When I turned my 2010 facebook status updates into a word cloud, I was unsurprised to see the word thesis looming large at the centre. It has certainly been one of the defining elements of the year for me, and facebook was a good outlet. By contrast, my twitter feed was probably more dominated by the election, and the associated politics; I can’t know for sure, as ’2010 in statuses’ didn’t seem to look back beyond the past few days.

On seeing my facebook status cloud, a friend, who has had a similarly thesis dominated year, suggested turning my thesis into a word cloud. So I did.

A word cloud of my thesis

About a week and a half ago I finally submitted my thesis, 40 months lab-work condensed into a document that was worryingly thinner than most. However, you work with what you have; padding the document with unnecessary figures and paragraphs will only serve to increase the length, to the detriment of the quality. As a secondary benefit, a short thesis also means that there is less to be familiar with for the viva, although I’m sure it will not work out that way in practice.

With the thesis submitted, there were few reasons to remain in Edinburgh; the viva itself isn’t until September. So last Saturday I headed south on the train, met my parents and a brother in Birmingham, and then headed off with my parents back to their house. For the first time in five years, I was back in my childhood room, not living out of a suitcase. It also meant, that for the first time in a year, I could get my desktop set up with a decent broadband connection again.

One of the problems with being back home, is the isolation. While I can’t pretend that my village is some rural backwater, without sewers, running water or electricity, it does lack basic facilities, such as a place to buy Jaffa cakes when you get a sudden craving at 8.30 pm.  This dire lack of Jaffa cake suppliers is made even more apparent when you consider the colour of my driving license: it’s green. The inability to drive may seem surprising for someone who grew up in a rural area, but despite the obvious usefulness of the skill, cars bore me, and early attempts at learning soon made it apparent that I wasn’t exactly a natural. Then it wasn’t long before I was off to university, and for the past eight years I have not only not needed a car, but have been living in situations where its often easier not using one. I’m sure I will learn eventually, but I’m wary of doing so, and then not driving for a few years.

Yet now I’m back in rural Wiltshire, and while I don’t intend to be here long, it is certainly far longer than I could cope with being housebound. On top of this, a somewhat lacking public transport system means that I’d be constantly relying on parents or other people for lifts, which is neither polite, fair, or convenient. This is especially true over the next two weeks, as my parents will be in Spain, and the drive back would require I give them a couple of days notice, hardly convenient; oh, and it might break the polite and fair requirements as well.

Without the ability to drive four wheels, I have instead settled on two, and have purchased my first bike for several years¹; it has also been ten or more years since I last cycled. While they say that you never forget how to ride a bike, I was still a bit cautious as I set out on it for the first time. Last night I began with a simple ride up and down the road to make sure everything was flowing smoothly, and today I took it for a short 6 mile round trip to a local walking spot. Fortunately it appears that I do still remember how to ride a bike, and failed to have any embarrassing crashes. The trip also revealed that I need to raise my handlebars slightly, and to tilt the saddle back, something that will depend on my finding a suitable Alan key. The bike however does give me mobility, and in concert with the rail network it should mean I can get almost anywhere. And who knows, perhaps even if I do fail to drive a car for a few years after learning, I’ll slip back behind the wheel with similar ease to slipping back behind the handlebars.

I hope to get back to writing some of the more structured blog entries shortly, once I’ve had a bit more consideration about how I intend to use this website in future.

1. A Trek 7.0 FX, if you are interested, or even for that matter, if you are not.

Collection of storage media

The photo here is fairly atypical, with the collection being of more interest than the photo itself. I’ve tried to gather together as much storage as I could, although stopped short of sticking an entire spindle or two of DVDs on the desk. Similarly the total storage capacity is based on advertised capacity, and thus ignores issues such as formatted capacity and differences between kilobytes and kibibytes. The floppy disk is there more for show than anything else, I don’t even own a floppy drive. While the diversity of formats and capacities is interesting in its way, what is more surprising is how many of them are redundant. The iamakey performs the role previously taken by a hoard of floppy discs, and even the blank CDs and DVDs rarely get used on a day to day basis. Indeed, formats and devices has become the determining factor in how many bits of storage media we’ll need, far more than capacity.

Meanwhile, in other news the thesis progresses, albeit slower than I may like. One of the most disheartening aspects of the thesis is seeing the flaws in your data, especially when you weren’t aware of them before hand. It is an unfortunate element of the PhD, that by the time you’ve learnt one of its lessons, it is often too late to do anything about it. Despite promising myself that I’m never doing another — A promise distinctly easier to keep than most — part of me still feels that if I did do it again, I could do a vastly better job. Of course, this ignores all the critical health troubles brought on by the further stress this would impose.

As well as the photography, I’ve also been giving consideration to this site. In the past I have bemoaned how the organic evolution of this place has caused a lot of the earlier content to have lost its context. This is becoming increasingly important when I realize that I shall be entering the job market shortly, and while I don’t intend to put my url on my CV, I can’t pretend that an employer wont Google me. When they do, I’d prefer that it is obvious what was written when I was sixteen, and what was written yesterday. Even the name of the website dates back to my early days on the internet; I haven’t gone by Jasp for a long time.

There is also the evolution of the web. CSS3 now has decent support in most of the web browsers, and HTML5 is close to being finalized. My online identity is spread across the worlds of flickr, twitter, facebook and several online forums. While pages like my lifestream help bring some of these elements together, I still see room for a greater fusion of these elements under a dynamic, exciting and modern looking website. Unfortunately seeing that this needs to be done is easier than doing it. I’ve tried several abortive designs, and all of them have ended up looking more bland than the current template. As a personal website this place provides no obvious theme to latch on to, and trying to represent ‘myself’ in design terms is challenging for someone who isn’t a professional designer. However, I hope to have a new design of this site up within the next few months, possibly with a new domain name to follow shortly.

In sorting through old CDs during a cleanout before a move, I discovered some old backups. The one from 2001 contained A-level coursework, and a ‘My Music’ folder of two albums. (Bless) The 2003 disc contained a txt file with the following:

TODAY I AM GOING TO EAT A PEACH. NOT A VERY BIG PEACH MIND YOU BUT A PEACH NONE THE LESS. TO BE FRANK I AM LYING, YOU MAY HAVE GUESSED THIS. I AM JUST STUCK AS TO WHAT TO WRITE AS MY PIECE OF CODE, SO I DECIDED TO MAKE SOME THING UP. DO NOT THINK I AM BAD FOR MAKING THINGS UP. I ONLY TOLD A LITTLE LIE, I COULD HAVE TOLD ONE MUCH BIGGER, LIKE I HAD A PET ALIEN OR WAS THE PRESIDENT OF A SMALL THIRD WORLD COUNTRY. INSTEAD I SAID I WOULD EAT A PEACH. IS THAT SO BAD.

I have no idea why I wrote that, or felt the need to back it up.

I’m tempted to rescue a few of the old website designs to show how this place has changed over the years.

I’m sorry that I haven’t been blogging recently, but unfortunately life is currently somewhat busy. I’m in the final three months of my PhD, and stress levels are rising. This has not been helped by having to arrange a move, as I’ll have to leave my current flat at the end of July. In Edinburgh this is somewhat difficult, as it means finding a place in the middle of festival season, somewhat complicated further by my requirement for a short term let.
I don’t mean to pretend that I’ve had no time for kicking back, but unfortunately it has meant that I’ve wanted by free time to be somewhat less productive than composing blog entries. Of course, I’m sure I’ll more than make up for this when I come to write my thesis, and blogging and twitter suddenly feel like huge distractions.

On Saturday I attended my first wedding of the year. The weather was absolutely gorgeous, and the whole thing went off seemingly without a hitch to the various guests assembled. Well, apart from the bride’s car breaking down, but what would life be if it couldn’t mimic a sitcom every once in a while. But in short, everyone was in a great mood, and the whole thing proceeded with a genuine sense of warmth, which was down to more than just the weather.
The fact that the happy couple were tying the knot wouldn’t come across as a surprised to anyone there. They had been together for many years already, and to anyone who knew them their marriage had become a matter of when, not if. Two people recognising and celebrating the fact that they love each other, what else could be more deserving of celebration?

You’d think so anyway wouldn’t you? Except for some people, a change of one small detail, one which I have in fact neglected to even mention in full, would change the above situation from something which should be celebrated, to something which should be prevented.

Today the Californian Supreme court voted to uphold Proposition 8, a dark stain which had made Obama’s victory in November, somewhat bitter-sweet. For the 52% of Californian voters who gave their support to the legislation, gender is far more important than love when it comes to marriage. Seemingly “Life, liberty, and the pursuit of happiness,” bears a footnote ensuring that it is somewhat tempered if you happen to love someone with the same genitals as you.

“The freedom to marry has long been recognized as one of the vital personal rights essential to the orderly pursuit of happiness by free men.”
-Earl Warren 1891-1974
Governor of California 1943-1953,
Chief Justice of the United States 1953-1969

Of course, America has been through this all before, albeit in a slightly different guise. It has been 42 years since Earl Warren, a Californian, overturned Virginia’s Racial Integrity Act, and ended race based restrictions on marriage throughout the US. I’ve borrowed a quote from him, which is as valid now as it was then, and I hope that he’d approve of its usage in this context, even if it would distance him from 52% of voters in his state, and countless members of his Republican party.

Sitting with a pipette here within my lab
Waiting for the cells to grow.
In perfect isolation here upon the plate
Waiting for the cells to grow.

However much work you put in, and however hard you plan your experiments, there will always be the occasion when every experiment you have running hits down-time at the same point. Whether this is waiting for cells to divide and grow until they reach usable levels, or for a supplier to send a much needed antibody, there will be occasions when you end up unable to do the experiments which you have prioritised.

When downtime occurs it is a good time to catch up with reading, polishing notes and sorting out benches. It is also a good time to make sure everything is in order, and to check that you have everything ready for the work to come. There is nothing more frustrating than reaching the middle of an experiment and suddenly realising that the key reagent you needed has been contaminated. However, what is surprising is that it is usually possible to fill this time, and it is rarely time wasted; sometimes these little tasks take far longer than reason would predict.

A few thoughts this week, mainly as none of them were substantial enough for a full blog post.

Swine Flu

Jumping in first on the topic which is most likely to generate general interest, I’d once more like to point people at the post I wrote covering the H5N1 virus. Anton Vowl, over at ‘The Enemies of Reason’ also has a bit to say about the way the media are treating the incident, namely: Aaaargh! We’re all gonna die! Noooooooooooo!

Still, I suppose it makes a break from everyone being unemployed and moneyless.

New Phone

This weekend also saw me upgrading my phone, as well as spending several hours trying to convince three that I really didn’t need two accounts with them. I realise that I should probably have followed their usual upgrade protocol, but the handset I wanted wasn’t in stock, and at the time they implied that meant I’d have to choose another handset. Turns out I could have still chosen the handset I wanted; it would just have taken a bit longer to arrive. When I tried to close the old account they decided to explain all this to me, and encourage me to take the new handset back, to allow me to obtain a new, identical, handset in its place, with all the heading off to strange delivery depots that this entailed. Sure I could keep my number, but considering that I had already sent out masses of text messages giving people my new number, this no longer seemed like such a benefit. I was also unconvinced by the fantastic benefit of the loyalty points I had accumulated, when I realised that the 32p per month saving on my tariff seemed to mysteriously match up with the 2.5% reduction in VAT, which three don’t remove until the final stage of the billing process. It took me a while to convince the ‘customer retention program’ of this, and involved being on hold for an hour to an empty office. Thanks three.

The main reason I was upgrading was to take advantage of an included data-plan, without any increase in my monthly payments. The ability to access the internet on the move would be incredibly useful for things like Google maps, price checking, and of course, twitter. As an added benefit, three also offer unmetered Skype traffic, , which is bound to prove useful.

When I entered the store I was interested in looking at the INQ1, which the three brochure had advertised as the only phone on the plan. The handset looked functional enough, and felt solid in the hand, but I was a little bothered by style, which felt as though it was aimed at a market a good few years younger than me. There was also the concern that many of the features were very embedded in the phone, and although accessing facebook while on the move is a nice feature, I’m not sure that I need it tied in to the very centre of my handset.

Instead I went for the more adult looking Nokia E63. I’ve had good past experience with Nokias, and hoped that the Symbian operating system would prove a bit more flexible than the INQ1′s proprietary system. The WiFi support in the E63 will also be a nice feature to take the load off my, admittedly huge, data allowance.

I had mistakenly believed that the E63 had an inbuilt GPS reciever, after misunderstanding an entry in the menu. However, on subsequently playing with it, I have discovered that its Mobile mast triangulation system is stunningly accurate, and Google maps was able to place me at the correct corner of a crossroads.

The end of my PhD is rapidly approaching, and suddenly it no longer seems some distant event. By the time Christmas comes around I very much hope to be out of the lab, and to have a good chunk of my thesis written up. However all of this means getting the lab work finished, or at least in a state in which it is possible to write up.

As things stand at the moment that goal has yet to be achieved, and there as still a few key experiments that need to be completed. The past week I gave the first run through of one such experiment, and am currently in the ‘debugging’ phase, in which I try to work out exactly where everything has been going wrong. Its one of those tasks which is okay in the short term, and can even be quite satisfying, but which gets demoralising if it runs on too long.

Fridays result was initially a bit confusing, until I realised that what it was actually telling me is that an earlier result was the misleading one. Fortunately everything is still in order, and it hopefully means that I’ll be able to address some of my problems on Monday. The rest of the problems however still need further scrutiny.

All this meant that I was in the lab this morning preparing materials for use on Monday. I have already decided that I’ll try and make the most of weekends between now and September, although that doesn’t quite mean pulling a 10/7. Don’t get me wrong, I’ve been no stranger to the lab at weekends, but previously I have tended to use them to facilitate the weeks work, rather than as working days in and of themselves.

This pre-poster post will probably be followed by a post poster post, post poster. I’ll keep you posted.

Well its not a post exactly, but I will shortly be presenting a poster at the Rubicon Conference in Lisbon. While this is my third European conference, it is the first at which I’ve had a chance to present. At previous conferences I have been somewhat hampered by a lack of data, but fortunately lots has come together in the last six to eight months.

Unfortunately academic posters are somewhat removed from the coloured pens and large lettering of the posters of primary and secondary school. However I’m still actually looking forward to having the chance to discuss my work with people who I don’t already see on a day to day basis. As a result I’ve been bringing together the relevant material and deciding what to present, and what to leave. My limited data means that this isn’t too troublesome, however it still isn’t possible to throw everything I have on there. Instead I need to decide exactly what story I want to tell, and what data is needed to tell it.

Unfortunately as it stands my story is still more interesting than the data I actually have available. As it stand, and data are all still suggestive, and although my hypothesis are logical, and based firmly in evidence, they haven’t yet borne fruit. Which is a shame, as there’s a good chance I have a very exciting orange tree, albeit one which could still easily yield lemons. (See what I did there! And you thought I was going to torture that analogy.)

There is also the issue of timing, which is going to make me sound like a right liar to anyone keeping count. Much of my poster is cribbed directly from a presentation I gave a month ago, and since then I have been making all the strains and materials necessary for the next steps. In the last few weeks I haven’t actually got any new data, but I have been reasonably productive. This however does mean that there are several important experiments that I have queued up to run in the immediate future. Thus the number of results I can legitimately claim to have ready in the ‘next few weeks’ is frankly a touch silly¹. There is also the serious possibility that I will get at least one of those results between printing the poster and attending the conference.

Sorry, that was a particularly rambling self interested entry. More of the pretentious pseudo intellectual claptrap, ill informed opinions, or embarrassing streams to derivative dreck classified as creative to follow soon. Not to mention plenty of self deprecating attention whoring.

1. Having said that, results in science always seem perpetually three weeks away. Just like all those inventions which are always five or ten years in the future.