All entries for August 2007

August 21, 2007

PEBBLE is Alive!

In other news, we may have spent a while filling a whiteboard with text, but the project now works! We can generate one million double beta decay events, complete with energies and angular distributions, in a little over a minute (on a 1.86GHz processor).

Today we’re going to tidy the code up a bit and complete all the documentation, then we can turn it into a library and interface with other peoples code, such as the CERN GEANT4 package, which will allow us to track the motion of the particles our program generates, as they pass through various detector materials.

Procrastination in the Morning: Repressed Memories

Last week the project was not going so well. We (Sam Smith and I) spent a long time waiting for the computers to do things (compiling, running, debugging) and we had to think about how we could fix the problems we were having. In the time this took, we achieved the masterpiece of "stream of consciousness" art which you see below.

Stream of (un)consciousness



We should try and cover the board in text - Samuel Smith, August 16th, 2007 (A Thursday, would you believe it?) Is this a dagger I see before me? No, it's a list of compiler errors as long as your arm, with your other arm cut off and attached to the end of it, and your legs cut off and attached in a similar manner. Then, of course, once the compiler errors are all distant, fond memories, you have the fun of dealing with linker errors, commonly held to be far superior in terms of the excitement and satisfaction which can be felt when one terminates such an error. And even then you're not home free. The runtime errors ride in force tonight, the ringwraiths iron clad. To code, or not to code. That is the question. Although it isn't written like one. One what? See that was written as a question. Do you have any idea as to the philosophical implications of the word "that"? That was a question as well. What's worse is asking yourself questions on a whiteboard. Fathom this one: how can a bodyless actor, in a conversation written by an external scribe have an idea about both the philosophical implications of the word "that", and the world as a "whiteboard", or, furthermore, their situation during this conversation about knowing what a bodyless actor can know about both the philosophical implications... I'm going to stop you there, you were getting recursive and that could lead to some serious stack issues. Of course, when one considers the futility of discussing such matters with a whiteboard, it should now be obvious to all but the most clueless observer that we are totally, completely and inescapably stuck, and should probably be thinking seriously about the ways in which we can dissolve the ... ... metaphorical glue which binds us into this state of helplessness and repeated writing on a whiteboard with no consciousness. That said, writing on a whiteboard which did possess the basic characteristics of sentient life would be a rather disturbing activity indeed. Imagine, if you will, a whiteboard that exclaimed "that tickles" every time you wrote on it. Well the whiteboard equivalent of " shock" would be drawing a set of axes, in an arbitrary coordinate system. Is it raining? Is it snowing? Is there any way of knowing? etc. etc. Something about the danger growing and the rowers rowing... and the whiteboard by now would have collapsed into a laughing fit, considering how much we have tickled it in the past moments. Imagine, for a brief moment, a probability distribution function. A Gaussian will do, for now, but something like (T1 + 1)2 (T0 - T1 + 1)2 would also be a good example. Now, try to climb it. That's right, like a mountain, or a particularly probabilistic boulder! That should give you a basic idea of how my dreams have been for the past three nights. If you think that is disturbing, try experiencing it first-hand! Consider, instead, a quantum mechanical whiteboard. Markings could exist only in discrete levels, much like the lines of text on this board. Furthermore, and without doubt a less obvious phenomenon, the interaction between a pure whiteboard state |WB>, and a pure marker state |M> would almost inevitably result in some kind of mixed state, probably with loss of quantum information (although perhaps such a result would be after application of the Eraser operator, such that, given a state <WB|M>, application of the Eraser operator in the form <WB|E|M> = <WB|WB>. An intriguing prospect). Even more disturbing: a whiteboard whose countless reams of potential information, in countless positions, written in countless orientations, displays all possible information that could be written on it at once. If the whiteboard were made out of a suitable material it could exist for hundreds of years, who doesn't love whiteboards? This means that a whiteboard somewhere has likely displayed the solution to the Navier-Stokes equation for such an infinitely small amount of time the world remained stable - the Navier-Stokes equation will bring about the apocalypse. Complete with the one horseman, and three pedestrians. The four hoursemen have probably retired by now anyway, so the apocalypse wouldn't be too bad. Just the end of the world, but no plagues / famine to be seen. The Americans took care of all of War's duties, and as or Death, well He would rather POTTER ABOUT IN HIS GARDEN, doing only those things to a garden that Death could do. I wonder where Blinky went? He is probably chatting to the Camels about the mathematical formulations of quantum gravity. I often talk to camels. It's fun. They have the craziest things to say. And they're rather irritable; must be because of all the sand! Imagine getting sand on a whiteboard... the philosophical implications of whiteboard physics were bad enough, lets not touch on quasi-stable structures on whiteboards that could one day show the solution to the Navier-Stokes equation. But occasionally the stabilities are fun to model! Do Samuels dream o velcro tape? Everything compiles and runs again, but just so that our eternal "fun" is guaranteed, the mode functions appear to be going crazy now! When will it end? Will it end? Is there even an end? Still, it seems faster than the original 13 hours, even now it is generating T2 and cos theta... albeit incorrectly so. I wonder who you are addressing. You're not talking to camels again are you? And who am I addressing? [Oh no, a gap!] that's who. Eat that home. But for now, assume Descartes first conclusions were correct; follow through the logic until you hit the phrase "cogito ergo sum", replace it with the more logically appealing sentence "I think, therefore something is". Thinking does not imply your existence, it implies there exists an unthinking process, with which you can contrast the process of thinking... I think... because I am. But I am not, At least, not the one who started this thought. So maybe I am, or at least I have the thinking process, but I am not Sam, and Sam is, so I think, even though I am not! A stone is, yet it does not think. A mountain is, yet it too does not think. I think, and Sam thinks, and we, too, are. I hereby find there is no statistical correlation between thinking and being, even though I have chosen to test Be => Think, rather than Think => Be. Revision zero, zero hour, zero-day, ground zero, 0+ - 0+ transition. What an interesting concept, that of nothing. How can one possibly imagine nothing when, by its very definition it is something? Such is the futility of all of this - it is time to go now. ======== COMPILING!! (See

August 16, 2007

Nearing the End

Max’s saturation of the URSS blog has made me feel slightly inadequate, which has prompted me to write a follow up as to where we are in our research. We have finished the first stage (analysing the conceptions of higher education in Britain and Germany), read the biennial Bologna documents and are trying to see to what extent the first has influenced the second. We have written reports and an annotated bibliography for the first stage, so at least we have something to show for our research, and seem to be on track. However, I believe the next stage will be difficult insofar as it will be impossible to conclusively say from where, for instance, the focus on quality assurance comes from.

Over the last couple of weeks we’ve also managed to go to the British library, which was probably more fruitful for Max, record a podcast in the RAW studio and get a decent overview of our project so far with meetings with our supervisor and discussions about our relative findings.

However, we do not have long left so hopefully we can find a conclusion of some sort that is worthy of being put on a poster.

Dan Davies

August 15, 2007

A wasted day

Personal Problems were a great hindereance to my output today. Luckily I was able to finish some rough sketch for the Podcast tomorrow and to finish my URSS student profile, but that was about it. I really need to find some track to get into make this last part of the research a success. Hopefully recording the Podcast tomorrow will be a beginning, because it may help to reflect on the work we have done already in a new and creative way.
In my URSS student profile I ended up writing far more than I originally expected, probably this only makes the point that we have already done a fair bit of work over the past weeks. The question to what I consider to do now after the URSS project first seemed a little odd, because I have two more years to study for. Nevertheless, I followed the input and booked an appointment with the careers service for tomorrow, to discuss how I can prepare myself for the search that is inevitably coming up. In many senses URSS was an eye opener in this regards, because beforehand I failed to appreciate how difficult research actually is and what kind of self-discipline it requires. On the other hand, it seems like I have two more years to catch up on both: Academic excellence and self discipline.

August 14, 2007

2nd day

I don’t know if it was related to the horrible weather today, but nobody in the lab was in the mood to work! Imonge went home at half 3 because she couldn’t be bothered to work any more, citing the reason that her ‘incubation would take too long’ and she’d miss the bus if she started it. Oh well!

Anyway, it seems the wet labs at Warwick come in useful! They were very handy today while I was making my media for my plants. I had to make agar plates with gentamycin for my transgenic plants to grow on. I also had to sterilise all those seeds I prepared yesterday and finished off this morning. I haven’t quite finished off the sterilisation, as there were a lot of seeds and the technique takes about 15minutes for each seed line, and I have about 40! So do the maths :p

So tomorrow I expect to finish off the sterilisation and start culturing some nice fungus in petri dishes!

Starting the final lap

The trip to London was definatly a right decision. Even though the British Library was less helpful than we originally expected, mainly because Dan did not get a reading pass; so for everyone who intends to go: Do not forget your ID and prove of residency and a separate confirmed card with your signature. Nevertheless, it was still a very nice day out in London, which we used to visit the British Museum and the National Portrait gallery (Dan saw it on his own).
Working in the British Library was great, despite the fact that it is even harsher than our library in Warwick, was great. In comparision I would even argue that Warwick University Library is a liberal paradise; in the BL you are for example only allowed to use pencils, not speaking about any form of drinks. The social science reading room, in which I worked, is an experience in itself, but I also found some interesting information for our research. Most importantly, that the Bologna-Process has its origins in the early 1990s, when the Commission published a paper that aimed at the economic importance of higher education in Europe. I became aware of this through a very interesting article by Tomusk, who has written quite extensively on the Bologna process, but to whose work I had no access before I went to the British Library. He also had some things to say about Warwick, which I am not going to quote, because we are thinking of using his quotes in our poster presentation.
After this day out, we did some proper work today, discussung our work done in phase 1 and 2, with our supervisor Ben. I think he was quite happy with what we have done so far, however, now the difficult part arises, finding some coherent themes between Dan’s and my work.
Additionally, we are planning to publish a potcast or a vidcast on our research for which we practice in the RAW rooms today. Thursday will be the date when we will hopefully record it. First, we will have to write something like a script, though; I am very much looking forward to it.

August 13, 2007

First day

I started my project at HRI today! Got there bright and early (a shocking 8:50am), and had the usual introduction with Katherine Denby, just basically going over what’s expected. Basically, in previous work, Dr. Denby and her team have identified three possible transcrition factors (518-A3, 518B-6 and NAC-3B) that may form resistance to Botrytis cinerea, which is a necrotrophic fungal pathogen. My job is to see if this is true.

I was given the health and safety induction and my own lab book (v. cool, although I’m not allowed to keep it at the end of the project, as it goes into the HRI archives).

Afterwards I meet another member of Dr. Denby’s team, Priya, who I will be working with most days. We go to the glasshouses to pick up six P40 trays (so called because they have 40 wells to each tray), and I also nearly destroyed one (oops!), ad then head to the dirty lab. Here, the soil needs to be soaked for 30 mins, as this makes it easier to plant the seeds. After 30 minutes though, hardly any of the soil is soaked, so we have to wait longer. Then comes to tedious task of pipetting the tiny Arabidopsis seeds: five seeds need to go into each well, to ensure that at least one wil survive and grow. If more than one grow, then they are weeded out. The trays are then covered in cling film (to maintain humidity) and placed in the environment chambers, which are set to a certain temperature, light intensity and CO2 level. My plants will be kept here for 4 weeks, then they will be ready for infection. In the meantime, I need to look after them, watering them every couple of days to make sure they grow!

After lunch I started sorting though some seeds that Priya had collected the previous week. This involves removing the seeds from the Arabidopsis plant and sifting them through a fine sieve to separate all the unwanted stuff from the seeds, which we do want. The seeds are then put into their own individually labelled Eppendorf tube.

I still have about 10 of those to do, which I will finish tomorrow morning.

August 12, 2007

Looking forward to London

At the moment the research is slowing down. Dan and I spend most of today and yesterday in prove reading each others text, doing only very little reading besides it. Well, at least I am now quite pleased with the report which I am going to send to my supervisor today and I guess we have now reached the stage where new input is needed. We need to decide how we are going to tackle the Bologna documents to come to our final conclusion.
I already have some ideas on how the German system interacted with the European Level; however, it seems very difficult to back my argument up. This is mainly due the fact that my current argument is based on a suspicion rather than factual knowledge. To me the Bologna documents appeared very vague, so that it does not seem far-fetched to argue that a lot of policies could be justified with it. This is exactly what appeared to have happened in Germany, as especially the Second National Bologna, quotes nearly all current higher education reforms to be in some relation to the Bologna process; to get more certainty, I guess interviews with people involved in the process would help. Maybe, I could ask Fran whether I could consult the material he collected.
Tomorrow, Dan and I are planning to visit the British National Library in London, to consult some of the literature that is not available in our Library and to have a nice break after having finished our first extended reports. The main book, which we want to read, is a major work on the Bologna process and might give us some new ideas, too.

August 11, 2007

NMR Week 8 + final 2 days

After last week’s work on optimising the parameters for the simulations, previous spectral simulations were redone to improve their quality.

At the end of last week my supervisor had asked me to prepare a talk for the next group meeting, which was to be held on the Friday morning. The majority of the week was thus spent creating the associated powerpoint slides, which I found to be a very useful exercise. The first thing I learnt was that you cannot include everything you’ve done into a talk; you have to pick out the sections that worked well and which link together in order to form a story. For this reason the talk omitted the simulations work, focusing only on relevant previous experimental work, my research and what they told about the possible structures of the samples.

I did a run through of the talk with a colleague, which was great for identifying flaws. After this the talk itself seemed to go fairly well :)

On Friday afternoon and the following Monday and Tuesday I started work on my poster.

Back in Devon now and enjoying the sunshine, but still with my poster to do. I’ll let you know when I finish!

NMR Week 7

Part of one day was spent looking again at the experimental spectral peaks we found and trying to come to some conclusions about whether it is what we expected.

Throughout the week we did absolutely loads of simulations work – some of which took quite a few goes to get:
a) atomic coordinates from molecule modelling programs and
b) input files written so that spectral peaks look as you would expect from experiment (there are several parameters that one can set)!

We tried a 2D simulation and did some 6-spin ones using coordinates from atoms that would be on adjacent molecules in a crystal.

When I started the project I was under the impression that simulations of our samples would have been completed by this stage. However I now realise that these things have to be done systematically and that you have to ensure that the basics are correct before moving onto the more complex.

August 2007

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