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.

NMR Week 6

We met Erwin Hahn! Who honourarily (?) graduated on Monday with the other physicists :) Go here to see him and the rest of us!

Work-wise I did more simulations using Spin Evolution, but this time using different pulse sequences. Amy did the equivalent using Simpson so we can compare.

Experimentally we had planned to run quite a few samples on the 600 MHz spectrometer but we had difficulty with various things so we didn’t get as much done as expected (research is seemingly a very slow process at times!).

On Thursday I did a 4-spin simulation using Spin Evolution. I chose atoms in the penicillin molecule to check that interatomic distances were represented on the spectum as expected. I also looked at the effect of changing the spinning speed and number of propagations.

Friday we ran a 2D experiment on sample B04. We got a lot of noise so left it running over the weekend.

August 10, 2007


Today was a day of consolidation, since I spend most of it brushing over my written work. Because I was not too happy with the flow of my arguments, in the text that I had already written, I decided to follow the advice of one of my tutors and to rewrite the whole text. This certainly improved my tipping, but if it was an efficient way of dealing with the problem I beg to question. Anyway, now the report has a complete body with introduction, conclusion and bibliography; moreover, I discovered for myself that I am getting more and more familiar with the subject matter.
Nevertheless, it continues to surprise me after all this reading that I am not able to write more on some topics, on which I have read whole articles about. I guess that shows me that I am not that confident after all.
Now I am intending to focus on summing up the Bologna-Process and its direct effects on Germany. In order to do this I will try to find some more sources tomorrow and see to get more commentaries on the matter. Especially, since I find it quite hard to find a decisive line that marks external inputs from endogenous developments.

August 08, 2007

More Bologna

I now finished reading the official Bologna documents and their corresponding national reports for Germany. Now I start to appreciate to have acquired some knowledge of the historical debate which the most recent reforms are only a part of. Phase two is therefore also quite advanced, in the sense that I am planning to stop researching for it by tomorrow midday and start to summarise my impressions of the German implementation of the Bologna-Process.
The reports themselves were, like the communiqués, very similar in their nature; however, even though some sections appeared like mere repetitions of previous reports, I still think that they are essential for my research. What I found most surprising was that, especially the second national report, was that all higher education reform was mentioned as an integer part of the Bologna-Process. Despite the fact that the Bologna documents do not include topics such as tuition fees or competitive salaries for academics. For me this is good news, because it provides some evidence for Dan’s and my thesis that the Bologna process has, in some way, led to a commoditisation of the higher education sector.
Also, I found a very good website on the current debate on higher education reform in Germany. The weekly newspaper Die Zeit has set up a section in their Website, in which all articles they published on the topic are assembled. Contributers such as Ulrich Beck and Anthony Giddens have given their view on the debate in Germany; this is gold for me (or at least I hope it is), because especially Giddens seem to resemble what I identify to be the main current ideology on higher education. Since for him it is illusionary to still use it as a national social policy tool, instead social policy should work at different level and universities shoul be allowed to go their independent way; still serving the public good, but no longer as part of the state.
All this fits very well into first year Politics.

August 06, 2007

Planning works!

The morning was very productive. I sticked to my plan and worked for about two hours on my report, which left me in a very satisfied mood afterwords. The project is starting to pick up some shape, which is a very good feeling in a sense. On the otherhand, the closeness of the the final lap is somewhat scary.
The official publications on the ratification of the Bologna process in Germany that I read today were not particularly thrilling. At least, my thought which appeared yesterday, namely that the university accreditation institutes open the huge possibility for a private market, seems to become more solid. To be sure though I defiantly need to get a better idea of what the exact mechanisms in Germany are and how they are changing.
Otherwise, most of what I read was concerned with homogenising qualifications authentication. A topic which I find personally very interesting, mainly because I am directly affected by i, but which has no further relevance to my research. Maybe, I should not have spend so much time reading it, as it did not bring any direct gain for my thesis. However, on the positive, it gave me a nice insight into the very positive aspects of the Bologna process, or the Lissabon convention to be precise; namely that people who spend long periods of time in education, will get a wider acknowledgement for their achievments. I am quite certain that this will improve the quality of life for many

August 03, 2007

Finishing Phase 1

I am glad to be able to say that I have overcome my writers block. A combination of further research and free writing was helped me most, no matte how good my own excuses were not to do exactly this. The more I wrote, the easier writing became, moreover, the whole subject matter started to make some sense. This shows me again that I should have done it much earlier, but than again I ask myself, what exactly I could have done differently in my preparation.
The Way I am working now is to write an annotated Bibliography, in which I summarise what I found interesting about a particular text. These summaries are not referenced, but completely emotive, as I found it simply takes too much time to note down any detail. In a sense, this works very well to get an overview over a topic, however, it consistently lets me down if I want to write more than a couple of bullet points on a subject. Because, this method also implies that I have to go back to each essay individually in order to find the particular passages that I need. Due to the time intensity of this, I do not make use out of all my material, because it is just simpler to stick to a confined number of sources. A vicious circle really.
I have written before on how great my enthusiasm for MindMaping software is and maybe it could offer me some guidance with this problem. Additionally to my annotated Bibliography, I could note down the passages that I believe to be relevant in my mindmap. Than, it should be relatively easy to access these parts, whilst I am writing my text. What I will note down and what will be left remains of course a question which no software will, hopefully, ever answer.
Content wise, I am consolidating my knowledge on higher education reform in Germany and start to look at the broader philosophical context. During my, gap filling, research I stumbled across some quite interesting articles that go beyond the report which I am just finishing of, but that may also be of some interest. One specifically targets the question of how European universities came on the path of marketisation at the end of the 1980s, so that should defiantly be of some interest.
Dan was also writing on his report for most of the day. We saw numerous parallels between German and British developments, especially regarding the expansion in the 1970s and the lack of funding in the 1980s. I guess, after that Britain took the more radical approach with electing Margaret Thatcher. Anyway, it is a real pleasure to discuss these things on the kitchen table, inspiring each other and spending new motivation. Hopefully this will stay the same when we start researching on the same topic tomorrow. But, I am sure it will because we are now both bringing in our own little field of expertise, which should equip us with some very individual way to analyse the same policy process


And where would we be without our dinosaur friends…

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