What we need more of is science.

Hailing the arrival of Spring appears to have been a tad premature, what with the whole cold and rainy vibe that has been going on ever since. I have made excellent use of my time since Sunday by watching the entire second series of Life on Mars. Without wishing to spoil it for anyone else, the ending is somewhat disappointing.
Trawling through ukbouldering in an attempt to stay sane in this god forsaken, flat, rain-soaked hell (I may be exaggerating), I found an interesting podcast. Craig Venter, who some may remember as the guy behind Celera (the private company involved in the "race" to sequence the human genome), has some interesting things to say about metagenomics, synthetic genomics and the future of biotechnology in general here (right click save as). Also of interest is the Science paper that outlines the chemical synthesis of an entire genome-sized chunk of DNA. Badass.
It's stuff like this, and some of the stuff being done by the synthetic biology cats that make you realise there is some fucking cool research being done. Mind you, a lot of the stuff being done here is pretty damn cool too.

On a completely different note, we heard back from Gregor (the mass spec guy), and he was very confident that we'd be able to do what we want to do with our lipid analysis with the equipment available. Score! So if anyone knows where I can get some ergosterol heptadecanoate, I would be most appreciative.

EDIT: you may or may not be as excited as I am about the fact that, should you want to, you can obtain a 25kg drum of cholesterol from China.

Spring in Cambridge

Spring arrived abruptly yesterday, in a flurry of warmness and sun. Ian (my supervisor) told me before I left that there was a reason why so many English poets have expended so much time and ink extolling the virtues of the period between Winter and Summer, and he was right. I went for a wander by the banks of the Cam, took some photos, and generally enjoyed the sunshine. It was all frightfully pleasant and relaxed. It's raining again today, but it's still quite warm, so no complaints really.

Lab-wise, I finally got to run some samples on the NMR. Juan's extraction protocol is the ducks nuts and allows us to pick up a swag of metabolites, but the signal intensity is quite low, so we're going to try doubling and quadrupling the biomass that we extract from, which will (obviously) increase the signal. NMR is quite a cool technique, and unlike MS based techniques people tend to share their spectra, making the identification process quite a bit easier.

On the ergosterol/steryl ester analysis front, I still haven't got a reply from the mass spec guy, although I know he's around because he's a climber and has been posting to the Cambridge Uni Mountaineering Club mailing list. I'd shake my fist, but I think it's bad for my elbow.

It looks like I won't be able to meet up with Franz and Terry for climbing in the Pyrenees because it would have meant taking a Friday, Monday and Tuesday off, which I just can't do. Still, Terry is going to be in the Peak in June, and I might get to visit Franz in Germany. It's unfortunate, but I need to get a thesis written at some stage.

A Font sequence

I got these photos from Ian, the guy who runs the BoulderBus. The problem is at Isatis - 5c, I think. I appear to be quite lanky - do I always look like that?

1. Starting off. Left hand is bad, right hand is a small incut crimp.

2. Tricky match to get left hand on the good part of the crimp.

3. Full stretch, barely sticking it.

4. Feet up...

5. Beached whale mantel - all style baby!

6. Further demonstration of how to do a mantel in the most stylish fashion

Wet weekend

This weekend was meant to be my wandering around and checking out Cambridge weekend. Unfortunately, the weather has been what the English like to call pants, or rubbish. Not the usual rubbish for half an hour then sunny, but genuinely cold and rainy for sustained periods. So I did something that will make my dad proud - I went to a bookstore. I picked up The Games Climbers Play, a collection of 100 articles about mountaineering. It's an excellent read so far, although I keep stopping to reflect on my own climbing, which I suppose is pretty much the point. It was originally published in 1978 and some of the articles have dated quite a lot, but many, including Lito Tejada-Flores' "Games Climbers Play" (from which the anthology obviously takes its title) are as relevant now as they were then. Tejada-Flores adds some thoughts here, which are well worth reading - I think I'll have to track down more of his writing. No doubt you'll find some more climbing related drivel on here before too long.

Speaking of climbing, I decided to takes Steve's advice on dealing with my sore elbow (he's old and knows about being injured) and went climbing anyway to see how it felt. Surprisingly, it feels better this morning than it has since I did it. I still can't pinch very well with my right hand, but it's definitely getting there. The bad news is that Captain Chaos is planning to meet up with Terry (The Hamburglar) in the Pyrenees in May, but I can't make it then. Hopefully we'll be able to sort something out, as Terry's tales of 400m all-bolted routes 600m from the valley floor have me very excited.

Something else that has me excited is the discovery that there is a flickr group devoted to bacon. Awesome.

Fish lipid protocols

I spent most of today cobbling together a method for extracting lipids from yeast cells for analysis by mass spectrometry. A reasonably straight-forward task you might think, but let me explain why you'd be wrong.

First of all, most of the time when I do journal searches I'm on a computer physically at UNSW, where I have a staff number, and probably a password that allows me to access their database remotely, but I have no idea what it is. No problem, I also have a UWS student number that gives me access to their database - except that for some inexplicable reason my access has been revoked, and they don't seem to want to tell me why. Still, I also have a UTS student number which gives me access to their database, and it actually works! I also have temporary access to Cambridge's resources, but unfortunately the combined UTS/Cambridge resources are still less than those available at UNSW. Neither, for example, has access to the journals Methods in Enzymology or the Journal of Lipids Research, which are both fairly handy when you're trying to put together a method for extracting lipids.

Things were further complicated by the fact that just about everyone, whether they're dealing with bacteria, yeast, plants, rats or humans, uses a technique devised by two individuals by the names of Bligh and Dyer in 1959 for analysing lipids from fish plasma. They published this method in the Canadian Journal of Biochemistry (or somesuch stupid journal - I'm typing this from memory and I refuse to look the bloody thing up again). Despite the fact that just about everyone uses it, no one really says anything other than: "lipids were extracted using the method of Bligh and Dyer", which isn't particularly useful, because I defy anyone to get hold a paper from 1959 that was published in the Canadian Journal of Biochemistry. I did manage to find a number of things online whinged about the fact that everyone cited the Bligh and Dyer paper without actually reading it, which still isn't particularly handy. So I tried a search on "lipid extraction yeast", and turned up a book chapter co-authored by Gunther Daum, who is pretty much the guru in yeast lipid biology. So things were looking up, except for the fact that neither Cambridge nor UTS had electronic access. UTS did have a hard copy, so if push came to shove I could see whether my sister was willing to go and photocopy the relevant pages, but that still left the question of how she would get them to me. My next step was to ask Pnar if she had a copy, but unfortunately she didn't. To cut a long story short, it turned out that both Steve and Juan had copies, and that for the 30-odd minutes that I'd been trying to get hold of it, a copy was literally 3 metres away in Juan's desk drawer. Shit.

However, the method outlined was adapted from a paper published even earlier than Bligh and Dyer's method, and was not going to be compatible with MS. Fuck. Somewhat exasperated by this stage, I decided to try searching some other databases, such as Google (that is an in-joke, people), and eventually turned up enough bits of information to sort it out. I knew it required chloroform and methanol in a 1:2 mixture, but it was the nuts and bolts that were eluding me. The methods part of my thesis will be easy to write though:

Lipids were extracted by the method of Bligh and Dyer (1959).

As a postscript, the good news is that I'll be able to measure both steryl esters and free ergosterol using direct injection ESI MS/MS, as well as get a shit-ton of data from a bunch of NMR experiments. All while working with Jules Griffin who is pretty much The Dude when it comes to metabolomics (his paper is the first hit when you type "metabolomics NMR" into Pubmed). So, um yeah. The phrase that springs to mind is a NoFX lyric: "Some people have all the luck, no matter how much we fucking suck".

Some of the above may have been exaggerated for comic purposes.

Climbing in the Pyrenees

My mate Terry, aka The Hamburglar, has just launched a business doing guided climbing holidays in the Pyrenees. Hopefully I'll get a chance to sample his wares in June (ooh-er!), but in the meantime check out his website:

www.climb-france.com

All quiet

So what's been happening? Not an awful lot, is the answer at my end. I have been getting my nerd on (it's Sunday and I am in the lab). I have managed to pick up some kind of RSI type thing in my right elbow from using the touchpad on my laptop, which I then managed to aggravate doing the theraband exercises that my physio gave me to help fix me up after I broke my collarbone. Shitty. Ice and ibuprofen gel seem to be keeping it mostly under control though.

Other than that, the main thing that is keeping me occupied is not strangling the noisy American asshat upstairs. Man, how I hate that guy, with his incredibly loud conversations with his parents until 1am, and his unnecessarily loud music and television. Not to mention the fact that he doesn't do his washing up. Asshat. Luckily, the other American guy is pretty cool. Marcus is doing a Masters in computer engineering/computational linguistics. He and Asshat are from the same university (in New York state somewhere) and I get the impression that he is also not the greatest fan of the guy. Apparently it's not term time at the moment, and all the other occupants of the house will be back soon. Hopefully they know how to shut him up.

Reading over that, it's possible that I actually got RSI in my elbow from shaking my fist while yelling "What school do you go to?" So cranky.

Football

Football, or "soccer" for the troglodytes, is pretty big over here. Who would have thought? Last week we went to the pub and watched the Arsenal vs Liverpool Champions League game at the pub (well, Alex and I did - Pinar, being Turkish, took everyone else to watch Fenerbahce beat Chelsea), and the return leg is on tonight. It's not the best time to be an Arsenal fan as their draw on the weekend all but puts them out of contention for the Premier League, so to beat Liverpool away would be great. Tonights games are televised on free-to-air TV, so no pub mission is planned, but seeing as I don't have a TV I'll have no choice. Bummer.

In other news, I have found a group to play 5 a side football with on Tuesday mornings. So fear not fellow Wombats, I will be fit and raring (sp?) to go for our next season. Just don't expect any raring tomorrow - so sore right now.

I love the semicolon

I love the semicolon
Originally uploaded by duncanmacinnis

I came across a brilliant article in the Guardian about the fate of the semicolon, and how it's demise is indicative of the decline of French language. It's a good read, but Irvine Welsh does put it into perspective a bit when he says: "People get worked up about that shite, do they? I don't fucking believe it".

The same author also penned an article tackling the pressing issue of identifying the shortest world leader. Such journalism should definitely be encouraged.

Cambridge

Well I've been in Cambridge almost a week now and have slain the lumbering giant of Bureaucracy, and have thus been rewarded with the Talisman of Building Entry and the Spell of Wireless Internet Access. Unfortunately the wireless does not extend to my house, so I need to come into the lab to access it, but no matter.

I should probably do a full round-up of Font, but can't really be bothered. Check the photos on Flickr, and believe me that it is an astounding place. We barely scratched the surface, Bas Cuvier alone (where we spent one rainy afternoon) probably has enough lines to keep you going for a year or more. I didn't climb anything super-hard - coming back from a snapped collarbone will leave you weak - but I did climb some beautiful aesthetic lines. The one problem is that you tend to get spoiled by the prevalence of perfect landings, and skip over anything slightly sketchy, which wasn't helped by the fact that the people I was climbing with weren't the best spotters. I'll be back though, of that there is no doubt.

I arrived in Cambridge last Sunday (today being Saturday). The weather was, amazingly, gorgeous, but I wasn't exactly sure where I was going. I knew I needed to go to the Porter's Lodge on Andrews St, but was not aware that "Andrews" and "St Andrews" were used interchangably. My navigation woes were not helped by the fact that the only map I had was on my laptop, nor by the fact that I was toting 35 odd kilograms of stuff in my 2 packs. Nevertheless, I eventually found both the Porter's House and 67 Glisson Rd; my home for the next couple of months.

It is an interesting house, with 10 rooms intended for post-grads. The only other 2 people I have met so far are 2 American masters students, who seem harmless enough. My room is big and has a view over the garden. The shared toilet has the terrifying sound and action of Niagara Falls, while the shower shoots water out at a crazy angle that is likely to take out the eye of some unwary student. The kitchen is well set out, and apart from the massive pile of unwashed dishes that I refuse to touch, is quite clean too.

My first day in the lab was a touch weird; no one knew exactly when I was turning up or what it was that I was going to be doing. This was compounded by the fact that Steve and Debbie (Steve's secretary) were away. However, we eventually worked things out, and I am pretty much settled in. Things are still getting sorted out from the lab's recent move from Manchester, but everything I need is here. Juan Catrillo is in charge of making sure I don't break anything while I'm here, and his support and supervision has been fantastic. He's given me lots of feedback on my project, as well as on the techniques that I will be using, and we are both confident that we can achieve some worthwhile things with the short time available. I've met with Steve briefly, and he's given me some useful feedback too.

The lab set-up is quite different to what I'm used to in Australia, being somewhat post-doc heavy. The people in the lab are Nianshu (post-doc), Pinar (post-doc), Konstantinos (post-doc), Alex (who started here the same day as me - post-doc), Juan (post-doc), Trevor ("lab technician, but really he's the lab manager) and myself. So there are plenty of people from whom to get advice, which I really like. Juan is taking a really active interest in my project too, which is amazing.

Apart from work I haven't been doing an awful lot. I went and saw the Liverpool vs Arsenal match the other night, and have sampled a pint or two from nearby pubs (whoever says that English beer is not good is wrong - hand pumped ales ftw). I've been to the climbing gym twice and found that it may not actually be as bad as I had first thought. A campus board and hangboard would be great though. Today was spent wandering around getting snowed/hailed/rained on and generally checking out the town. It is, it must be said, a very pleasant town, even when you are being hailed on.

Two important things have happened back home while I've been away, Steve got a job in Melbourne and is off to join Meg down in cold town. "Cranky Steve" has been a good climbing partner for a while now, and has held the rope on a lot of my most memorable leads. Good luck mate, we'll miss your cranky lankiness, and indeed your lanky crankiness. More importantly though, my niece turned one while I was away! Happy Birthday Bri!