My Path Through Research

The Trials and Triumphs of Doing a PhD

I <3 Straight Lines

I have one love which surpasses my love of graphs, and that is my love of straight lines in graphs!

But why am I bringing this up now?

I am currently in the process of analysing some of the data I have been collecting over the past few weeks. I was looking to monitor the change occurring during degradation of my photographs by calculating the rate of change.

Now, if you look back to your maths classes, you might remember that rate of change can be determined by the gradient (i.e. slope)  of a time-graph (i.e. graph of how a value is changing against time). This is quite easy to analyse if you have a straight line, as the gradient is just a single value. However, if you don’t, you start running into more complicated problems!

So I plotted my data.

To my satisfaction I did get a regularly changing line (i.e. there is some significant effect in what I was measuring), but to my dismay, it was a polynomial (i.e. curve), not a straight line!

You can get a straight line from a polynomial curve by taking a derivative of the equation. However, as my brother wisely pointed out to me, you do lose quite a bit of information in doing that, which is not ideal.

My other option was to find a value which DID change linearly with time. So I converted my data into other monitoring systems, and…tada!!!..I got straight lines!

I am happy that I managed to get my straight lines without a lot of data handling. Of course, the more you work on your data, the more information you lose. However, in this case, the two ways I used where just two different ways of measuring the same thing only using a different standard.

Filed under: Experiments and Methodology, Research Process, , , , , , , , , , , ,

And another paper…

If you follow my twitter feed, or have just looked at the publication list on the right you should already have figured this out. What’s the news? The second paper concerning my PhD work has been accepted!

The paper will be published in the journal Polymer Degradation and Stability. We had submitted the original paper at the end of May. Then this week we received some minor comments which we dealt with, and on Friday we got the final confirmation that it has been accepted for publication.

So far I don’t have a link to the paper, but I will provide this as soon as I do. However, here is a brief overview of what the paper is about:

The title of the paper is ‘Stability of chromogenic colour prints in polluted indoor environments’. In it we have reported work I have been doing on comparing the effects of acetic acid, nitrogen oxides and formaldehyde on the stability of chromogenic prints. The pollutants were chosen as previous work we had done showed that these are the main pollutants found inside archival boxes (you can read that full paper here). We also discuss a way of non-destructively monitoring the degradation of the photographic dyes using a colourimeter (image below). This work builds up on chromatographic work I had done during a research visit to the Universita di Pisa last year.

All in all I am really satisfied. By the end of the second year I will have had two papers published, which fits in quite well with the original plan of publishing three papers throughout the whole PhD (especially considering that as the work is finalised towards the end more work can be published).

If you are not in academia you however might be wondering about why is publishing so important. Having your work published in a well-known journal is a way of showing that the work you are doing is of a certain level. This should hopefully come in useful when I come to write my final thesis as I would already have somewhere to start from. Furthermore, once I submit the thesis, having already published the work in a journal helps me show that the work has reached a certain standard. And of course, any help you can get when it comes to the final submission is always good!

Filed under: Experiments and Methodology, Research Process, , , , , , , , , , ,

Photographic Necklaces and Aching Muscles

One of the problems I had to figure out before starting experiments was how to place 50 photographic samples in one 100mL glass vial without any of them touching each other or the glass. On top of that it was essential to be able to easily get them in and out of the vial for them to be analysed, and that means each sample needs to be easily identifiable.

I spent quite some time on and off thinking about this conundrum. Most of the methods I was thinking about were either not very practical for later identification and analysis. This was before I stumbled on the idea of sewing all the samples together onto one piece of string. A form of necklace of photographic samples. A good idea…but how to fit them into the glass vial without any of the samples touching?

The answer to this second part of the problem did not actually come from me in the end. One of my office colleagues walked over to see my efforts with constructing a supporting structure from stainless steel wire and very calmly suggested: why don’t you form it into a coil? Brilliant idea! My having a coil I can extend the stainless steel coil and easily wrap the string around it, before compressing it again to fit into the vial.

This happened quite a while ago. So why am I writing about it today?

I started preparing samples for the next set of experiments yesterday. This morning however I woke up with one of my upper abdomen muscles hurting. It’s not a muscle I ever knew existed and I couldn’t remember anything I did yesterday which could have conceivable resulted in this.

The puzzlement however only lasted till this morning, when I returned to the lab to finish the sample preparation. As  soon as I went to punch out the first sample for the first necklace, the muscle ached! It seems like every time I pressed down on the puncher I tighten this particular muscle. Doing it ten times might not hurt, but as I found doing it hundreds of times certainly does!

What have I learnt from this? Well, I either have to grin and bear it or spread the sample preparation over more days I guess!

Filed under: Experiments and Methodology, Research Process, , , , , , , , , ,

Christmas time in geekland!

In the geekland formally known as ‘my department’, Christmas has definitely arrived early this year!

Why?

Up to now the lab we had access to was a tiny room with a big chamber in the middle of it, leaving a small L-shaped corridor around it to work in…shared by around 5 people at one go. Let’s just say that this was not ideal set-up for a lab! It was really much more than a room with bench-space rather than a lab as I understand a chemistry lab to be.

The day finally arrived when we got our new lab last weekend! While I was busy enjoying the Cheltenham Science Festival, some of my colleagues made a start on getting the lab all nice and ready for Tuesday. Why the deadline? Well, we had an important delegation coming to our department then so we needed to make sure that the lab was all nice and ready for their visit.

I entered the lab first time on Monday morning. I was definitely impressed! The lab is much bigger than I ever imagined! And there is so much space to move around in, bench space to work on, and storage space for anything needed.

Up to now going to the lab has been a not-so-pleasant experience…a descent into a windowless, crowded basement room. Now? I think I just might find any excuse to go their. Experiments here I come!

Filed under: Experiments and Methodology, General, Research Process, , , , ,

Progress of Work

I realise I haven’t written much about how I am doing in my research. However, don’t worry, this has not meant that I am not doing anything.

One of the things I have been working on has been a paper on the results I have obtained from environmental monitoring as well as data I have been provided with from other sources which I could include in this paper. This paper, which we have been working on since the summer, has finally been submitted last week or so. So now we wait for the comments from the peer review process, and hopefully they will be favourable and I will see the paper in print.

Apart from that my work has been on a stop-start situation. Being in a quite new centre has meant that there is very few pieces of equipment available. This has meant that I need to order most of the equipment and material I need myself. This has been both positive and negative. It is negative because it means that time is ‘wasted’ waiting for the equipment to arrive, putting it together, figuring out how it works etc. However, it also means I get new equipment which hopefully is not continuously breaking down!

Well, last week I think (! I don’t want to jinx the situation right now) I received the last of the equipment I need, at least for the time being. Thus, for the past week I have been busy getting my samples ready and the equipment ready to be able to start the experiments next week. I have set up most of the equipment, and done around half of the pre-ageing measurements of my samples. Hopefully next week will see me starting the experiments and then I will have results to look at and admire (and discuss!)

Will keep you updated!

Filed under: Experiments and Methodology, Research Process, , , , ,

Pisa…A Research Visit

In the last post I left you with my arrival in Pisa. Now, having completed my time there, I am back in London. But how did it go, and why did I go there?

The first aim of my visit there was to determine a method for the extraction of the dyes from my photographs, followed by their separation using chromatographic methods. Thus, the majority of the first two weeks was spent trying out the methods mentioned in literature for similar methods (since none were found for my exact requirements), and then depending on the results obtained modifying the methods to obtain the best methods we could. This is proably one of the most tricky parts of a research project, since it can take a very long time till the best combination is determined. Luckily, we found something we could work with, and thus could get on to the next part of the work. This involved analysing aged photographs using chromatographic and colourimetric methods and correlating the two. What about the  results for this? I must say not all the results are perfect, but at least I proved what I was there to do.

What about the other aspects of the research trip? I must say it was great! I enjoyed the work, the people, the lifestyle…everything. Being in Pisa also meant I could get to other parts of Tuscany quite easily…so I visited Florence, Siena, Lucca, Cinque Terre, Certaldo etc. I also had people visiting me, which was nice.

I think that it is not enough from these research trips to take only the work, but it is so much better if you can experience a bit the life in that place…you really do gain a lot…not just in friends, and results, but also in other skills such as project management and time management (since you are there for a limited period of time).

Filed under: Events and Activities, Experiments and Methodology, Research Process, Travel, , , , , , , , , ,

Research Trips

A good point to doing a PhD is definitely the travelling you get to do (especially if you have a supervisor who supports you and is interested in sending you to conferences and in working with other people). Luckily I have one of these supervisors ;). So far I have been to a workshop in Ljubljana, Slovenia, where I attended two workshops: One on the use of GC-MS to analyse small quantities of mixed organic materials by a research group from Pisa, Italy. The second workshop on the next day was on the use of NIR/Chemometrics in Cultural Heritage (which is something which I will use quite a bit in my PhD).

But this is not the only research-related trip for this year. Around the beginning of March my supervisor asked me if I would be interested in going to do some work in Pisa (with the research group I attended a workshop by in Ljubljana). I immediately said yes, both as I like travelling, but also as I knew that there I could get work done which would be difficult to do in London on my own. So my supervisor started some correspondence with this research group, and luckily they accepted to host me :). I then I applied for a grant through COST, “an intergovernmental framework for European Cooperation in Science and Technology” by the end of March. Beginning of April I received back that I was accepted for a grant through this programme…and Voila’! I’ll be in Pisa for the month of May!

I arrived in Pisa last weekend, and will be here till the 1st of June. So far I am really enjoying myself, and the work seems to be happening (it is still the first two days, but at least we are working on something). I am so glad for this opportunity. Will let you know how it goes!

Filed under: Experiments and Methodology, Travel, , , , , ,

Preliminary Studies

As I said in the introduction to this blog, I have started what I am calling preliminary studies. What I am doing in these studies is that I cut some photographs into strips. Following this I am heating the photograph strips in an oven (a very crude way of speeding up the ageing process).

I started this study highly optimistic that I would start seeing something change in the colour of the photographs quite quickly. However, after the first few days, I immediately realised that my optimism was misplaced. The photographs seemed to want to spite me and not degrade (or at least not as fast as I would have hoped for). After a couple of weeks of this, we decided to try introducing some humidity for some of the samples. This didn’t seem to particularly speed up the degradation process, besides totally ruining one sample were I added the highest level of humidity I tried, where the gelatin melted and I got a glob of dyes and gelatin at the bottom of the flask I was trying this out!

What to try next? Last week we decided to increase the temperature a bit more, and see how that goes. I wasn’t too hopeful, having been deluded before, but today I decided to have a very good look at the samples, comparing strips I have removed before from the oven to those still in there…and guess what? Success! All samples registered a change which can be seen with the naked eyes from where they started off! Though the way wasn’t as fast as I had originally thought it would be, it feels great that we are getting somewhere now. That was definitely some good news.

And that wasn’t the only good news today 😉 But I’ll tell you more about the rest when it is confirmed.

Filed under: Experiments and Methodology, , , , , , , , , , , , , , , , ,

Lessons in Manual Writing (and Supplying!)

This is a rant…I apologise for this coming so early on in the life of this blog (hope I don’t put you off ;)), but I have been fuming about this issue for quite a while now!

Since our department is still quite new, we are continuously buying new equipment, which of course we need to figure out how to use. Now, since I am the one needing some of this equipment first, this means that it falls to me to figure out how these instruments function. Easy task right? Just follow the instructions!

That’s what I thought too! But the situation is not always as easy as it seems. Why?…

Well…first of all I think that some of these companies need to learn a bit about manual writing. Even a simple thing, like how to switch an instrument off, is often missed out! Some of them are quite straight forward (though that is not a sufficient excuse according to me…what if the person who should be using isn’t the brightest in the world, or just simply cannot figure it out at the moment? Shouldn’t that be included?), but in other cases, the switching off procedure requires you to press a combination of buttons, or depress the same button for at least 5 seconds, or something like that…not everything is exactly intuitive. They should also understand that the people using the instrument are new to the instrument…they may not understand the jargon you include, or cannot do the assumption leaps you do! (This is especially the case when for some reason the pictures/text described in the manual is different from what is happening in your instrument, or, worse, when pressing the buttons directed in the manual give you a totally different result to what you expect [worse off is if the button options are all scrambled up throughout the manual, so it’s not like one combination has been switched with just one other! Believe me…I have a manual like that right now…it took me some time to figure out what is what!]).

Ahhh! And once you write them? Send them to the people buying the instrument! Or at least make them available to your customers and tell them how to find them! I am sick and tired of getting exasperated at figuring out an instrument, only to e-mail the company, which replies saying…this is the manual you need…so why didn’t they send it immediately with the instrument like they sent I don’t know how many instruments? 

Worse off however was one company which send us an instrument, which I was trying to connect to my computer (it should have had the capabilities!). One problem…we were supplied with around 5 software applications on the CD…which one to use?…Well, most of the applications had at most a 1-2 page colourful description of what they should do (if anything), which was more advert than help! I installed all applications…still couldn’t figure it out. Hmm…at my wits end I decided to call the company

Call 1: I am told that they sent us an old version of the CD (We bought it end of 2008, and the new version of the application came out in 2007!). OK…I could download the new version on-line. I download the new version, but still nothing happens!

Call 2: I am told that the new version does not necessarily work on Vista…but I have Vista installed! OK, one of the research assistants has XP, so I try it on hers…still nothing! The computer doesn’t seem to be able to recognise the instrument.

I leave some time pass…

By this time I was highly frustrated, and I didn’t want to disconnect before they told me exactly what  I had to do…I was a girl on a mission! I wanted to get this instrument and the computer to communicate! It was essential that they do! (otherwise this would have meant me jotting down over 15,000 values by hand!!! Not a pleasurable task!

Call 3: A new person answers…as soon as I start explaining, he said: I know what your problem is, give me your e-mail address, and I will send you the instructions! WOW…OK…I gave him my e-mail and 5 minutes later I had the instruction sheet in my inbox.

I arrange the settings to the new settings…and…

  • drum roll*

It worked! They connected! They recognised each other! WOW!

What I didn’t understand was why they didn’t supply that sheet with the instrument itself, since evidently it is something they know about (if you talk to the right person). Not having it meant that I spent I don’t know how many hours trying. Do these people enjoy making life for others more difficult?

Oh well…I will shut up now, and go back to my happier self.

But really…people…write decent manuals and supply them to your customers!

Filed under: Experiments and Methodology, Rants, Complaints and General Malaise, , , , , , , , , ,

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