I had always intended to use this blog as day-to-day record of what it’s like being a PhD student. Unfortunately this proved to be unsuccessful. I never even got round to giving it a sensible title.

Most of the posts I found myself writing were about silly mistakes that I made in the laboratory. Sometimes these mistakes were pretty funny and I thought it could help people by sharing them. But then I had a crisis of confidence: do I really want to admit to the world that sometimes I am completely and utterly stupid?

On a similar vein, I have quite a wacky sense of humour and sometimes I like to write about really silly subjects (see: the iguana post). Writing in a more light-hearted way was a welcome relief from serious science, but I worried that I wouldn’t be taken seriously by being quite oddball on my blog. I think I would be really embarrassed if someone who didn’t realise how nutty I am really came across my blog.

Sometimes I found myself writing about what I was working on and wondered about how much detail it’s safe to go in to prior to publication. Another issue is that I am quite private with my online identity and struggled with how wise it would be to put my name and face to what I was writing.

I would be interested to get feedback on what I’ve written, so please feel free to leave a comment.

Having to yell “MY ECKSPERRYMENTS DIDN’T WERK AGAYNE” in despair at the end of each day.

• When they swim they can’t be bothered to use their legs. They just let their limbs dangle casually as they propel themselves aalong with their tail.

• Got your tail trapped in the car door? No problem if you’re an iguana – they can just casually shed it and carry on with their day no problemo.

• In central and South America they’re called “chicken of the tree”. This is because they live in trees and go well in stir fries.

• They have 3 eyes, man. Like cyclops, tripled. The third eye is a transparent scale on the top of their head. They use them to make sure there’s no dragons circling above their head waiting to devour them.

• Even though they’re pretty fast and swift and speedy, they like chillin’ man. Sittin’ on a log casually chewing on a plum, lazily creeping a few inches or two ever so often. Listenin’ to Bob Marley. With a steely glint in the eye as if to say “I’m gonna CUT you, punk”.

• Look at their teeth:

• In wintry Florida, iguanas get really cold and go into a comatose state. They lose their grip on tree branches and go splatt onto the tarmac below, giving them the nickname “kamikaze iguanas“. When it gets warm again they revive and waddle off.
• “I knew of a gentleman who was collecting them off the street and throwing them in the back of his station wagon, and all of a sudden these things are coming alive, crawling on his back and almost causing a wreck.”

• They’re manly enough to eat cacti.

• If you throw one off the roof of your house, it’ll be fine. They can fall from 15 metres and survive. Whether this is dependent on having random foliage around to grab on to on the way down I am not certain.

• Their collective noun is “a mess of iguanas”.

• Male iguanas have two penises. So if one gets stuck in the car door along with the tail, all’s fine.

• They like living in trees so much that they’ll only come down to have sex (or to lay eggs, or move to a more exciting tree).

• Evidently they like extreme dieting. If all humans averaged 2m tall and weighed 5kg…we’d be so thin that we wouldn’t even exist.

• Just look at it. It’s cool and it knows it.

Yeah, I know, this article kinda deviates from the norm of this blog. But I figure it’s vaguely related to science, and it’s nice to have a bit of excessive frivolity once in a while (if my posts aren’t frivolous enough already).

French pressing squashes cells under loads of pressure until they go POP. The press consists of a hydraulic pump and a piston in a hollow metal cylinder which contains the cells. It’s a bit like making coffee in a cafetiere but much, much, worse. The cells are pushed through a valve where the plasma membrane/cell wall just can’t take it any more and breaks. Apart from being an excellent torture device for naughty cells, French pressing is useful for the isolation of various cell gubbins including membrane vesicles. Unfortunately, French pressing is not particularly enjoyable for anyone.

If you’re a non-bio-scientist and didn’t understand a word of that, it doesn’t matter – the point is, I have to do it, and it is horrible, and I am going to tell you why.

• Things can get incredibly messy. There is huge potential for cell juice to come squirting out of various holes at great speed if you’re not careful enough. The first time I ever French pressed, the whole thing exploded as I was lifting it onto the hydraulic pump, coating me in gloopy green bacteria. I even managed to swallow some (it tasted of soapy soil).

• The pump is noisy, and it takes ages to do one sample. It emits a high pitched mechanical whine, a bit like if you pitch shifted up the sound of a chainsaw cutting through a noble old oak tree. Everyone peacefully working in the lab has to work through this constant grating noise. The whole squashing process happens twice or more, once you think the press user has stopped, the racket inevitably starts up again a few minutes later. Our French press only does batches of 40ml, so woe betide anyone who has any more cells to do than that.

• I am pretty feeble, and the French press cylinder is pretty heavy. I’d compare it to trying to balance 40 house bricks on one hand. Once you’ve put your cell sample into the apparatus, you have to lift it onto the pump whilst carefully (gingerly) holding it so that your precious cells don’t dribble (explode) out everywhere.

• The jokes get old. No, the apparatus is not named after a sort of torture device used during the French revolution.  Hur hur, do the French call it English pressing? French press – that’s what they call coffee makers isn’t it, are you going to drink your cells lolllllllllll. Even more frivolity occurs if you happen to have someone from France in your lab. It’s actually named after a bloke called Charles French, which is rather disappointing really.

• The poor little bacteria get squashed to death. I typically splatt my cells at 3,000 psi, which is just over 204 atmospheres of pressure. Just imagine having all that sitting on your head! I expect you’d be greatly vexed.

I am now going to go back on everything I’ve said and declare that I actually love French pressing. It is a means to an end and I love my science. This is most likely because I am a n00b PhD student. I haven’t been beaten down by years of tedium and failure yet. Also, squashing your cells until they burst is a great form of stress relief.

Thank you for listening. Goodbye.

I am now officially, WILLINGLY, New England Biolabs‘ slave for life. They sent me a new researcher starter pack for freeee. It is so awesome that I just want to buy everything from them, whether I need it or not.

I got:

• Floatee (for incubating my Eppendorf tubes in a water bath)
• Very snazzy 1GB data stick on a string, so I can wear it around my neck like a pretty necklace.
• Eppendorf opener (pretty much the most useless bit of plastic in existence).
• Permanent marker to label my shizzle (I need to scrawl cryptic numbers and dates on bits of plastic on a daily basis).
• Sleek looking black pencil.
• Charts with the electrophoresis running patterns of various DNA and protein molecular weight ladders. To make things more exciting, they’re magnetic.
• Sample of DNA polymerase . Bit dubious as to whether this’ll actually work as it’s been in the post and is meant to be stored at -20degreesC.
• Massive academic year planner wall chart.
• Loads and loads of information on biochemical signalling pathways including a couple of wall charts. Insanely useful if I was actually in this area of research. I will hang the wall charts in my living room, just to irk my housemates.
• Thousands and thousands of leaflets about various NEB products.

And this is just SOME of it, sitting proudly on my desk:

The packs are all gone now, so I’m afraid YOU CAN’T HAVE ONE. I expect they’ll be doing the offer again next September though.

In addendum: I had some confusion with delivery of the pack (due to my ignorance of how the department mail works) and Ms NEB helper lady, Dawn, was very helpful. Talk about customer service, srsly.

I was doing some centrifuging today, spinning my bacteria shizzle at 40,000 rpm (185677.44 g). “Wow that’s zoomy and spinny” I thought. It came up in conversation “how fast could you spin a human in a centrifuge?”

According to my friend Sophie, a person can survive up to 9 g at constant rotation. The average width of a person is 22 inches, so a ‘rotor’ width of 50 inches would accommodate a person. This adds up to 80 rpm in a person-sized centrifuge.
Humans can withstand higher G forces for a shorter period of time, and 179.8 g is the highest ever survived by a person (David Purley in an F1 crash). Sophie is very clever and interesting.

The original topic came up when I was worrying about breaking the centrifuge. They instil so much terror about it in my department that it’s a real anxiety. I said that if I broke the centrifuge, I’d just hide inside it. It was pointed out “I hope no one turns it on and starts you spinning”.

I’ve been silent for quite a while; I’ve been gadding around having fun and being cultured for the past few months. Now it’s time to get back into the scientific swing of things. I start my PhD in a couple of weeks, eep!

Whenever people ask me what my PhD is in, they generally expect an answer like “biology” (in which case they assume you’re about to turn into a plant), or chemistry (in which case they assume you’ll end up blowing yourself up before you’ve managed to hand in your thesis). In my case, things are a bit more difficult.

My PhD project title is “Low dimensional chemistry”, but I’m located in a Molecular Biology/Biotechnology department…but I’m funded by the Engineering and Physical Sciences Research Council.
I guess that means my job description is just “Scientist (all disciplines (except social..gawd what do you take me for?!))”.

To make things a bit clearer it’s “something to do with photosynthesis”.

How vague and unilluminating. More later.

Post script: sadly “low dimensional chemistry” sounds significantly less exciting and impressive than it actually is. I’ll refrain from disclosing that description in future.

Addendum: AAARGGGHHH I DON’T KNOW WHAT I’M DOING I’M NOT CUT OUT FOR THIS I DON’T KNOW ANYTHING I’M JUST A TERMITE AARRGHH.

Currently circulating around a social site I frequent is a news article from 2007 about a “miracle drug that cures cancer but no one has taken any noticer”. There is much outrage from users about why little has been heard about this drug since then. Conspiracy theories are popping up left right and centre.

As a lone scientist amongst the masses, I decided to set things to rights. I spent a couple of hours researching the drug in question (dichloroacetate).

What happened in 2007 is your typical media frenzy that occurs every so often when a scientist says “this might be something that could help with cancer” and turns into headlines declaring a “miracle cure”. In this case, the hype snowballed because New Scientist (a reputable science magazine) did a news piece on it, and at the time it did seem promising.

In a nutshell:

Recent studies have shown that dichloroacetate may indeed be effective in helping battle cancer. Other studies have shown that it is ineffective or even harmful to the body. It is by no means a cure, and is a long way off from being licensed for use as an anti-cancer drug.
Drugs undergo years of testing before they’re put on the market. Just because something shows promise in early trials (in this case) doesn’t mean it’ll be proved effective in later tests. The media likes to over-hype things (particularly the tabloid press). Be wary.

This is a much better article, explaining things in a lot more detail, that I found later.

Unfortunately my research was futile. Despite a year of my masters degree being about drug design and mechanisms of disease, I was told I’m “unqualified” to contribute to the debate because I am now working in photosynthesis research. I was also told to take my ego-tripping elsewhere.
If sharing of knowledge, and having access to research papers, is ego-tripping then there is no hope for the world.

The worst thing was that I was accused of being a plant biologist. This is the worst insult I could possibly imagine.

I think they were just upset to be told that they’d been taken in by hype.

Michelakis, E., Sutendra, G., Dromparis, P., Webster, L., Haromy, A., Niven, E., Maguire, C., Gammer, T., Mackey, J., Fulton, D., Abdulkarim, B., McMurtry, M., & Petruk, K. (2010). Metabolic Modulation of Glioblastoma with Dichloroacetate Science Translational Medicine, 2 (31), 31-31 DOI: 10.1126/scitranslmed.3000677

To put it simply: The process of photosynthesis involves lots of little protein components. If we find out the structure of these proteins we can start to understand how they work. We can find out the structure by crystallizing the protein and then firing X-rays at it (and doing some complicated maths).

Photosynthesis proteins are notoriously difficult/frustrating to crystallize (because they live in the cell membrane and don’t dissolve in water). I like a challenge, so 4 years ago I decided to myself that I really wanted to try to get some crystals. Working in a lab that deals with photosynthesis this year has enabled me to give it a go. Today I have these crystals – of a protein called LH2, which absorbs light in the first stage of photosynthesis in a bacteria called R. sphaeroides.
I’ve been developing purification and crystallization (or at least continuing the good work of my predecessors) for LH2 in order to get a better structure than the one we have already; the best for this species is a 6 angstrom EM projection map (Walz, et al., 1998 – J. Mol. Biol 282, 833-845).

The crystals I obtained were distinctly badger-shaped (or at least some other woodland creature, or beaver). Unfortunately these will be pretty useless for X-ray diffraction but they’re amusing nonetheless.

I also got some more likely-looking crystals, which should grow bigger in the next few days. At the moment it’s fantastic that I even got crystals, so if they diffract it will be an additional bonus. My future work will involve refining the purification/crystallization procedure to get better crystals.

(More badgers)

I also got some crystals growing along an eyelash I dropped into the experiment!

On a side note, it’s a bit odd for me to get excited about a 6 angstrom resolution, considering the best structure I had last year (of a soluble protein) was to 1.7 angstroms.

In other news, I have secured a PhD position for next year. More on that story later.

I’ve been pretty busy with my Masters and have been neglecting my blog. I came up with a cunning plan to spew my “scientific” nonsense: video diaries. They’re quicker to make than painstakingly pondering over words. However since I am so brain blattered and tired, things are liable to get silly. In addition, I prefer writing. Still, at least I’m postin’.

[youtube:http://www.youtube.com/watch?v=cEFVlLs76Qk]