evenings turn to nights, red-cheeked patrons drag the sliding doors closed, and the fireplace against the back wall is fed. The sour smell of hops is replaced by thick, warm, smoky air.  The fourth year alchemy students take their position in the plush armchairs by the fire, and roll exotic cigarettes. The merrymaking turns to quiet conversation about philosophy, theology, or the essay on Lebor Gabála Érenn that is, horror of all horrors, due next week. As the fire dims to glowing embers, the remaining students file out of the pub, yawn and stretch and stumble across the manicured lawns, maybe run their hands along the cold bronze of the Fountain, then scuff along the cobbled paths, under the stone archway, and back to their dormitories.

Time of year

29 Oct

It feels really lovely today. Rain outside, an achievable load of school work to get through, and a nice dream last night about my British fiancé insisting that we have the wedding in Australia because that would be easier on my family (he’s very understanding of my sister’s difficulties with travel and my mother’s phobia of flying). His wedding present to me was arranging to have my bookshelf and all of my books shipped to our tiny, sparsely decorated flat in central London. Also, I have a milk crate.

This is possibly my favourite track off the most recent Woods album, Sun and Shade.

Love to your mothers.


27 Oct

I don’t want to write about carboxylesterases any more.

Hurry Up We’re Dreaming – M83
Epic and mind blowing. Listen to it now.

Days – Real Estate
I wouldn’t call it surf-pop. It’s a bit monotonous, but very listenable.

Father, Son, Holy Ghost – Girls
Catchy, poppy, nice non-threatening guitar music.

Sun and Shade – Woods
If you liked At Echo Lake, you’ll like this. Woods don’t change much. It’s nice.

The Whole Love – Wilco
Art of Almost has an incredibly intense build-up. I like it a great deal. I’d rate this in my top 4 favourite Wilco albums.

Psychic Chasms – Neon Indian
Ah! Really really good! Electro where you can hear all the filters and it’s all just awesome. Yes.

Hunger and Thirst – Typhoon
Some really catchy numbers on this. I need to get their most recent album A New Kind Of House, because it has this song on it:

Okay, back to work now.

Haven’t washed since

21 Oct

This came up on shuffle this evening and it basically sums up how I’m feeling today/about summer approaching/in general:


Also, it made me remember the last time I saw Cat Empire live, and how good it was, and how they’re easily one of my favourite live acts, and how I shook Felix’s hand and then nearly passed out.



15 Oct

The ocean’s big and deep and blue,
The sky is much the same,
And if you turned them upside down,
You’d just get salty rain

Organophosphate breakdown

15 Oct

Procrasti-posting is about to kick into gear for the semester. This one is semi-relevant to what I’m supposed to be doing right now though.

Google image search for ‘mechanism for breakdown of organophosphates by esterase 3’ yields this fantastic shot:

I like to imagine that these are biochemists who like to LARP in their free time, and that they’ve named themselves The Esterase Three. They roam about of a weekend, and slay any esters of phosphoric acid that dare cross them.

Might make myself some more procrasti-coffee. Or learn this riff, because it has been wedged firmly in my head for about 48 hours now:

Love to your mothers.


11 Oct

I’m as bad as the lot of them,
Or worse, maybe.

Mine are irrational, nonsensical,  half-magical, all-spectacle,
And they don’t result in me giving to charity.

So I conclude
My superstitions
Are just as bad
As most religions

I find a four-leaf clover, my week will be excellent.
I see a shooting star, I can close my eyes and wish.
I hold my breath all the way through a tunnel
while repeating a name in my head
and that person will stay safe today.
Misplaced pin, falling leaf,
SAVETHEWHALES charity band
infused with Melville-esque significance,
Silver star on a chain, like a crucifix.

A woman of science who counts the number of crows perched on street signs.

One for sorrow,
Two for joy…

And what gets me, what really irks me, what annoys me like nothing else, is the simple fact that it always works.

Which rationally, cannot be the case. I know this, I know it, I swear.

But my eyes are always open to the little rays of sun that clear away clouds when I put a Beatles record on.



Song 2

1 Oct

Like you’re unlikely to have ever heard it. It’s pretty.


“That’s a fat plane”, observes guitarist Graham Coxon, slowly. “You’ve got the sun on one side,” says Damon. “It’s like the moon.” “Let’s all cut out little silver fish shapes out of silver foil,” suggests Graham, “so we have something to play with.”

Damon is still watching the plane, entranced. “That’s the sea and we’re the sky.”
This reminds Graham of something: an episode of Daffy Duck where Daffy turns the picture upside down so that the water becomes the sky and the sky water. Graham remembers it well, and painstakingly recounts all the cartoon japes which follow from this inversion. We listen with the indecently keen interest of the sozzled.

“It’s Gide, man,” mutters Alex James, bass player. “When fishes die they float up to the surface. It’s their way of falling.” (He is paraphrasing a famous remark by French novelist Andre Gide in his journals.)

“Going to heaven,” mutters Graham sweetly. It is the calm before the storm. There ensues a fierce arguement about whether fish really do float to the surface when they die. Right now, on this particular peice of rooftop, it really matters. Alex and I firmly believe that they do. Damon and Dave, the two years sober drummer – dispute this. “The sea would be fucking covered in fish,” argues Dave. Damon tries to insist that Dave’s opinion should carry most weight , as he is not drunk. Graham is more concerned with stirring the debate. “Most fishes,” he ingeniously lies, “when they think they’re going to die, get themselves wedged in a fucking rock and stay there.”
“Fish fall up,” mutters Alex
“They don’t fall up!” explodes Damon. “I have no respect for Gide.”
“Bodies float,” argues Alex.
“They do not float,” roars Damon. “That’s bollocks! Do you want me to ring 999 and ask ‘do bodies float?’ That is crap.”
“This is Gide’s beautiful thought,” says Alex quietly, “and you’re calling me a c**t.”
“You are a c**t,” says Damon.
“Don’t call each other c**ts,” Graham beseeches them. “All I did was try and explain a brilliant Daffy Duck cartoon.”
Personally I think these are reasons to like Blur.

— Blur interview. The Face, 1995