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).

Remembrance

This is a fairly well-known passage, although I don't recall the name of the writer. But these are the words I would want to say to people who remember me after I am gone, if they could hear me.

Death is nothing at all. I have only slipped away into the next room.

I am I and you are you. Whatever we were to each other that we still are.
Call me by my old familiar name, speak to me in the easy way you always used.

Put no difference in your tone, wear no forced air of solemnity or sorrow.
Laugh as we always laughed at the little jokes we enjoyed together.

Play, smile, think of me. Pray for me.

Let my name be the household name it always was. Let it be spoken without the shadow of a ghost in it.

Life means all that it ever meant. It is the same as it ever was.
What is death but a negligible accident? Why should I be out of your mind because I am out of your sight?

All is well. Nothing is lost. One brief moment and all will be as it was before.

For my friends and loved ones who have already left before me. You are always by my side, lending me your strength.

Is happiness a choice?

I read a magazine article yesterday that debated whether or not you can 'choose' to be happy. The arguments for and against were very polarised, and as usual, I found myself agreeing with both and neither at the same time.

You might not be able to 'choose' to avoid situations and events that will make you unhappy - or rather you can, but you will not be actually happy if you have just opted to ignore the problems that won't go away. Self-delusion is normal and necessary for us to stay sane but there must be a limit to how far you can or should trick yourself. If you let it go too far you end up hurting both yourself and the people around you.

Happiness, or perhaps to say sadness, is something that depends greatly on events that happen in your life, when there is illness and bereavement and stress it's very hard to be happy. And understandable if you aren't happy. If you think about a large proportion of the world, there is so much to be UNhappy about, people who have to worry about food, shelter, political unrest, abuse, the list goes on. For those of us who are much more fortunate we worry about illness, work, money, family and friends. The issues may appear to be of different scales but that doesn't mean that these problems aren't just as REAL to each of us. Or, for that matter, that these problems aren't important.

So your own happiness is something that you have no control over? How depressing.

But I believe that to some extent you can make a choice. Not whether you are happy or not, because that feeling of joy bubbling up inside you is something that comes when you aren't thinking about it. But you can actively choose how to deal with problems, choose to some extent how far you let yourself become upset over a situation. As a simple example, many of my friends have been considering career changes recently. Some of them complain a lot about their current job and say how unhappy they are, but they focus so much on this negative side that they don't gather the energy to really look for a new job. They become depressed and easily discouraged by every set-back they encounter. Others have bitten the bullet and spent a lot of time on their applications and preparation for interviews, and kept going even when the rejection letters have kept coming back. The difference in energy and sense of purpose is so evident even when I've been on the other side of a telephone being updated by what has (or hasn't) been happening in their lives.

Although we cannot control events that happen around us, nor predict what may happen next, perhaps we can try and stay optimistic and look for the silver lining to keep us going. Although how easy or difficult it is to do this depends a lot on your personality, that doesn't mean that we can't change. Maybe instead of always striving for happiness, we should strive for contentment and satisfaction in what we can achieve, without being complacent. Then with a calm and welcoming heart we might be able to experience the streaks of colourful emotion that can strike every now and then, and with any luck might be true happiness.

chocolate banana cake (a la Sam)

Weigh out roughly 200g plain flour - recipe actually calls for 225g self-raising flour but that's close enough. Add three and a half tsp of baking powder, you forget how much you're actually supposed to use.

Don't bother to sift. Just put in mixing bowl with 2 tbsp of cocoa powder and 1 tbsp hot chocolate because you've run out of cocoa.

Stir in 75g light brown sugar (you should use 115g, but you only have 75g or so left). Mix.

Make a well in the centre and add zero tbsp malt extract (as you never had any ever), roughly 2 tbsp golden syrup, 2 eggs (minus 1, because you forgot to check how many you actually have), 4 tbsp water (in lieu of the skimmed milk that's not in the fridge), 3 tbsp vegetable oil.
Also add 2 large ripe bananas (plus an extra half banana, to make up for there not being enough egg). Realise you were supposed to mash them beforehand so mush them up with a spoon in the bowl (but you HAVE remembered to take the skins off first!). Mix everything together.

Pour into a cake tin you never bother to grease and line.

Turn body to put tin into oven that housemate is using at roughly the right temperature. Move rapidly to one side as said housemate dashes past and asks to use the grill first 'for just a minute or two'. Sit at kitchen table for next twenty minutes, until oven is finally free. Sit cake tin in oven even though the grill has heated it up to 200 degrees celsius at the top (but have presence of mind to put it on a lower shelf). Turn thermostat to 160 degrees celsius and go away.

Come back later having realised you forget to check the time when you put the cake in. Then find it doesn't matter because oven has turned itself off anyway. Test cake by stabbing the middle with a knife. Still not done. Turn the timer for another 15 minutes and go away again.

Come back after 25 minutes. Cake is done. Surprisingly good, though still too sweet, despite using less sugar and less golden syrup.

Go back to desk, ignoring the imp that's been sitting on your cerebral tissue randomly jabbing needles into your pain sensory centre all day. Blog about it because the imp is making it too difficult to blog about all the things you really care about, like GM crops, biofuels, medicine availability and child worker exploitation.

Eat cake after blog entry has been written.

Drama

Latest issues that have appeared in my social and work circle lately, worthy of any self-disrespecting soap opera.

1) Love triangles/quadruples/polygons

2) Unrequited love

3) Disputes over the balance of power in the lab (luckily, not my lab)

4) Infidelity

5) Weddings - four at least to attend this summer alone

6) Births and christenings

7) Friends stressing over the lack of partners to get married to or reproduce with.

8) Family disputes. Arguments with parents/siblings/extended family.

9) Siblings MIA (mine)

More sobering;

10) Cancer and illness

11) Bereavement

Specifically for the PhD students;

12) The end is NOT in sight. Panic over looming deadlines and depression over the lack of foreseeable job prospects.

13) Student-supervision relationship break-down (not mine, thankfully)

14) Stressed undergraduate friends and supervisees close to mental breakdown in the run-up to exams (wait til they start a PhD. Then they know what mental breakdown really is)

15) Everything else. Life.

I've finally realised why I got so much more work done when I was far away in Oklahoma.

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.