All things ginger #6: The Rise and Fall of the Ginger Lizards

While there are many examples of red-haired creatures in the animal world, the revelation that even dinosaurs could be ginger is something of a surprise.

Ginger and scaly and feathery? I normally stick up for my kind, but that's just weird.

Women in science

In the same week that Athena SWAN commended university departments which it considers are making positive steps in encourgaing women working in science, engineering and technology, I stumbled across a new governement website called 'Science: [so what?]'. I shan't let the overly 'cool and edgy' use of punctuation detract from the fact that I am delighted to see a site aimed at engaging non-scientist members of the general public with the science that underpins both the natural world and human innovation around them. But why, you might be asking, am I mentioning these two things in the same paragraph?

Well maybe it's because, of the scientists featured, the biomed people were female while the engineers were almost exclusively male. Maybe it's that they made a point of mentioning that Rachel Riley, co-presenter of Countdown, was "the only girl to read mathematics" at her Oxford College (shame on you, Oriel!) And that she beat beat 1000 other women to the job. Were men debarred from applying? Is she the maths brain, or eye candy? Oh, and let's chuck in "she was bullied at school for being clever."

The site may well provide some answers to how things work (although the content seems a bit thin on the ground at the moment). But if it harbours any desire to inspire people to go into science careers (and this page would suggest it does), then it's awful. In summary, I have learnt:
1. Biomedicine is for women, engineering for men
2. Girls studying maths at uni are a unusual
3. If you're smart and sciencey, you risk getting picked on.
4. Their suggested link for careers advice does not recognise the scientific field I work in when you search their site for it.

Helpful. Thanks for that.

Overcoming certainty

Given that even the credit crunch has failed to prevent the ordinary folk from having to pay taxes, it's nice to know that not everything is set in stone. According to the BBC, taking a more positive view of life can actually help you to cheat death! The key to eternal happiness has been found!

This discovery was announced the other morning on the BBC News pages as follows:

Quite a claim! While pessimists are busy shuffling off the mortal coil, the probability of the cheerier souls following suit is considerably less. Presumably some of them cheat it entirely, judging by that headline.

Perhaps, unsurprisingly, the text subsequently changed to the somewhat more prosaic "Why optimism may be key to a long, healthy life - at least for women". Shame the editor didn't follow through and change the article itself. It still starts as follows:

What they actually mean is that over the years in which the study was conducted, the death rate among optimists was lower than that among the pessimists. This is not the same as having a lower risk of death. Let's be clear about this - the risk of death for every person on the planet is 100%. 10 out of 10. As certain as taxes. Is the Pope a Catholic? Yes. Are you going to die? Yes.

That's not to dismiss the research itself - one's state of mind can have a profound influence on one's health and longevity. Whether life is 'nasty, brutish and short' or otherwise, one might as well find a way of enjoying it, and a sunny disposition may well aid you in receiving a telegram from the Queen. But is it too much to ask that people charged with writing science stories actually proof-read what they've written, and check for logic? No, I suppose not, or else we might have been spared this effort today:
Isn't 'downing a drink' a tad colloquial for a 'quality' news site? Are we dumbing down English as well as science? Mind you, it looks like the proof reader had had a couple.

Sigh.

[In case you are worried I'm plotting to usurp Dr Goldacre from his post as Chief Health Story Inaccuracy Pointer-Outer, I won't. He does it with far more skill than I, and I haven't got the time. But I reserve the right to carry on shouting at the telly when they say stupid things about health. And I may well subject you to a rant about swine flu coverage at some point. Sorry.]

Bad Science

I was delighted to hear Ben Goldacre on The Now Show the other day, not least because I'm currently in the middle of Bad Science, a book that I imagine I will badger everyone I know into reading before the year is out. He says an awful lot of things about the relationship between the media and health research that I would like to communicate, but in my case I end up shouting at the telly and getting too aerated to construct coherent blog posts, whereas Dr Goldacre manages to focus his frustrations into far more concise and persuasive arguments.

If you'd like a taste of his perspective, here's his slot on The Now Show:

Well, quite. My only gripe is that The Daily Mail Oncological Ontology Project (surely the best named blog ever) ran for a mere 4 days before ceasing to progress. Perhaps the author spontaneously combusted under the strain of reading all the crap spouted by the Daily Maul. Given the general ignorance about the difference between correlation and causation, I feel confident in stating (on the basis of this scant 'evidence' which I have extrapolated from an observation) that reading the Daily Mail is bad for your health.

Making a pig's breakfast...

Sorry I've been a bit quiet lately. I seem to have misplaced my magic blogging dust somewhere along the line, but I spect it'll turn up behind the sofa.

I did start writing a long ranty post the other week about swine flu, and how it was another example of the media distorting the facts for their own agenda. In my view the approach of the WHO and health authorities here was entirely approriate to the situation. The media, meanwhile, seemed to be gagging for panic on the streets.

But as usual, other people are more adept at putting across a message more succinctly. Here is a recent offering from the wonderful PhD comics. (click to enlarge)

So very true.

Gingerism in science

The other day I was looking for information about a category of genetic variants called SNPs (Single Nucleotide Polymorphisms i.e. variation of a single 'letter' in the DNA code of a gene). In my hunt, I stumbled across SNPedia, which provided me with the information I needed.

Having a further look around the site, I found references to SNPs in the genes that contribute to red hair. It was at this point that I discovered that 'red hair' is categorised, alongside cancers, mental health problems and heart disease, as a 'medical condition'.

Hmph.

Future UnCERNtainty

So, apparently the world might end tomorrow. Out of all the screw-ups I ever made in the lab, it's safe to say nothing I did was ever likely to have that kind of effect.

I'm actually having a few days off with no fixed plans. It occurred to me that something I could do is find someone else at a similarly loose end and meet at the Underground. If we both board the Circle line, but headed in different directions, what would happen at the point at which our paths cross, if we managed to make eye contact? Would the Underground grind to a halt? Would Bob Crow be silenced forever? Would Boris's hair get even wilder?

But do I really want to fork out £5.90 on a travelcard if the world's going to end? Does PAYG work in a black hole?

News round up

Nowt major, just a couple of things that caught my eye in today's news:
1. The grammar pedants have won, but still might not be happy. Tesco has caved in to pressure from the Lynne Truss brigade to change their express checkout signs from '10 items or less'. But rather than the more grammatically correct, '10 items or fewer' they're going for 'Up to 10 items'.

A spokesman for the Plain English Campaign said:

"Saying up to 10 items is easy to understand and avoids any debate."

Unfortunately, I would beg to differ. '10 items or less', though jarring, is totally comprehensible and unambiguous in everyday speech . 'Up to 10 items' makes me think that perhaps it could mean 9 items or fewer. Did they never learn the difference between the '<' and the '≤' signs in maths? Surely for totally clarity it would have to be 'Up to and including 10 items'. That would make for a very large sign. I think they were better off before.

2. "Farm Pregnancy 'cuts asthma risk.'" I wish that science news editors would be a little more discerning regarding what is 'good, interesting science' and what is 'good, interesting science that is of relevance to the general public'. The discovery that pre-natal exposure to a farm environment may reduce risk of developing asthma in later life is scientifically interesting. It might give clues to immunologists who are trying to develop a better understanding of the basic biology of asthma. I don't, however, think that it is information of great use to anyone else - it's the kind of story that makes you go, 'So what?' What are we supposed to do with that information? Tell pregnant friends to get themselves along to the nearest pigsty? Congratulate rural friends on the likelihood that their future children will have good respiratory health? What exactly?

Funny Science (part one)

The stereotype of a scientist doesn't usually include a lot of laughter, unless directed at the poor unfortunate nerd. But that's not necessarily an accurate representation of the truth. A lot of us can be quite funny if we put our geeky minds to it. Have you ever seen what happens if you fill a latex glove with dry ice, and then let it expand till it's as big as a medium-sized pig? No? You haven't lived.

Anyway, given that science and comedy are two major interests of mine, I've decided to present for your viewing pleasure snippets from three fairly contemporary scientific TV comedy efforts. First up we have Lab Rats, a new offering from BBC2. Set in a British university lab that seems to change its research focus week by week, according to whatever odd requests are made of the staff, it's got quite a cartoony, surreal feel to it. It's certainly not going to feature in my 'Top 10 list of most funny sitcoms ever' but I do feel like championing it a bit, if only cos it's the only programme I've ever watched being recorded in a studio. Yes, ladies and gentlemen, I can testify that the laughter isn't canned, although now I do understand why it can sound like it. The series does seem to have improved as it's gone on, but here's a clip from the first episode (the one I saw being filmed), showing Cara at her most deliciously daft:


Second, across the pond to The Big Bang Theory, which is kind of like Friends or Will and Grace but with physics geeks. The Women in Science blog didn't seem desperately impressed by it, and I can understand why. There are only really two female characters, one of whom is a gorgeous fashionable blonde, the other a speccy, curly haired deadpan type. Guess which one is a physicist, and which one is the love interest from across the hall? Having said that, the guys don't exactly come out of it looking like fine specimens of social aptitude in action, so I feel more inclined to be affronted on behalf of sciencekind, rather than womankind specifically. Here are Sheldon and Leonard engaging in a very geeky kind of macho posturing:

My last offering (for now) is Look Around You which beats the other two hands down in its commitment to pure scientific endeavour whilst simultaneously presenting a big old heap of nonsense. It ran to two series, the first of which parodied Open University-style schools programmes, whilst the second targeted Tomorrow's World and the like. I gave a DVD of the latter series to a friend of mine who's just qualified as a science teacher - I hope he shows it to his pupils someday. But not the first series - to the untrained brain there is just too much potential for confusing fact with fiction. Here's what the Look Around You team have to say about MATHS:

So there we have it. I have to admit, although I can quite happily watch all three, I do wonder to what extent they might appeal to the general, less nerdy, public? Do the 'science bits' seem off-putting, regardless of how (in)accurate they are? Can science and comedy mix? I'll come back to this another time and explore a few more examples.

Finally, I do realise that it is totally necessary to suspend a certain amount of reality when it comes to TV shows of any kind. But there is one inaccuracy I really can't tolerate in all of the above. How on earth did Cara, Lab Rats' tiny technician, manage to get a lab coat that fitted her perfectly? When I was an undergrad, the smallest lab coat the uni shop sold still required me to roll up the sleeves. Maybe we'd get more women into science if the safety equipment actually fitted them. ;-)

Ginger is no longer in a relationship with her PhD

"The time has come," the Walrus said,

"To talk of many things:

Of shoes--and ships--and sealing-wax--

Of cabbages--and kings--

And why the sea is boiling hot--

And whether pigs have wings.

And why Ginger has taken the slightly dramatic step of quitting her PhD."

-Lewis Carroll (and others)

Yep, that's right. Your blogging hostess is officially a PhD drop-out.

I realise that, from the perspective of my blog, this might seem like a bit of a bolt from the blue. Sure, I've had the odd grumble, but mostly I've kept my disgruntlement to myself. But trouble has been a-brewing for a while now, and recently I made the big decision to call time on my research project. Without wanting to go all 'group therapy' on you, I thought I might use my blog as a way of offering an explanation. Not least because I found Googling 'Quitting a PhD' quite a helpful way of seeing what other people's experiences of this kind of situation had been before I made my final decision.

So, where to start? Well, I entered into my project with the best of intentions, and the desire to see it through to the end. And it's not like I went into it blind - I'd already worked at the lab in question for 10 weeks before I committed myself, as well as gaining lab experience elsewhere. And things were fine to begin with. I had the newbie enthusiasm, the naively optimistic 'get back on the horse' attitude to the odd experiment that failed here and there. But as time went on, things began to unravel. A bit of extracurricular reading introduced me to the existence of a different field which got me far more intellectually and emotionally fired up than the one in which I was working. I began to realise that, post-PhD, I'd rather work in that field and cease lab work altogether. I still remained committed to seeing it through though.

But then... well, there were the experiments that failed to work over and over again, gradually eroding my self confidence, and occupying weeks and months of attempts before I finally managed to show that it wasn't actually my fault. The realisation that the technical problems plus the consequent demotivation meant I was at least six months behind schedule. The dread with which I was filled at the thought of carrying this on for another couple of years, and the long hours it would entail, when my heart was no longer in it. And other problems I won't go into on a public forum.

I do appreciate that everyone goes through 'second year blues' where it becomes overwhelmingly apparent that you have no data, and the end is both a bloody long way off, and yet too soon to get everything done. And I don't think that any one of the reasons I cite constitutes, on its own, a need to throw in the towel. However I do think that, in combination, there was a compelling argument for my decision. I did not want to give over a major part of my life for the next 2-3 years to something in which I no longer had any confidence, had lost passion for, and which was no longer directly relevant to my future plans. I have a deeply ingrained 'I'm not a quitter' attitude, but I am beginning to appreciate that sometimes there is virtue in walking away and not flogging a dead microarray.

Something that has surprised me is how much kudos I seem to be getting for making the decision. PhD/science web-fora seem to be full of people saying 'I want to quit, but I don't want to let my parents down' or 'I wish I'd quit a year ago'. I am fortunate in that my family and friends have been supportive of my decision. What came as a surprise was that people seem to view it as a brave step to take. Certainly, I know it's one of the gutsiest decisions I've had to make, but I was fully prepared to have to justify myself and fight against the perception that I was a wuss who didn't have the courage to meet the challenges of a PhD. It's been a pleasant bonus not to be burdened with that label.

Right, having managed to spout cliché after cliché, it's time to get on with the rest of my life...

Quotation of the week

Nicked from a t shirt:

Engineering forsight: An escalator can never break. It can
only become stairs.

"For the Good of the Company"

Dull epiphany

I realised recently that I spend more time holding a pipette than I do a pen.

That's all.

*sigh*

Anatomy of a PhD

Most PhD vacancies in the UK come with 3-4 years funding attached; even if you haven't written up your thesis in that time, the research council will stop paying you.

Now the layman might reasonably assume that this structure suggests that the student spends 70-90% of the available time gathering data, and the remainder writing this* up in the form of papers and a thesis. Fourteen months into my lab-based PhD, I'd like to suggest an alternative structure:



Year 1
Month 1
- Learn where stuff in the lab is kept.
-Try to understand the title of your research project.
Month 2-12
- Learn the basic techniques for your research. This may involve having them demonstrated, trying them for yourself, then repeatedly needing reminders of the finer points of which you forget a different one each time you carry out the experiment.
Month 2-8
- Potter
Month 8-12
- Feel like you're starting to get some command of what you're doing. Then learn a whole new bunch of techniques and feel like a newbie again.
- Have an unsettling conversation where someone says to you 'Oh, did nobody tell you that X is done like this...?' Feel a bit peeved/confused/stupid.
- Be told that something is easy/straightforward and then come up with every mistake in the book.

Year 2 Getting down to some serious work. This may involve:
- Generating weird data that prompts every senior/more experienced person you consult to say, "Ooh, that doesn't look good. I don't know what's causing it though."
- Fail to find any helpful advice for your problem in the literature. Know deep down that your bizarre data is ten thousand times more likely a glitch in the experiment than a significant discovery.
- Develop a force field that causes every piece of equipment you want to use to break or malfunction.
- Write 15 drafts of your transfer report (to have your study upgraded from 'MPhil' to 'PhD' status)
- Have serious doubts about (i) your research methods (ii) the validity/importance of your overall study (iii) the purpose of your own existence.
- Discover that coming in on a Saturday is no longer a weird concept.

Year 3 (please, God)
- Finally get some of your experiments going.
- Bid farewell to any residual social life
- Generate that much longed-for data.
- Write up.

So I'd estimate around 6 months of useful data generation in the whole process, and a few marbles lost along the way. I hope the taxpayers are happy.

*Yes, I know 'data' is a plural, but talking about 'these data' sounds a bit unnatural and poncy outside of the context of a research article.

Blood on our labcoats

It always sucks when you discover an organisation you're associated with is not quite what it seems. Particularly if the hidden side isn't one of which you approve.

I strongly feel that universities should be apolitical institutions with respect to their governance. Not that students and academics within them shouldn't argue for or against various political concepts and ideals - rather that the institutions themselves are free from the sway and trends of politics, as might be imposed on their operation.

Working from within that framework, I find it both disappointing and disturbing to discover just how many UK universities have shares in arms companies. What place does arms dealing have in what is supposed to be a climate of academic thought, learning and research? It's somewhat disconcerting to realise that the tuition I sought to try to make a positive contribution to society was indirectly supported by an industry whose products maim and kill. 'Disconcerting' is probably not the word to describe the sensation experienced by those on the receiving end of such 'products'.

It gets worse (and more bizarre). Reed Elsevier, a major force in scientific journal publishing, also run arms fairs such as DSEI, which attracted protest today. I cannot begin to fathom what kind of board meeting resulted in that decision:

"Right, ladies and gentlemen, we need to do something to increase our revenue. Any ideas?"
"How about we become pioneers in Open Access publishing, thus benefiting the academic community and perhaps society as a whole?"
"No, not profitable enough. Any other thoughts?
"Well, we could run arms fairs and invite military from around the world to come shopping?"
"Excellent idea!"

As it happens, Reed Elsevier have decided to sell off this enterprise at the end of the year due to criticism from a number of sources. I'm glad of this, as boycotting KitKats because Nestle are evil bastards is one thing, but trying to avoid Reed Elsevier's publications whilst simultaneously trying to make a reasonable stab at this 'cancer research thing' is rather more problematic. It's a strange old world where civilian war casualties are somehow linked to cancer patients in peaceful nation states, but such is the complex web that underpins commercial enterprise. Whatever my purist ideals about working in academia and not industry, I'm becoming increasingly aware of my need to get to grips with commerce and economics if I want to try to live an ethical life.

Necessity is the mother of invention.

But who can say that they've ever needed a device to turn their electric hand whisk into a power tool?

One of many wonderful offerings from a blog I discovered today that seems to chronicle a history of bizarre inventions. Have a look at Modern Mechanix, and have a chuckle.

Slow progress

BBC NEWS Entertainment Queen star set to hand in thesis

Oooh. Hope for me yet.

Something to work on

As the first anniversary of starting my PhD draws very close (gagh!), I've realised that, whilst I am committed to what I'm doing, I still have a long way to go as far as being a good technician goes. There's certainly a bit of a discrepancy between what I write in my lab book and what it will need to look like in a paper one day. For example:

"Sample X – not entirely great

Slide messy – wash went a bit awry "

Precision. Yes, that's what's needed.

Not so white coats

People go into scientific research for different reasons. Some people in response to an intellectual obsession. Some because they want to Make a Difference^TM. Contrary to what old horror films would have you believe, few people go into it for nefarious purposes. So I did feel some degree of pity when I learnt about the unfortunate Thomas Midgely Jr., an American scientist who not only developed CFCs, but also put the lead in petrol!

It's quite something to make one discovery that has damaging consequences, but two is a little excessive. (For the uninitiated, CFCs are the refrigerants that have damaged the ozone layer, and leaded petrol contributed to air pollution). Mind you, whilst Alfred Nobel's regret that his invention of dynamite earnt him the moniker 'The merchant of death' prompted him to create the famous peace prize, Midgley didn't seem to do much to extricate himself from promotion of leaded petrol, even though he himself experienced the negative health effects. Ironically, it was one of his other creations that resulted in his death; having contracted polio, he created a pulley system to aid him in getting in and out of bed, which unfortunately resulted in his strangulation a few years later.

It can be difficult to predict the future implications of scientific endeavour which appears to be morally and technically sound at the time. I feel that scientists do, however, have a responsibility to try to act if it turns out that unexpected harm is a consequence of their work; to tame the monster they have created, as it were. Midgley didn't seem to try, and this is one of the reasons that, for all the technical validity of his major works, his is not the sort of career one should look to when wanting to find examples of good scientific practice.

Britain's Finest Minds

There are certain expectations when you tell people you're doing a PhD that you're reasonably bright. I think a fair number of tax payers would be rather dismayed if they knew the reality. Someone came to service one of our centrifuges at work yesterday (comme ça). It's been playing up rather. We presented the technician with a list of problems, and hoped that he would be able to fix them. When he was finished, he called us in to explain what he'd done:

• The reason the display was in German, not English, was most likely because nobody had ever read the manual to see how to change it from the factory settings.
• The reason that the display was also virtually unreadable was not that the backlight had gone - someone had probably lent on the button that adjusts the contrast.
• It helps if you clean/oil the parts. Maybe weekly as he suggested. EVER would be a good start.
• He also retrieved a shard of plastic and a couple of wooden beads from the interior. The former may well have come from the time I set the machine spinnning without realising there was a loose tube inside. The latter was definitely from when one of my colleagues changed the sticky mat next to the machine and jumped up and down on the clean layer* with such enthusiasm that her necklace snapped.

All things considered, I'm not sure that the future of biomedical research is in safe hands.

*It sounds childish, but I bet you'd do the same if you were there.