Joining the ranks of the employed

Well, I got the research job in Rothamsted. I am happy, but somehow not as excited as people seem to expect me to be. Partly that's due to the tizzy my supervisor has got into (and therefore infected me with) over my approaching thesis deadline, and the lack of thesis thus far. It's hard to be excited about a new post-doctoral job when you're still worrying about getting the prerequisite doctorate degree...

The other part is probably because I've been anticipating working in the US, and in fact I have a job less than 50 miles from where I am now (Rothamsted is near Luton). Not that I'm overly fond of the USA, but I feel that if I want to do a post-doc there before I settle down elsewhere, it would be sooner rather than later. I know there'll be other opportunities though.

Of course, to cap it all, I've spent weeks and weeks collecting together the samples for an experiment, only to just now find that it didn't work. It will now join the 'inconclusive data' section of my thesis.

I'm sure that the excited, happy, optimistic side of getting a job that seems really interesting with people who are really friendly will kick in progressively. So not to worry :P

update

Having moved back home to Manchester for a few weeks to write up my thesis, I've been on the phone much more than I have been in the last six months. However, I have not seen anyone except through my house windows for several days now, and not stepped foot out of the front door since Saturday.

The house is in a row of terraced houses, although in fact there is a private alleyway running down one side of my house, so we only have one adjoining building. The sounds from around my house do carry though, as is the norm for old terraced buildings, so that sometimes I have to refrain from running downstairs to check that there isn't an intruder when I hear doors banging, seemingly from the ground floor of my otherwise empty house.

Despite this relative isolation, work is going very slowly. I seem to spend all my time planning the thesis and not actually writing it. Today though, I'm adamant that I'm going to start work in earnest on my first results chapter.

So this is just an update, to let everyone I'm still alive, and to put down in typing that I really am going to get this chapter done.

Toes crossed and fingers ready to fly across the page.

a worthy competitor

Due to the lack of other fourth-year PhD students to compete with, my lab mate and I have decided to compete with phd comics' Cecilia, who is also thinking about writing up her thesis. Given that Cecilia is an American (and we all know how long PhDs in the USA take) we're going to be really gutted if we lose to her (especially since she's imaginary).

In addition, my lab-mate and I are competing against each other. Whoever loses buys the other a pint. It would be buying each other a pub dinner, but as we have no job lined up as yet, and our funding has run out, we decided to make it a more economical prize.

Hopefully we won't die of thirst first.

the last of the fourth year students

Aaargh
I'm officially the last one of my batch of phd students not to have submitted their thesis!! And I haven't even left the lab yet.
I'm hovering between panicking and complacency now that I'm the last one - I can't be any more last than last. Except I know that people who started after me are also starting to write up.

Oh and yes. I finally set up my cantab address. Not that I'll be leaving anytime soon.

shooting practice

I spent a very frustrating couple of hours on the laser capture microdissection machine on Saturday. The aim was to capture a sample of about 250 cells from a fixed leaf section of 5 microns thick and extract the RNA from them, to use for RNA analysis. The basic idea is very simple - you have a 'cap' of thin plastic film which you direct the machine to position above your tissue section. You can then look at a microscope image which is projected onto your computer screen and mark which individual cells you want to capture. The computer then relays this information to the laser arm which fires a laser beam for a period in the microsecond region at the cap above each point. The film then melts, adhering the cell as it reforms, so that when you lift the cap off the desired cells should be adhered to the film.

Very cool, and I've had brilliant results from it. The hardest part is only really optimising the laser parameters, as it has to be strong enough to melt the film, but not so strong that it burns a hole in your tissue. However, it seemed that the laser just didn't want to play on Saturday. That or it was too eager. It jostled between not melting the film, only making dents in the surface (see top image) or burning a black hole in the middle of the target point. As the RNA in the tissue section only remains intact for an hour or so after wax deparaffinization, by the time I had the laser optimised there was no time to capture the cells I wanted.

Not yet defeated by this failure, I prepared a second section, and set about re-optimising the laser for this sample (you have to re-set everything each time you change samples). Again it wasn't playing. My cap looked like it'd been used for target practice.

In the end I gave up. It was only when I was removing my caps from the machine and complaining to a friend that he noticed a dust-hair on the surface of the cap. Those very fine ones that float about. But it was enough to prevent the cap from sitting flush against the tissue surface - hence my problems with the laser. Sigh. At least now I know, so I'll be cleaning the cap holder very well before using it in the future.

spoke too soon

It turns out that the end of the light of the tunnel was really just the headlights of an on-coming express train.

I've been trying to put together the figures for my *first* paper (yay). It's a mix of my work and some results from a PhD student who finished last year. My supervisor's writing the main bulk of the paper, which is good because it saves me time, but he's assumed we have images and figures that we don't have, which is BAD. We have the data and some of the photos, but they were meant for our own records and not of publishable quality. The other problem is that the previous student's thesis is a nightmare to trawl through, there are so many different plant lines and he's laid out the results for each experiment in a slightly different format each time (why oh why?!!!) .

Some of these issues I need to bring up with my supervisor, but in true traditional supervisor fashion, he sent me the rough draft on monday and then disappeared for the week on tuesday. I need to give him a mock-up of the figures at the start of next week, and there's been no word from the previous student in response to my cry for help (and data in a more sensible form).

At least I'm lined up to be joint first author on this paper, rather than the second author I thought I might be. But it's a hefty amount of work I need to do to get it.

a single keystroke

I need to start writing up in earnest.

The end is in sight

Over the last few days, I've thrown out 7 shelves of plants - that's 45 trays or 315 tobacco plants. I did take samples from them, so they didn't die in vain. More to the point, I'm in the last stages of processing my data from over 300 samples.
I've also heard that each growth chamber at the plant growth facilities cost us £4000 a month to maintain. As I've been using half a chamber, that's £2000 a month I've been clocking up for the lab bill, if the rumours are true that is. Our group alone use the better part of 5 rooms, adding up to a ridiculous amount of money spent on lighting and humidity control alone...

Anyway, hopefully not too long left doing experiments!

overworked

My blog may become a shrine, or at the very least, an advertising space for PhD comics, but they're just so accurate...
The rate at which things disappear FROM my to-do list - 3 lines/week

The rate at which things appear ON my to-do list - 12 lines/week (or if you take the rate of interest over the time period during which I have a meeting with my supervisor - 2 lines/5 minutes)

That latter is limited only by the speed at which I can write down and make semi-sense out of his comments.

more confocal images

I'm using a 'new' GFP construct! It's not newly made, but it's one I haven't used for microscope work before.

Danger alert

Today's new phd comic is very fitting. John has been let loose in our lab. We did clear his desk for him first, to reduce the danger potential [think radioactive plants (though under a lead-lined perspex box), syringe needles and razor blades]. We have a summer student and a visiting PhD student, and John likes to use the opportunity to put a lab coat on and show them what to do. We would feel a lot safer if John wouldn't keep explaining how to make liquid nitrogen and dry ice bombs, and wave his hands around whilst holding bottles of toxic chemicals.

We've printed the comic strip out and stuck it to his door. I think he may get the hint.

Hurdle. Jump. Hurdle. Jump. Splat.

Let me see.
Experiments. PhD third year presentation. Grow up plants for more experiments. Keep virus stocks going. Form for fourth year plan comes in. Strike one.
Kill off plants from the last experiment. Dissertation plan form comes in. Strike two.
Data compilation. Find out you just killed off plants before collection of all the desired data. Groan. Strike three.
Crash, bang, wallop.

I thought I'd finally sorted out all the paperwork and jumped all the hurdles that the Graduate Studies Board wanted from me before the last BIG hurdles of thesis and viva. Finally I can concentrate on actual experimental work. As usual, wishful thinking. Only a few weeks after I gave my third year presentation, I've now got a form entitled 'Graduate Student Fourth Year Plan', with all the questions we don't want to be asked.

1. Have you finished your data collection? (I wish)
2. If not, when will you have finished collecting data? (sometime this decade I hope)
3. Please provide a list of abbreviated chapter headings for chapters already completed and the date when these were handed to your Supervisor. (BLANK)
4. Please give an estimate of when you will give a complete draft to your supervisor. (more blanks)

signed (by Student)
signed (by Supervisor) (indicating that they think this is realistic) (sigh)

I spend more time than I can afford over these things. And guilt over the number of trees that have died unnecessarily so that I can do this PhD and the blasted paperwork that goes with it. Plus it distracts me from my work.
All this paperwork to make sure that we are on track to finish our PhDs. But I need to do the experimental work to have something to put in my thesis!!

In theory, I know it's meant to be 'helpful' and not a bad idea really. In reality, a reply consisting of running jumps, River Cam and AARGH comes to mind.

weighed down by family ties

These last few weeks have been even more busy than usual for me. My experimental load is increasing all the time, especially since I'm now moving into my last few months in the lab. I don't imagine that I'll be able to do all the loose ends up in time, but at the very least I'm trying to identify which are the structural threads of my project and finish the framework for a model. Add to that presentations that need writing, and experiments that have to jump the priority list queue for impending papers. Add to that lots of lion-dancing again, moving house, and various weddings and celebrations that need to be slotted into my schedule.

So I'm very thankful that my friends and family have been so understanding about the way I've been neglecting them lately. It's been several weeks since I've rung my parents in Hong Kong. Every two weeks my poor mother gets three lines of e-mail telling her that her only daughter is too busy to ring her and that she'll try and do it NEXT weekend instead. Having said that, my parents were supposed to come back to the UK at the end of July. They're now contemplating a holiday to Korea and so may not be back til the end of August. Suddenly I've become our family's 'official representative', as my brother puts it, at various family weddings this summer.

But when you're working to deadlines and have a long list of things to do, it's a massive relief not to have to worry about other people as well. In that respect, I feel very very lucky. Last weekend, one of my friends came very close to breaking down. She's also a final-year PhD student with similar deadlines to mine to meet, so I know how stressful the workload is. But in addition, at the moment her mother and family are going through a rough time and she's holding her mother together both financially and emotionally. She and I both want to continue in academia, but whereas I have the freedom to look for a research job in the country of my choice, she will be unable to do that. She can't afford the uncertainty of being on a three-year contract with no guarantee of a job after that, especially with the low salaries that post-doctoral researchers get. But whilst she's holding her mother together, who's holding HER together?

Over the last few years, several of my friends have essentially had to give up their freedom and independence either to look after their families or in deference to family pressure, or both. It makes me very sad to see them have to put their dreams and hopes on hold, maybe giving them up completely. Perhaps that's why I've become increasingly impatient and less sympathetic with friends who have drifted along for a long time, with no apparent pressing commitments. Although I understand how easy it is to lose direction, I find it hard to offer as much support and sympathy as they seem to ask of me.

Oddly, or so it seems, the friends who are most supportive and considerate to me are those who have the most on their plate. Or maybe it just feels that way. But I'm very thankful that I don't have to feel weighed down by my responsibilities anymore, as they've been lifted off me one by one over the past year. In fact, I feel obliged to spread my wings and aim as high as I can, because there's nothing stopping me from trying. Maybe that is also a burden, but at the moment it's a very light pack to carry.

Weather forecast on the confocal

The weather is being a bit funny lately. As usual. Sometimes I wonder what we would talk about in the UK if we actually had a more stable climate. Not that we don't have meaningful conversations, but it does mean it's easier to have random conversations with complete strangers on a rather non-controversial topic. Even if the weather behaves for a while, we can still comment on whether the BBC weather forecast has, for some reason got it RIGHT for once (though that's probably just due to the laws of probability - it has to be right at some point. Surely). Or if we'll have a drought this year (it never ever ever has but we still get hose pipe warnings). Or flooding in the summer as soon as it starts to rain again (i.e. two days later).

It was nicely hot and sunny last week, so much so that when the air-conditioning was broken in one of the labs I got visitors whilst I was in the chilly confocal room. Actually, I didn't mind being in the dark and cold for once, although it meant I was missing out on the sunshine outside. For one thing, now that it is officially 'summer' the sun goes down so late that I still got some melanin-inducing rays after work. For another, after sitting in the sun at lunch I was thankful for the cool temperature the microscope has to be kept at.

Now that it's gotten cooler again, I've reverted to wearing a jumper and gloves in there.

'Britain doesn't have climate. It has weather.'

By the way, the whole point of this entry was to show off some of the images I've been getting recently....

Defying the laws of probability

So I plate THIS number of seed lines onto selective media but only FOUR lines grow (the green plants are those growing on normal medium).

Not only that, but all four lines are different plant-transgene combinations, they don't even have the decency to be two lines of the same combo. So not useful for publication. AARGH

Surely this must be all against the laws of probability?

Though it only serves to confirm Murphy's law. Thus goes the story of my PhD (a rather thin but sorry looking pamplet).

Three questions you should never ask a final year PhD student

Anyone who is over six months into their PhD knows not to ask these questions.

1) How's lab-work/the project/work going?

2) When are you planning to start writing up/submit your thesis/graduate?

3) What do you want to do after your PhD?

If you do have the misfortune or stupidity to ask these questions, make sure you have a) lots of tissues, b) lots of comfort food, c) hidden all the sharp objects and, in extreme cases, d) be ready to intercept said student before they attempt to dash their brains out on the nearest table or wall.

six months to go of lab work

I haven't updated my blog for quite a while now - there's just so much I want to discuss, but which topic to choose first?

Maybe something that my fellow final year PhD students and I have been discussing lately - it seems as if it's only as we enter our final six months in the lab that we've really started to understand our projects. I've had a few rare flashes of clarity lately, as I've finally caught a glimpse of the direction my work should take, and what experiments I should be planning. Unfortunately, almost immediately these have been followed by another flash - I'm only funded until the end of September, after which I need to beg a friend to take me in off the streets as I write up.

At the moment I'm screening my putative transgenic plants, and systematically going through my seed lines. This is something I should have done about a year ago, if I hadn't been too demoralised by that point. Unfortunately, my past has come back to haunt me, and it's a choice between doing it now or having a big fat blank for the first 18 months of my PhD. It has now joined the long list of experimental work that's jostling for my attention right now. Yesterday I spent four hours sterilising 32 seed lines (only another 72 lines to go!) and two and a half hours today laboriously plating them out. My right thumb will need some time to recover....

My friends and I unanimously agree that if we were to re-start our PhDs now, we would have got to this stage in our work at least a year earlier than it's taken us this time round. But that's the whole point of doing a PhD in the first place - it's a learning curve. The process of doing a PhD means that we get training, not only in experimental technique, but also in the skills of project management and planning, of taking responsibility for a project that is ultimately our own. Sure, it's difficult, and often frustrating - not for nothing do we PhD students kid that we are actually undergoing Permanent head Damage - but then, so is 'real life'.

For the biological and chemical scientists, the UK PhD system is fairly unique in that most of us are expected to be finished and written up in four years maximum. In the US six years is fairly standard, and seven or eight years is not unusual. After all, PhD students are cheap labour, and after the first few years we 'should' be well trained up enough to join the paper-generating machine that is needed to boost their supervisor's PubMed ranking. In one way, I would now welcome the possibility of another six months' funding for my PhD project, as there are so many questions I want to follow up and so little time to do them in. But then, I think it is precisely this tight deadline that has forced me to think about which aspects of the work are most interesting and what I should concentrate on. It's a shame that I didn't reach this stage of clarity, and indeed, maturity, earlier!

P.S. The comic above is from PhD comics. If you haven't heard of them, you're obviously not a PhD student. It took a long time for me to decide which comic strip to use for this post, but I decided this one summed up a PhD the best. Despite my new-found confidence in my work, I have no doubt that I'll be back to my normal stressed self next week.