a room of my own

The Dynamic Personality of Dorothee Kern

2011-10-01T18:11:00.011Z

This post was written for Ada Lovelace Day – an international day of blogging to celebrate the achievements of women in technology and science.
http://findingada.com/

Dorothee Kern often starts her biochemistry talks and lectures with a movie of a basketball game. Not what you'd expect perhaps, but then how many science professors used to captain an international basketball team? Kern's research focuses on protein dynamics, an area of active research worldwide (and indeed the subject of my own PhD project). When I started delving into the literature, her name came up again and again, one Science or Nature paper after another from her lab at Brandeis University.

Protein structure - the way a chain of amino acid subunits folds on itself to form the three-dimensional structure of the active protein - is a much-studied problem. And as proteins perform such a vast variety of roles in the cell, and represent therapeutic targets for many drugs, understanding these structures is essential. X-ray crystallography is the method of choice. We trap proteins in crystal 'cells' and fire X-rays at them, and the resulting diffraction pattern - the way in which the X-rays are scattered by the protein atoms - allows us to deduce the relative geometric positions of the atoms, giving the structure. In the early days, when Dorothy Hodgkin was solving the Nobel-prize winning structure of insulin, and Rosalind Franklin was producing her famous DNA structures, the process involved complex mathematical calculations and constructing elaborate physical models by hand. Fortunately now, with the help of computational methods, the process has been speeded up to the point where solutions can be churned out with relative ease, and tens of thousands of structures are available in the online Protein Data Bank. So much structural data is available that it looks as though the problem is solved.

But it is not so. In fact the dependence on crystal structures for our understanding of proteins could be seen as having distorted our view of what they are and how they work. Traditionally proteins are considered to be fairly static structures, except when a particular action is required to perform a certain function. But in fact they are in constant motion - if we could look close enough to see their motions, we'd see the vibrations of individual atoms and bonds, functional groups moving as coherent units: sometimes we'd see the two halves of the protein opening and closing like a seashell, like a breathing living thing. A protein does not have just one structure, but many, constantly shifting from one to another. To understand protein function, we need to consider not just structure, but dynamics.

This is one of the big paradigm shifts in protein science, pioneered by Kern in a seminal paper, The Dynamic Personalities of Proteins. Here she challenges the traditional 'static' view of proteins, proposing instead the use of energy landscape models more usually associated with the protein folding process, and makes a bold attempt to bridge biology and physics in a unified view of proteins from atomic structure to biological function. She and her research group used a variety of experimental and computational methods to determine the dynamics of a model protein on various timescales, discovering previously unknown states that occur with low probability but are vital to the overall function. And the results also showed that the seemingly random, miniscule, fast movements of individual atoms in fact contribute to the slower, large-scale motions of the whole molecule - the organisation is hierarchical, multi-scale in both time and space. As Kern explains in a characteristic basketball analogy: each individual player in the team is continuously moving, 'with or without the ball', each contributing in their own small way to the concerted actions and achievements of the team.

My own research uses mathematics to model and predict the multiscale dynamics of cell-cycle proteins involved in cancer and other diseases, with a view to being able to develop inhibitors to interfere with protein function in a predictable way. It was easy at first to take the dynamic model of proteins for granted; it had already become such a well-established part of modern protein science. But like so many great ideas in science, although it looks simple with hindsight, it took an imaginative, unconvential thinker to realise it and to challenge existing orthodoxy.

Kern is a believer in pursuing interests outside science - energising, creative ones; her colleagues describe her as the most energetic scientist they know. It's easy to forget sometimes, especially when it comes to biology, that science is as much about creativity and abstract thinking, as about churning out results. That's why, this Ada Lovelace Day, I wanted to talk about Dorothee Kern.

Doing science justice

2011-09-10T10:47:00.004Z

BBC4's Justice: A Citizen's Guide to the 21st Century was not your average television documentary. After a brief introduction from Harvard professor Michael Sandel, we were straight into his first lecture, listening along with a hall full of undergraduate students as he discussed Aristotle's Politics and its relevance to contemporary moral and political questions. Some concentration was required to follow the lecture; there were no pictures or movies, no interruptions by a friendly narrator to summarise for us in simple terms. It was a challenge for those of us with no background in philosophy or academic politics.

In Beautiful Equations, on the other hand, we were introduced to Einstein's equation by an 'art critic' who boasted about his ignorance of mathematics and found the very concept of equations to be baffling and incomprehensible. He might have been better advised to stick to his usual job, which appeared to involve creating oversized finger-paintings on walls, alarmingly suggestive of giant toddlers running riot. Surely the BBC could have found someone a little more qualified; even, we could dare to imagine, a mathematician? Of course the purpose was not just to present mathematics but explore a connection with art and beauty. But it is probably fair to suggest that there are more mathematicians with a deep knowledge of and genuine interest in the arts, than there are artists proficient in mathematics. The producers perhaps wanted a narrator the ordinary viewer could identify with? But we don't see literary discussions presented by people who can barely read or have never picked up a book. Why is the standard so much lower for maths?

We have certainly seen maths presented by experts. In The Story of Maths, Marcus du Sautoy gave us a fascinating history of mathematicians and their work over the centuries. But his efforts were limited by a bizarre reluctance to allow any actual mathematics into the content. However skilled the communicator, it is just not possible to explain the Riemann hypothesis in any meaningful way without showing the Riemann zeta function or the complex plane, to convey any understanding of the Mandlebrot set without a definition of the set itself, given by its generating equation. To attempt is like trying to describe a great work of literature or poetry without ever using a sentence: a remarkable achievement if you can do it, but why would you wish to?

A similar problem afflicts so much science programming. The BBC's Horizon had good intentions in its recent exploration of 'extreme astronomy'. But it looked and sounded better than it was: we saw sweeping panoramic shots of mountain and desert scenery and dazzling starscapes. Stirring and triumphant music played loudly, while the narrator intoned grand statements about scientists 'uncovering the secrets of the universe'. But so, so little content. And the result as always is that the non-scientist is left with the vague impression of 'scientists are doing some stuff' while the rest of us are frustrated: how does it work? What is the data and how did you process and interpret it? What does it mean?

So let's have some undergraduate lectures from Harvard or Cambridge (or Imperial!) in maths and physics, astronomy, genetics, engineering. Why not? We might not all understand every word, but surely it's better to be challenged and educated occasionally, than patronised and soothed with pretty pictures and music? After all, we have the Landscape Channel for that.

The big syrupy placebo effect.

2011-02-05T16:10:00.003Z

Winter is here, and it's the time of year when coughs and colds are spreading alarmingly through the population. Fortunately our local pharmacies and supermarkets have their shelves well-stocked with remedies, not least those bottles of cough syrup to be taken by the spoonful in a reassuringly quaint manner, preferably while tucked up warmly in bed. I remembered hearing a little about the dubious efficacy of many cough medicine preparation so had a look at a Cochrane review on the subject. The Cochrane reviews provide a systematic search and analysis of the evidence available for a particular medication or practice, and look at both the results of trials and studies and the quality of the study and what exactly it was measuring. They're deservedly considered the gold standard in evidence-based medicine.

The drugs used in cough medicines can be divided into major group depending on their purported mode of action. Anti-tussives are cough suppressants, reducing the sensation of needing to cough, an appealing idea when you hav a dry irritating cough that keeps you awake. Expectorants are more or less the opposite, helping you to cough up the 'gunk' that builds up in your lungs and mucolytics work in a similar manner, thinning out the mucus and making it easier to shift. The final class is anti-histamines, often given together with decongestants.

The trials of anti-tussives show them to be remarkably useless, providing little or no improvement in symptoms compared to placebo, though it was interesting to see there was a significant reduction in symptoms seemingly due to the placebo effect, cough perhaps being a symptom particularly amenable to placebo for some reason? Anti-histamines and decongestants produced similar results. The expectorants and mucolytics appeared somewhat more promising, with some trials showing a statistically significant benefit compared to placebo, however the quality of trials giving such positive results was described as 'dubious', with flaws in both trial design and interpretation of data. The overall conclusion was that we have no reliable evidence that over-the-counter cough medicines in fact have any effect at all on cough symptoms. So what's that brightly coloured array of bottles and packages doing on our shelves, and what's actually in there?

The expectorant guaifenesin seems to be the usual active ingredient in the 'chesty cough' preparations. Dubious evidence being slightly better than none at all, it's reasonable to think this might be worth a try. But the best of all is the version for dry cough. A 'strong' version of most brands is available from pharmacies, containing a cough suppressant and a decongestant, which is...interesting when you the evidence . But if you think it's somewhat brazen to take people's money for a useless medicine, then look at the version you get on the supermarket shelves. Check the ingredient list, and it is exactly the same as the 'chesty cough' one, except without the active ingredient. So just the syrup base. This one is literally a big syrupy placebo. I guess the syrup might feel soothing if you have a sore throat from coughing, but would be very surprised if there was reason for it to be any more soothing than a spoonful of honey or syrup from your cupboard at home.

The packaging is also a thing to behold, robust red and royal blue for the ones that help you get up and get on with it, soft blues and lilacs for the ones that are supposed to help you sleep (though interestingly the mild anti-histamine sedative may be one of the few ingredients that does have a proven effect), consistent with the evidence that shows colour of a drug influences its effectivity. Graphics showing the flow of air through the bronchial and nasal passages, miraculously restored, images of the human body bathed in brilliant white healing light like a blessing, a warm golden glow focused at the site of the affliction. It's an absolutely fascinating study in advertising and the cultural and psychological connotations of 'medicine' as a concept, though it's difficult not to wonder whether if as much effort and money went into developing new products as into designing packaging and advertisments for the old ones, we might get more relief from our winter coughs.

But maybe not. Because perhaps the biggest flaw in these products: that they haven't been shown to work any better than placebo, is also their greatest strength: that they do work really quite well as placebos.

Bias

2010-10-10T19:56:00.007Z

Would you treat a little Connor or Chelsea differently from an Alexander or Elisabeth on their first day at school? Or be impressed by a male violinist's virtuosic playing in comparison to his female collegue's 'smaller technique' even though they performed with equal skill?

You'd probably like to think you wouldn't. Most of us don't mean to be irrationally prejudiced, and would be upset and offended at the suggestion that we harbour such ideas about people based on their gender or name, never mind more politically sensitive attributes such as race and skin colour. But we are, and we do. Orchestral auditions, while possibly not the most critical area in which we need fairness, are a good illustration of the problem - it was shown that when musicians performed their auditions behind a screen, so that judges were unable to know their gender or other personal characteristics, the probability of women being hired increased significantly.

On a similar note I wonder how many of the choirmasters who insist that young boys' voices have some elusive 'special quality' that girls just can't emulate would find themselves able to distinguish accurately between boys and girls in a screened audition. Just for amusement value I'd like to see if coffee snobs could really tell their Nescafe from Starbucks from Proper Italian Coffee in a controlled test.

And then there's my own experience, in the corporate world, on both sides of the interview process. I remember being told in feedback for an interview that my voice did not sufficiently covey 'confidence and authority' in the group discussions and presentations, compared to that of the other candidates (all male). Because the City is no place for feminist analysis, I politely accepted the feedback rather than questioning whether social conditioning and centuries of cultural baggage might just cause the interviewers to unconsciously associate those traits with the deeper sound of the male voice. And from the other side, hearing my colleagues discuss a candidate they'd just interviewed, technically very strong, but they wondered whether she would be a good fit for the team, would she be up for the banter? Easier maybe to just hire someone just like themselves. No one explicitly said they didn't want to hire a woman, but that, whether they realised it or not, was effectively what they meant.

I recently wrote an article for The F-Word about the need for women-only literary prizes. I want to be clear that I don't think the judges in such competitions are intentionally judging women differently, but that all of us are human, which means we are not nearly as objective and rational and free of prejudice as we would generally like to think. What to do about it is a more difficult question.

Does segregating women in their own competitions make the problem worse, or risk being seen as patronising to women, implying female authors are in need of special treatment or unable to compete fairly? Possibly, and acclaimed literary author AS Byatt for one would say so. But for me the obvious response is to ask why, centuries after the Bronte sisters and George Eliot had to hide behind their male or ungendered pseudonyms, in a world supposedly now free of gender prejudice, she chooses not to publish her work as 'Antonia Byatt'.

This is by no means a problem limited to the literary world. I am unlikely to ever be nominated for a literature prize, however I would definitely hope to publish some research papers in the next few years. So what about academic peer review, the process of criticism and approval or rejection by other academics that a paper has to go through before it can be published in a reputable journal? But unlike the Orange Prize question, this seems to me a problem with a simple and easy solution.

In science we recognise our inability to be objective in other situations, for example in evaluating the effect of a drug or medical treatment, which is why randomised, controlled and double-blinded clinical trials are considered the gold standard. Otherwise we can't know we're not subconsciously cheating ourselves. Even outside of clinical trials, in scientific experimentation we place great importance on knowing whether what we really know what we think we know.

So it's remarkable to me that even in science we send papers to be reviewed with the authors names clearly indicated. There's no good reason for this not to be an anonymous process, like orchestra auditions, and in fact similar studies have shown a similar increase in women's representation when 'double-blinded' review is used. But it still isn't universally or even widely adopted.

For now, one possible alternative solution is to take a leaf from AS Byatt's book and use initials only, which cleverly disguises the gender of the author, and indeed this is common practice anyway. But that only works until the reviewer looks you up on your institution website and you're betrayed by your girly photo and the feminine pronouns in your bio. And gender is not the only issue. Both given and surnames tell us a certain amount about ethnic and cultural background, and social class. In the 'naughty children's names' survey, for example, it's notable how many Irish names appear in the list of boys names viewed negatively by teachers, though I'm sure most of them would vehemently deny any anti-Celtic feeling.

Double-blinded peer review seems the only practical way to overcome these problems, and no one should be offended at the implication that they are racist or sexist or some other -ist, unless they are offended at being considered human.

Two scare stories: #2

2010-08-30T09:07:00.002Z

Following shortly afterwards was a rather disturbing report in The Lancet about antibiotic resistance. This is actually much more worthy of concern. Antibiotic resistance is a real and serious problem, and this latest finding reminds us of its importance.

But I noticed how the reporting of this was very confused with many writers clearly not knowing what an enzyme is, references to the enzyme 'living' inside bacteria , and this:

'New Delhi metallo-ß-lactamase-1, or NDM-1 for short, is a gene carried by bacteria...'

'NDM-1 (or more precisely the DNA code for this enzyme) '

Wait, so is it a gene or an enzyme? Does the person writing this know the difference, or are they just using the terms interchangeably (*)? And 'DNA code for this enzyme', but didn't you say it was a gene, and surely a gene is a 'DNA code' itself...

It's just so confused and is transparently, obviously, a case of someone who really doesn't understand what they're talking about trying to put together some fragments of sentences they've read or heard and hoping it makes sense, because they personally have no idea how to tell whether it does or not. And I'm not pointing this out to mock the journalist who wrote it, it's too easy for critique of science writing in the mainstream media to turn into pointless pedantry and mean-spirited sniping, and that's not what I intend. I really do sympathise with the person who wrote that, because I've been there and I know exactly what they're doing.

In one of the first interviews I ever had for a programming job, I was asked for my opinion on Solaris. I didn't know what Solaris was. I had some vague idea that it was some open-source thing, something to do with servers, but was it a programming language? An operating system? Something hardware-related? I didn't know, but didn't want to say that. So I had to make up some answer as well as I could, though I didn't know what I was talking about, the interviewers knew I didn't know what I was talking about, as much as I tried to make it sounds vague and plausible and probably would have sounded all technical and impressive so someone equally or more ignorant than me, to an informed audience I probably just sounded ridiculous. It would have been better if I'd just admitted I didn't know. Needless to say, I didn't get the job!

I understand there's not always a science correspondent available to write the 'breaking news' science stories, but it would be nice maybe if journalists etc were drawn from more diverse backgrounds, so there was a reasonable chance of a 'generalist' writer having had some science education. Also if there was more scientific literacy among the population in general, so even if someone's formal education background was not science, they'd have at least a basic idea of what words like 'gene', 'enzyme' etc meant.

But if none of this is possible, then they should just admit it, like me in that interview. Instead they seem to attempt a sort of cargo-cult science, where they write something nonsensical with sciencey-sounding words like 'gene' and 'enzyme' scattered randomly in it, depending on the fact that most people who read it will just skim and see that it looks all technical and sciencey and everything and be impressed by that, and not make any attempt to actually analyse the content.

The other approach seemed to be the apocalyptic one, like "Are you ready for a world without antibiotics? in the Guardian.

This is about carbapenem resistance in Gram-negative enterobacteria like E. coli, so really it wasn't very relevant to talk about 'incurable' tuberculosis, transplant surgery becoming impossible etc.

And the concern here is that it overstates and overdramatises the case, and much like peak oil and climate change, becomes something that everyone knows 'experts' predict but no one really things is going to happen. Which detracts attention from the very real problem that is antibiotic resistance, and the need not to overuse or misuse these drugs and the need for research into new drugs and emphasis on basic hygeine. Mostly I wondered if this was also just a 'cover' for the writer not really understanding the specific issue here and so wheeling out a generic The End Of Antibiotics story instead. Or assuming that the readers would be incapable of understanding any specific detail nuance in a science story, so not bothering to even try to write about it. Either way it doesn't look good for science journalism.

(*) Guessing this particular confusion came from the standard terminology of giving the gene name in italics to distinguish it from the protein name, a distinction that probably went unnoticed by the journalist...

Two scare stories: #1

2010-08-14T16:34:00.002Z

I was pleased to see the generally low-key reaction to the recent attempt by the media to stir up panic and 'controversy' (their favourite thing!) about use of cloning in cattle farming.

The story was basically this: a UK farmer bought some animals that were the offspring of a cow produced by cloning in the US, where such techniques are legal. Some products of these offspring (early reports said milk, later was said to be meat) were sold for human consumption. This is technically a breach of FSA regulations as:

meat and products from clones and their offspring are considered novel foods and would therefore need to be authorised before being placed on the market.

and clearly this case had not gone through the proper channels and the relevant authorisation had not been sought.

Cloning is obviously not a good replacement for 'conventional' breeding of animals. There are animal welfare issues - cloned animals have reduced life span and rapid aging thought to be due to having abnormally short telomeres (the sequences at the end of DNA strands) and can have particular developmental and health problems as a result of inaccuracies in the technique. Also the whole reason sexual reproduction (as opposed to just splitting down the middle like single-celled organisms or putting out runners like strawberry plants to produce natural clones) is a good thing because it's a major way in which diversity is introduced to a population, allowing adaptation and evolution and ultimately survival. So cloning is no substitute for this (not that anyone suggested it was). But I can imagine it can still be a useful technique in its place.

But there was no excuse at all for the scaremongering headlines, e.g.

Shocking evidence of how 'super calves' have secretly spread into our food system

and stories reporting 'concern' and 'unease' in the general population without evidence that there was any (my experience is that there wasn't) and asking 'Is It Safe' as though that was a matter to be decided, and repeatedly referring to these unnatural products 'Entering The Human Food Chain' (whatever that means) in a desperate attempt to create 'controversy' where there was none.

I suppose 'farmer makes harmless administrative error' wouldn't really sell so many papers. But I was pleasantly surprised to see people reacted sensibly and generally just did not care.

Women in science

2010-07-18T20:33:00.003Z

I was interested to see Rowenna Davis' article in the Guardian last week looking at undergraduate course choices by gender, and questioning why women's participation in certain subjects was still quite low.

But I thought it was unconvincing on two counts. First, the data didn't really look too bad. Life sciences, medicine and vet science courses were significantly female dominated, and there was 'only' a 60/40 bias against women in the physical and mathematical sciences, which is not particularly dramatic. Computer science was highlighted as a particularly male-dominated field, but that probably surprises no one, and especially as it got a recent 'dishonourable mention' as the undergraduate subject most likely to produce unemployed graduates, it's hard to justify why you think more women should pursue it. Things aren't so bad at undergraduate level, leaving the feeling for many readers that this was trying to make a story out of nothing - the real problem, possibly, is further down the line when well-qualified and competent women disproportionately drop out of scientific and technical professions for various reasons.

Secondly there seemed to be an implicit assumption in the article that every subject should have a perfect 50/50 gender split, with no explanation of why - and understandably a lot of commenters picked up on this, criticising it as an irrational and idealistic insistence on 'equality of outcome' for no logical reason.

There are two arguments about why such equality is a good thing. The first, and best in my view, is that its better to draw from as wide a pool of potential scientists as possible, so as to maximise the chances of getting the best and most talented people. This one works both ways; as well as women who would have done very well in hard sciences or engineering, a gender bias the other way means nursing and teaching and early years care miss out by men being put off these professions.

The second, which is a bit annoying, is that we need more 'girly' traits in science and technology. We need people who can communicate, who can multi-task, who have the 'soft skills', the people skills, who can collaborate and be nice. Which may well all be true, but why put that burden on women? To me, the 'we need women for their people skills, because we men are just so bad at it' translates as 'we need women to do all that boring soft/admin/non-science work for us, because we really don't want to make the effort', wrapped up in a compliment (women love getting compliments, you see). A little like 'but you're just so much better than me at doing the housework'. Not only does it reinforce in the workplace the idea that that sort of thing is women's work, it's another reminder of how invisible those women are who don't fit the feminine stereotype. Is it not possible that a woman might make a useful contribution to science for exactly the same reason a man would, not just because of her people-pleasing skills?

It also adds to the invisibility of women who don't happen to fit the feminine stereotype - and we have a difficult enough time anyway, excluded from the 'geeky' men's social circle because of being female, and not really fitting in with 'normal' women either...

On Overeating

2010-07-10T18:00:00.001Z

Apparently the new government are cutting funding for the healthy-living 'Change4Life' campaign, which they hope will be funded instead by snack food companies in exchange for 'freeing' said companies from further regulation of their products. Because they're not the big, bad evil monsters they've been painted as, and it's not their fault if some people choose not to eat in moderation.

It's easy to say - people like high-fat, high-sugar foods. It's what we've evolved to like, from the times when humans struggled to get enough calories to survive. The companies sell what we like, what else would we expect them to do? But it's very much more complicated than that. Yes we probably have evolved to favour fat and sugar, but still I feel little inclination to eat sugar by the spoonful from the packet in my kitchen cupboard, or to raid the fridge for butter or to drink the olive oil. These things in themselves do not produce the intensity of craving or lead to eating binges in the same way that certain prepared and packaged foods do.

People frequently describe the feeling of being 'out of control' around certain foods. I would have dismissed as them being 'just greedy', but then...it happened to me. I found myself overeating. I'd find myself eating another slice of pizza after I was already uncomfortably full, then another, and it would be as though I was watching myself and wondering what on earth I was doing. I found myself getting up from my desk at work, thinking only of having a break, getting away from the stress of the busy, noisy trading floor, to find myself wandering down a short corridor where I was confronted with The Vending Machine, surrounded by a gentle white-noise whirr, lit by a soft glow displaying the rows of snacks wrapped in shiny paper, red and gold and silver like Christmas gifts. So I'd buy a chocolate bar and eat it, feeling the textures and smoothness in my mouth, the coolness, wrapped up in how it felt to bite through layers and discover more flavours, uncover new sensations in each one. That was, well, kind of nice. So I'd usually buy another one, and another, and feel myself drawn back for more, and if I felt sick of chocolates and sweets there were always the delicious salty crisps and corn chips and cheese-flavoured crackers, or cold, cold, fizzy drinks. I felt a bit embarrassed by my behaviour sometimes, but I couldn't long resist The Vending Machine and the simple, private, non-judgemental transaction, the card in the slot, the numbers punched in, my every desire dropping with a satisfying 'clunk' in the vending tray below. So without dwelling further on my personal binge-eating adventures, this experience made me feel there was something going on as well as me being greedy.

I read recently David A. Kessler's The End of Overeating which examines the phenomenon of compulsive over-eating and is also a detailed expose of the food industry (in the US in particular), his argument being that dysfunctional eating habits involving foods produced by this industry are not coincidental, and not even an unintentional, evolution-driven result of the industry, but are intentionally created and exploited.

Because these products are not just foods, they are complex 'multi-sensory experiences' designed with great care to produce addiction-like reactions in those who taste them. I was shocked and slightly in awe of the weight of biochemical and food science and psychological research, the vast quantities of time and money and expertise, that has gone into designing these products/experiences, at just how much there is to the food industry beyond the simple logistics of preparing and transporting and selling the food. At how much of it is about designing something not just to look and taste good, but to produce a specifically engineered pleasant-but-fleeting sensation in the mouth to encourage another bite, another portion. To dissolve quickly in the mouth without need for chewing to facilitate eating as much as possible in as short a space of time as possible. To behave in the stomach environment in such a way as to artificially delay the sensation of fullness, to encourage the eater to cram in more and more.

That's before we even start on the advertising to encourage people to consume more, more often, on more diverse occasions. A good example is a particular sugary breakfast cereal, which is now being heavily advertised as an ideal snack for when you get home from work. Don't just have it for breakfast. Have it other times as well, perhaps times when you wouldn't normally think of eating. Eat more of it. And more. And there's my personal nemesis, the vending machines in workplaces and public spaces, owned and sponsored and carefully positioned by the companies who produce the products, of course, displaying them enticingly, making them available in places where there wouldn't normally be food, encouraging you to eat right here, right now, making eating easy and acceptable everywhere and at all times.

The flip side to this is personal responsibility. I don't want to downplay this, and I know that in criticising the food industry there's a risk of portraying us all as passive consumers, unable to do anything but what the advertising tells us, unable to put down the packet of biscuits or walk past the fast food restaurant or say no to another donut or chocolate bar. Of course we can say no, as has been helpfully pointed out to me, it's my hand putting the chocolate in my mouth. It's hard to do, but then doing the right thing often is. It's our responsibility to look after our personal health and weight and wellbeing as far as we can, and I'm not necessarily saying the food industry should be excessively regulated, though I'd certainly like to see more people know about how it works.

But, that doesn't stop it being a hugely jarring juxtaposition to have a 'healthy eating' campaign funded by companies whose very business model is to trick and manipulate their customers into eating as much as possible, as frequently as possible, of food products containing substances known to be harmful to the health in large quantities.

PhD

2010-05-31T14:35:00.002Z

Whenever I read about PhDs and post-docs and academic/scientific life in general, one of the main themes that comes up is career paths. Specifically, the problem of finding a permanent job in research or academia. It's common to hear people express the view that they wish they hadn't done the PhD at all, that it has been a waste of their time, that they wouldn't advise anyone else to do one etc etc. I can understand the frustration if they have been depending on the PhD being a ticket to a particular position, or a guarantee of a secure, well-paid job.

But the best advice I have read on the subject, is to do a PhD because you want to do a PhD. Because you want to spend those four years researching that particular subject, becaue you feel you can make a contribution, because you want to do something significant. Yes, it will likely open up a wider range of opportunities for you in the future, but it seems backwards to me to look at the PhD as something to be endured. Similar to the common view of an undergraduate degree as something that you have to 'get' in order to get a job afterwards, rather than something you actually want to do for its own sake.

And a PhD (and a post-doc) are not in my view 'education' in the same way an undergraduate or Masters degree, not even really 'training', and comparisons between training to be a plumber and training to be a researcher certainly seem to be missing the point. When you start a PhD, you are already doing research. You're not in training to become a researcher (though of course you have a lot to learn, and will learn a lot during the process), you are a researcher already. You're contributing to the body of scientific knowledge, if only in a small way, you're making discoveries and publishing papers. That seems to me a remarkable way to spend four years (or more if you do post-docs as well) and it would be a shame to spend those years worrying and complaining about what's going to happen next. It also seems to me that a period of research is very much worth doing, both for yourself and for everyone else who benefits from and builds on your findings, regardless of what happens next. If you feel that it was just a waste of your time, you really have to question what you think your time is for. If you think it's for amassing as much money and status as possible for yourself, then you're probably right, research wasn't the right choice for you.

Perhaps I look at this from a different perspective compared with the 21 year olds starting a PhD after continuous education since they were 5 years old, but I think part of the problem is seeing 'my life' as something that will start happening just as soon as this annoying period of education is over with. Or something that will only start happening when you have a permanent, paid job. Not so. Your life is happening right now, and has been for some time, and this is part of it.

Daily Fail Causes Cancer

2010-05-02T14:55:00.002Z

I had to laugh out loud when I saw the Daily Mail's latest cancer scare:

Simply turning on a light at night for a few seconds to go to the toilet can cause changes that might lead to cancer, scientists claim.

Of course, 'scientists' claimed no such thing at all, as the University of Leicester pointed out the following day. As far as I can tell, the Mail didn't bother to publish any correction or apology for horribly misrepresenting the research, and indeed just making some of it up.

The research in question actually looked at factors affecting circadian control of cell division. It's well established that living organisms have a 'biological clock' (circadian oscillator) with an approximately 24 hour cycle, apparently an evolved response to changing conditions over the 24 hour day, and this is observed in single-celled organisms as well as higher animals. It's also been observed that cell division operates on an approximately 24 hour cycle in some organisms, and it appears to be the case that the circadian oscillator is controlling the cell division.

The circadian oscillator operates via transcriptional feedback loops. This is where the expression (i.e. production) of proteins in the cell is controlled by the levels in the cell of these proteins - it can be a single protein exerting feedback on the expression of its own gene, or there can be several proteins and genes involved. There's a lot of feedback loops and many changes in expression of genes and levels of proteins in a cell over the course of the cell division cycle. The numbers of genes and proteins involved and the complexity of the feedback loops and protein-protein interactions makes it a very difficult process to untangle, and some parts of it are surprisingly poorly understood. It's an important one to understand though, as the regulation of the cell cycle is fundamental to the development of cancers.

And the research by Kyriacou and Ben-Shlomo looked at the effect on the expression of various genes during the cell cycle in mouse brain cells, and the effects of disrupting this cycle by, among other things, administering hour-long pulses of light during the 'night', i.e. the dark part of the artificial circadian cycle created in the lab. They found that the light pulses affected the expression of several genes in the cell cycle - some of these changes led to higher expression of proteins associated with cell-cycle arrest (i.e. the cell stops dividing), some were increases in proteins implicated in uncontrolled division and tumourigenesis. Whether the overall net effect of all these changes was an increased or decreased or unchanged risk of tumours developing in the brain tissue - they don't say, as that's a far more complex question and beyond the scope of the study, which was intended to observe the expression of cell-cycle genes.

So it's quite a long way from 'OMG YOUR BATHROOM LIGHT GIVES YOU THE CANCER!!!'. Why do I care if the Daily Mail wants to be stupid? Well, it's annoying to see genuine and interesting and important research misrepresented in this way, it reinforces the view among the general public that 'scientists' are always coming up with new, bizarre and unjustified health scares (when it's actually the newspapers that are doing this) and therefore it's reasonable not to listen to any health advice from scientists or doctors. Or that if everything causes cancer anyway, you might as well do what you please. Which means ignoring actual evidence-based advice (like maintaining a healthy weight or giving up smoking) that really is known to affect your risk of cancer and other diseases. So I guess indirectly the Daily Mail causes cancer. Will we see that on their front page?

Girls love pink (again)

2010-04-18T16:13:00.002Z

The BBC reports on results presented at a recent conference showing that children under a year old favour gender typical toys.

The study looked at children from nine months to 3 years old (they say 36 months in most of the stories, not sure why, except that perhaps they assume most readers can't or won't bother to divide by 12 and realise that we're not talking about small babies at all) which seems plenty old enough to have been subject to significant socialisation at home and nursery/playgroups. It seems very likely to me that the children would be likely to reach for familiar toys and colours, and also that there are very few homes where children would have a gender-neutral environment and choice of toys. Even if as parents you try to let your child's gender identity develop naturally and in his/her own time, there are well-meaning relatives who will try to drown your little girl in a sea of pink dresses.

It's unlikely of course that the researchers are completely unaware of this, and may have made some attempt to correct for the confounding issues, though it's difficult to see how this can have been done in any meaningful way. I tried to find the original paper, however it seems that there isn't any paper, at least none that's been published yet, so it's impossible to comment on the methodology used or how significant the results were.

Interestingly it appears to be someone's undergraduate project, in which case they've done well to have it presented at a conference. Still I wonder how well it goes down in the academic community when you use over-simplified results and socially provocative statements in order to promote yourself in the mainstream media.

Living dolls

2010-04-04T13:56:00.002Z

I read this article recently in the Guardian about parents who choose to select/control the sex of their child. It focused on white, middle-class British parents, so this is not the usual context of the Chinese ‘one-child policy’ or India’s ‘lost girls’, and in fact the main focus was on women who wanted to have a girl child.

Most of the objections discussed seemed to be around the idea of sex-selection as ‘unnatural’, or ‘interference with divine will’. I’m not even going to discuss that much, as I don’t have any objections along those lines, and the whole idea of what is and isn’t natural, and the relationship between ‘natural’ and ‘good’ is a logical minefield and never leads to any useful conclusions. For me, the alarm bells were more around the reasons the women gave for wanting girls.

"But, Susan says, "I got sick of walking down the high street past BabyGap and seeing these delightful little girl outfits in the window and just getting this pang.""

"Nicola says. "I remember seeing someone in town with a little girl all dressed up. I thought, 'I'm never going to have that.'"

This, to me, is just crazy. It’s all about the clothes. It’s not the first time I’ve heard such arguments, women desperate to have a girl, women who already have several children, determined to create a completely new human being, just so they can have a living doll to dress up in little pink outfits. I’m not particularly maternal or fond of children, but this much I do know - a child is not a doll or an accessory, but an individual person with her own personality and identity. The child small enough to dress up only lasts so long. What happens next? Suppose she doesn’t want to wear pink any more, or have long hair like a princess doll, or suppose she likes science or sports better than shopping and fashion and inane gossip. Suppose she turns out to be lesbian or even transgender? What will you do then, send her back to the shop and ask for the ‘proper’ girl that you paid for?

The assumption seems to be that if you can determine the sex of your child, you have automatically determined exactly what their appearance and personality will be like, and that will be your stereotyped image of what a ‘girl’ or a ‘boy’ is like. Unfortunately, or perhaps fortunately, people are a bit more complicated than that. And children, which the breeders often seem to forget, are actually people. There can be enough pressure on a child anyway to meet their parents’ standards of behaviour and gender conformity; how much more will there be when your parents have paid significant amounts, perhaps taken out a large loan or remortgaged their house, for the sole purpose of ensuring that you will be a child that wears pretty dresses and has long, pretty hair, and not a messy, energetic one? Wouldn’t it be better for everyone if the dressing-up obsessed ‘mummies’ just bought themselves a doll?

Maybe they feel that having a girl would be like going back in time to meet themself as a little girl, armed with all the knowledge and experience they have now and able to help her have a better life than they did. I can understand that up to a point. Now of course my guidance (I like to think) would be better, I’d like to tell my younger self to let go of the religious guilt and shame about myself, to have more confidence in my abilities to not worry about what others think of me. Whereas the women in the story presumably would go back and smother their younger self in pink frills and princess toys and impress on them that the most important thing in the world is to be visually pleasing to others. But for both them and me, that’s just fantasy and not relevant to having a child of our own. Your daughter is not you, not a second attempt at becoming yourself, though the woman who refers to her daughter as a ‘mini-mummy’ doesn’t seem to have grasped this. Fortunately she seems to be content so far with her 'mini-mummy', so "completely different from the boys in every respect", though perhaps suffering from a massive case of confirmation bias.

I don’t think sex-selection is a bad thing in itself, and I don’t see the purpose of banning it, particularly if the requests are not biased significantly towards one gender or the other. It could be a good thing if it prevents each woman producing a brood of unwanted ‘wrong-sex’ children in the obsessive quest for one with the right set of genitals. What I do object to, and more violently the longer I think about it, is the reasoning behind it in every story I’ve heard on the subject, the strict gender-policing of behaviour and dress and even of the personality one is allowed to express, which these parents are imposing on their children before they are even conceived.

"To clarify, I am not a Santa researcher..."

2009-12-28T15:50:00.006Z

So the 'Santa causes obesity and drink-driving' spoof article in the BMJ was (mis)reported all over the place, from the Today program on the radio to the free papers on the train, and even the supposedly serious papers.

This article, I thought, highlighted an important issue - the author himself suggested that maybe the confusion arose because journalists just read the press release and not the original article itself. I suspect this is very common, judging by the number of science stories that are almost word-for-word copies of the press release they're based on.

Is it actually unreasonable to expect a science correspondent to read the paper or article when reporting on scientific research? There's the issue that not all papers are open access, but you would think that the BBC, for example, could afford subscriptions or pay-per-view? And there's the question of whether the journalist could make sense of the paper once they'd got it. It's a reasonable point, after all researchers write their papers with their peer group as the intended audience, and a general science or health journalist can't be expected to be an expert in every specific field or every scientific discipline.

But still, things could be better. Journalism is supposed to be about investigating and finding out the truth - so they could at least try to read the paper, and they should have to be suffficiently qualified that they can make some attempt at understanding the gist of it, even if they're not familiar with all the details of the methodologies etc. -they can surely do some learning themselves, or contact an 'expert' in the field or indeed one of the authors of the paper with questions - and have some familiarity with statistics and be able to make some judgements of their own.

An interesting exercise I once had to do as an undergraduate was to look at several papers (selected by the lecturers), some of which were 'good' and some which should never have made it to publication - there were some obviously terrible ones, for example graphs missing error bars or meaningful labels/units which fudged the results, or ones where grand conclusions were drawn which couldn't really be justified by the results. It shouldn't be too much to expect a science or health writer to be able to do something like this at least.

Medical writers, for example, usually need a PhD, or at least a BSc in a relevant medical or life sciences discipline, or relevant experience - and there's a good reason for that; it just doesn't work to have people writing blindly about a subject they don't understand, using words like 'virus' and 'bacterium' interchangably because they don't know or care about the difference, and lacking the education or intellectual ability to critically evaluate or understand what they're writing about. The situations are not the same, of course - a confused or ignorant medical writer could cause disastrous consequences, whereas the equivalent journalist usually does nothing worse than annoy pedants. But bad science journalism can occasionally have serious consequences of its own - a good example is health scares such as the MMR/autism 'controversy'.

Also, why don't the BBC ever link to the original research, for those who want to read it for themselves? I feel it's time to write a letter...

All very tiresome

2007-03-13T23:04:00.000Z

Of course, Jane Austen herself could have said all that far more concisely...

"But history, real solemn history, I cannot be interested in. ... I read it a little as a duty, but it tells me nothing that does not either vex or weary me. The quarrels of popes and kings, with wars or pestilences in every page; the men all so good for nothing, and hardly any women at all — it is very tiresome."

(Northanger Abbey)

Pride and Prejudice

2007-03-09T18:27:00.000Z

Last week, Jane Austen's 'Pride and Prejudice' was voted the most popular book in a World Book Day survey. Clearly this disrupts the natural order of things, so the BBC have carefully selected people to explain why, in their opinion, Miss Austen was not in fact a great novelist, satirist and social commentator, but really just a bit dull and silly. But it's something I've noticed before - some of us love her, but others not only don't enjoy her writing, but have a kind of contempt and antipathy for her novels, her choice of subjects, her style and everything about her and her work. Much of it from men, but not all. It's strange. You don't often hear the same comments about many other authors, although of course we all have those we like and dislike.

I think possibly the main force behind all this is anger at Austen's perceived audacity at focusing on women's issues, which are automatically assumed to be inferior to anything men might be doing at the same time, such as fighting a war -- one of the common criticisms is that she didn't write much about the Napoleonic wars which took place during her lifetime, and didn't appear to have much interest in them. How dare she ignore the men, and fail to express the proper reverence for their military adventures?

But as with every war, hundreds of years go by, and few people really care about the outcome, or can remember what it was all about. But the truths about human nature and society in Austen's novels are as relevant today as they were at the time she was writing, her characters and storylines are just as complex and life-like as ever, the pathos is just as moving and the humour is as funny.

And why should she have written about these issues? There are already plenty of books about military and political history. In fact, when reading history or historical novels I often find myself asking the opposite question: where are all the women? What were they doing while all this was happening, how did they fill their time, what issues were important to them, what did they have to say? Why have they been seemingly erased from the story? I think the male-centred story has become so much the norm that anything else seems odd, as if history from a woman's point of view is not 'real history', not about real issues. But it is absolutely as real, unless on some level you believe women don't count as 'real' people. This of course was the reasoning when feminists coined the term 'herstory' -- although misunderstood and mocked, this was actually a tongue-in-cheek attempt to draw attention to the invisibility of women in history.

Like feminism itself, Jane Austen was not anti-men, just not particularly interested in most of them. And that seems to be the biggest possible insult to male vanity.

update

2007-01-23T14:35:00.000Z

I haven't had much time to blog recently, but from my site statistics I seem to still have the occasional visitor here. So for something new to read, look at the new addition to my blogroll, codebunny.
If you got here by searching for "can two numbers be equal?" the answer is yes, however if you were looking for confirmation that "0.9r is not equal to 1", you are unfortunately wrong. See below.
Also adding Life in a Suitcase to the blogroll, since Amanda has kindly linked to me under the heading "Cool Folks". Who knew?

read the whole thing

2006-12-20T10:29:00.000Z

A few selective quotes:

Last week a primary school teacher was sacked for telling her young class that Santa does not exist.

The supply teacher apparently decided the pupils - some as young as nine - were too old to believe in Father Christmas.

A governor said: 'It's not just Father Christmas that's the problem. We also have issues with things like the Tooth Fairy.

"It is like a loss of innocence. Children should have the right to stay innocent for as long as possible."

Sometimes I suspect the Mail is just one huge parody of itself. Unfortunately that wouldn't make any difference as the readers don't seem to notice...

On the same subject...

2006-12-14T18:07:00.000Z

I found this here:

dollars==cents?

2006-12-11T22:21:00.000Z

There will hopefully be some more mathematical blogging soon, when I have time to write properly about this. But for now, a blogger's valiant attempt to teach primary-school maths to call centre staff:

G: [big sigh] Okay, I think I have to do this again. Do you recognize that there's a difference between one dollar and one cent?

A: Definitely.

G: Do you recognize there's a difference between half a dollar and half a cent?

A: Definitely

G: Then, do you therefore recognize there's a difference between .002 dollars and .002 cents

A: No.

G: No?

This goes on for about half an hour. Would you have the patience?

(also listen to the call here)

Satisfactory

2006-11-23T16:06:00.000Z

Seen here:

One in eight secondaries, 13%, are judged inadequate and another 38% satisfactory, a category the chief inspector, Christine Gilbert, called "not good enough" as she presented the annual report on standards.

A radical new definition of 'satisfactory'?

interesting

2006-10-11T16:15:00.000Z

Sofie from Volsunga writes about a new call for the government to "consider the scientific, medical and social changes in relation to abortion that have taken place since 1967, with a view to presenting options for new legislation."

This is obviously nothing new at all, but it was interesting that some of the commenters saw it from the opposite point of view, i.e. that a review of legislation could actually result in things going in the opposite direction, for example removing some of the arbitrary restrictions. Interesting because I tend to be wary of any attempt to 'review' the legislation because I can only imagine it getting worse, not better.

Elsewhere in the blogosphere...

2006-09-23T15:51:00.001Z

Molly and Amanda at Pandagon are answering questions on everything feminism related.

And there's a new Carnival of the Feminists here

And BitchPhD comments on the shocking (shocking!) suggestion that women in science and engineering are hindered by

"a pattern of unconscious but pervasive bias, “arbitrary and subjective” evaluation processes and a work environment in which “anyone lacking the work and family support traditionally provided by a ‘wife’ is at a serious disadvantage.”"

rather than by their inferior feminine brains.

Read the comments for a good discussion of the issue including some opposing viewpoints. Everything original I could think to say about it has been said there already...

what goes into crisps goes into you

2006-09-23T11:16:00.000Z

Have you seen this campaign from the British Heart Foundation which aims to 'expose hidden salt, fat and sugar in common foods' - not that the fat in crisps is particularly well hidden, and even if it was you could always take a look at the back of the packet.

But anyway, this annoyed me immediately, because '5 litres per year' is completely meaningless unless you put it into some context, i.e. how much fat are we supposed to consume in a year, and what percentage of that would 5 litres make up? Because without that, there is no way to tell whether it's excessive or just normal.

5 litres does sound like an awful lot of oil. But is it really that much when you think of it in small amounts over a whole year?
I did some calculations, and 5 litres of sunflower oil per year actually works out to 12.6g per day
I also had a look at the nutritional information on a packet of Walkers crisps, and the fat content is stated as 11.7g. So 5 litres per year is a slight overestimate, but it's accurate enough. But is it a lot? Well the recommended fat consumption is 70g for adult women, so assuming I eat a fairly normal diet that would mean the equivalent of drinking over 30 litres of cooking oil a year. Is this looking meaningless yet? I can't find the GDA for children, but even assuming it's significantly less than that for adults, a child eating a healthy diet would still be 'drinking' many more than 5 bottles of cooking oil every year, if you want to use that metaphor. So it's really not looking like such a bad thing.

No of course eating too many crisps is not good for anyone, for many reasons. But isn't there a better reason than claiming 5 litres of sunflower oil in a year is a lot, when in fact it's actually a lot less fat than we should be getting in out diets?

Drinking cooking oil straight from the bottle would probably be a bit disgusting. I wouldn't really want to try it. But if you could stand the taste and the texture, and you drank 13.7 ml per day for a year, it would be really unlikely to do you any harm. Sunflower oil is not such a bad thing.

And it's patronising and irritating that we are supposed to make the logical jump that since cooking oil doesn't taste very nice, eating crisps is bad. Yes maybe this is aimed at children as well as parents, but shouldn't we be encouraging logical and critical thought in children, not irrational panic?
This made me think about a wider issue, which is this: is it ok to lie to people for their own good? That's got to depend on who is doing the lying and who is being lied to, for example it's generally considered ok for parents to lie to their children to encourage them to behave better or eat well or whatever.
It's generally considered not ok for the government to lie to the voters, or for a company to lie about its product in order to sell it (*). But the British Heart Foundation is not the government and is not selling us anything, in fact they're discouraging us from buying crisps...but I still don't like it. Because encouraging people to eat a healthy diet and give their children good food is a good cause, but if it is so good, then surely we can come up with some real reasons for doing it, rather than inventing reasons that aren't reasons at all.

(*) Who else has seen those adverts for the toothpaste containing 'liquid calcium'? The melting point of calcium is over 800C, which is a lot hotter than my toothpaste tube tends to get even on a very warm day. How can they possibly ever get away with claiming that? How can anyone ever believe them? This is worse than the 'limescale is just calcium that sticks' thing. And the myth about milk being a good, in fact necessary source of dietary calcium.

Poor calcium. Was there ever a metal more misrepresented?

subtext

2006-07-12T19:58:00.000Z

In other news, Subtext Magazine is finally here.

more badgers

2006-07-12T19:37:00.000Z

A few months ago I wrote about the DEFRA consultation about badger culling...well apparently the response was very positive if you're on the badger side - 96% of responsdents were against the cull.

Maybe it's not quite as good as it sounds - after all it doesn't mean that 96% of the population in general are against the cull, just that 96% of people who feel strongly enough about badgers to bother writing are against it - which is probably less surprising. But then there were over 47000 responses, so that's a whole lot of people who feel do strongly about the issue.

Can two different numbers be the same?

2006-06-22T11:16:00.000Z

I saw this in the Guardian this morning, and it made me very happy because I love mathematical puzzles, even more so when there's some 'trick' involved that's essentially invisible to the non-mathematician, which makes it look like magic.

The problem was this: is 0.9r (recurring) equal to 1? If so, how can this be? How can two different numbers be equal? The proof given in the article was a 'challenge' to find some real number between 0.9r and 1. Of course you can't find any such number, and the question doesn't even make a lot of sense, but just because you can't find something doesn't mean it isn't there.

This is what I think. It's not very helpful to think of 0.9r as a simple number, in the way you'd think of an integer or a fraction. The best way is to write it as an infinite series like this:

with line 4 using the clever formula for sum to infinity of a geometric series, which we can use in this case because |1/10| < 1.
This makes sense to me, so when I Googled the problem to see what others thought, I was surprised to find it's quite controversial, even among people who seem to know what they're talking about. It looks like a lot of the controversy comes from the problem of defining exactly what we mean by 0.9r. But if you define it as the infinite geometric series above, it seems obvious that it is just a different way of writing 1. So maybe the question really should be 'Can the same number be written two different ways?'

If you disagree, I'd be interested to hear!

I also saw a different proof, which was to assume 0.9r is the largest real number less than 1, which leads to a contradiction. I think that's the same as saying the set (0, 1), for example, has no least upper bound within the set (the lub is 1).

The arguments in the comments section of the article have already started. Note the comment about 'lesbian algebra' after mine. I'm not sure if that's referring to me, or to the girl mentioned in the original article, or Britney Gallivan (the paper-folding woman), or someone else entirely. But I think being accused of being an academically-minded lesbian is supposed to be an insult. Strange...

voodoo vets?

2006-06-19T18:16:00.001Z

Their words, not mine!

This is about the Veterinary Medical Directorate planning an amendment to their regulations to allow homeopathic remedies to be registered and authorised to be administered to animals. As you might guess, this is controversial, and a lot of people are unhappy about it.

This is interesting because one of the most common arguments is that if the effect of homeopathic treatments is 'just' the placebo effect, then why would they have any effect on animals (and babies or small children). The obvious problem of course is that while the placebo effect wouldn't be expected to work on an animal or baby, it could well work on the owner or parent, who is probably the one reporting the improvement in symptoms. And of course on the doctor or vet administering the treatment, which is why drug trials have to be double-blinded.

The 'against' opinion seems to be divided between those who think 'why shouldn't people use homeopathic treatments if it makes them feel better', which is what I tend to think, and those who think that this is deception of poor ignorant people, or at least self-deception, and therefore bad (of course you could have a similar argument about religion and faith, and probably a lot of other things). And that what we need is study of the placebo effect itself, with a view to understanding how it works so we can use it in the most effective way.

There have been interesting studies into how homeopathy might work, with some tentatively interesting results : see this and this in New Scientist.

But the big problem is that homeopathic treatments have never been shown (in a large, randomised, double-blinded trial with replicable results) to work any better than placebo, either in humans or animals. That's not to say there is nothing interesting happening at a chemical level, or that it shouldn't be investigated further. Or that people shouldn't use them. But it does raise the question of whether it's ethical to advertise or sell them as a cure for anything.
And when they're given as treatment for animals - well, if there's not evidence that they work, how is that different from giving no treatment at all? And isn't it neglectful and cruel to refuse to seek treatment for a suffering animal in your care?

I think a lot of the problems actually come from treating 'alternative' medicines as a separate category. That only makes sense if you think they work in some magical way that can't be detected and doesn't show up in trials - in which case they really can't be said to work at all in any meaningful way. If they do work in a real way then they should be regulated like every other medicine.

One of the best quotes I heard on the conventional/alternative dichotomy was from a letter to the Guardian - this was a few months ago but I still remember so it made an impression:
I don't buy into the artificial distinction between "western" and "alternative" medicine: there's medicine that works and medicine that doesn't work.

and that is exactly what I think as well!

Of course the idea of 'western' vs 'eastern' medicine is a problematic thing in itself, and I always thought there was something patronising and slightly racist about the idea that people from the 'East' are more primitive and more in touch with nature or whatever. Anyway there are plenty of traditional herbal remedies that originate in European cultures, and I think the first we know of homeopathy itself was in ancient Greece.

Anyway, the point of all this was to say that the VMD are currently accepting comments for their consultation. If you have an opinion, and want to let them know, then read the consultation paper here and email your comments before 7th July. I'm not sure how much attention they'll pay to letters from random people, but it can't hurt.

all new

2006-06-15T19:13:00.000Z

So this is the new blog, really very similar to the old blog. I've even copied a few of my recent posts across to make it feel home-like, and may copy more of them in the future in case anyone wants to re-read them!

Hopefully there should also be some new content here soon...

test

2006-06-15T12:41:00.000Z

test

more Austen

2006-05-30T09:55:00.000Z

I've been meaning to write about the new editions of Jane Austen's novels, which have apparently been repackaged in the style of 'chick-lit' to encourage "women put off by the idea of reading a 19th century writer", and presumably also women put off by reading anything that doesn't have a pink cover. I don't have time to say a lot about this, and the argument about what exactly chick-lit is will have to wait for another time.

So instead you should read Zoe Williams in last Saturday's Guardian and remember why you love her:

"The accompanying press release reads: "Who is the fairy godmother of women's fiction? And who is still packaged like a dry, academic author, reaching only a tiny fraction of her potential audience? The answer, of course, is Jane Austen!" This, I feel it's worth pointing out, was printed in pink. There are few things that irk me more than the idea that women will pay more attention to things that are printed in pink. Just track back the thought process: here are some words; their colour will add nothing to their significance; nevertheless, those black ones are boring! Black is for stuffy people! I like those pink ones better, I'll bet they smell really nice, too ... oh no, they don't smell, they're words. Come on, this is five-year-old territory. What say we give away some My Little Pony stickers with every third copy of The Mayor Of Casterbridge? How about reviving the flagging reputation of Dickens with a cover-mounted Kinder egg?"

on the subject of weight

2006-04-17T09:37:00.000Z

and just because I'm irritated by seeing these on buses and billboards everywhere I go, this is from the Greater Manchester cycling campaign:

What exactly do they mean? Fat people shouldn't cycle? People who use cars or buses are all fat? How do I find out whether I'm thin enough to use one of their cycle lanes, and what will happen to me if I dare to cycle while fat?

I hate seeing them do this, because I like what they do - encouraging cycling and campaigning for better, safer cycle routes. That's important, because while I like cycling, I also like being alive, and for that reason I haven't even brought my bike to Manchester. Compared to the towns I've lived in previously, provision for cyclists is terrible, and it just isn't safe for me to cycle to any of the places I need to go.

And that makes it more disappointing when they do something like this.

diets

2006-04-12T16:22:00.000Z

Via Mind the Gap:

Almost a third of women worry about the way their body looks "every waking minute", a survey suggests.
The poll of over 5,000 women for Grazia magazine found just one in 50 was happy with the way her body looks, with women wanting to lose an average of 19lbs.
...
It concluded that the average British woman worries about her body every 15 minutes.

Except this says nothing about the average British woman, just the average Grazia reader, which I hope is not the same thing. And not even the average reader, but the readers who are concerned enough about body weight/appearance to bother filling in the survey. It's a small, self-selecting population, and even Grazia readers should know that you can't use something like that to make conclusions about the 'average woman'.

It's a bit like that Tesco Diets survey where this conclusion was made:

The majority of women would prefer to be slimmer than have a higher IQ, instant wealth or a date with the celebrity of their dreams.

Nineteen out of 20 of the female population say that they place a higher priority on having a smaller waist than on their intelligence.

with the lovely title "Most women would rather have a small waist than a big brain".

I don't know what the point is of running these articles that push the idea of most women as silly little people who teeter through life on their high heels, clutching a tiny handbag and a copy of Grazia with their fluffy little heads filled with nothing but anxieties about their fat thighs. I'm sure if a similar survey was run in a magazine like 'Ms' or 'Bitch', the results would be different. Or why not ask women who read 'New Scientist' or 'Nature'?

Does it work as advertising for Grazia or Tesco? Is that why they do the surveys in the first place?

On the subject of diets, I just noticed the headline "Why portion sizes matter when you're on a diet" on the MSN homepage. I didn't click. I think I can work it out...

that new pill

2006-03-30T16:46:00.000Z

Super pill to cut cancer and end PMT

Wonder drug PMT cure

Wonder pill for women

It's called mifepristone, and this is what is looks like if anyone's interested:

It's a steroid, with the usual 4 fused rings you can see in the structure: 3 cyclohexanes (the six-sided ones) and a cyclopentane. All the steroids have these, as far as I know, and it's the other groups that distinguish one from another.

Natural hormones like progesterone are also steroids, and this is a competitive inhibitor of the natural hormone progesterone. Competitive inhibition is when the inhibitor has enough similarity to the original molecule that it can also 'fit' its receptor, so it competes with it for access to the receptor. In this case, mifepristone can bind temporarily to the progesterone receptors, competing for the binding site with actual progesterone molecules and hence reducing their rate of binding (unlike non-competitive inhibition, where the competitor permanently binds to the receptor)

Here's progesterone, to compare:

If mifepristone sounds familiar, that's because it isn't actually anything new, it's one of the drugs used in medical abortion. That means it's likely to be controversial, but this is an entirely different use and the contraceptive effect is caused by preventing ovulation.

A lot of the news articles seem to focus on the possible reduction in breast cancer. I'm not sure whether this just means it doesn't elevate the risk the way the 'traditional' pills do, or whether it actually has a protective effect. It's possible it does, since apparently mifepristone may also be useful against ovarian and endometrial cancer.

This paper was published in 2004: Low-Dose Mifepristone Inhibits Endometrial Proliferation and Up-Regulates Androgen Receptorand amazingly the full text is free online.
Also this from 2002: Daily Low-Dose Mifepristone Has Contraceptive Potential by Suppressing Ovulation and Menstruation

I can't actually find anything more recent, but I guess there must be something new behind the recent announcement. Maybe it isn't published yet?

Science education

2006-03-16T01:55:00.000Z

The BBC says:

Science interests split the sexes

"The sexes are split on science interests, researchers say, leading to calls for gender-specific syllabuses."

I thought it would be a good idea to first have a look and find out what "researchers" actually did say. It mostly comes from The Relevance of Science Education, an international research project studying attitudes towards science and technology and mostly focusing on 15 year old school students. There were actually a lot of interesting results about the effects different factors might have on attitude towards science, including nationality, culture, social class, how rich or 'developed' a country is etc. It was not all about gender, though the BBC's article might lead you to believe that, but then it's always nicer to have your pre-existing prejudices confirmed than to have to bother to think about anything new.

The article was based on several studies, and the statement

"A survey of just over 1,200 pupils in England found the hot topic for boys was explosive chemicals while girls were more interested in the human body"

gets them mixed up, because the research that apparently showed that particular result was one involving 15 year old school students in Norway.

The English survey (results here) was actually about attitudes towards science in general, with questions about whether we should trust scientists, whether science and technology are important to society etc. Interesting, but a different thing.

The second source was actually a PhD thesis, that of Camilla Schreiner from the University of Oslo, and this is where the list of "top ten" interests for and girls came from. There are several problems with this top ten. Firstly, the items were picked from an ordered list of 30, and whoever compiled the top ten apparently picked the ones that appeared to best support stereotypes about the genders and put them in random order.

Interestingly the answers given by girls were divided so strongly into two clusters that the two different "types" of girl were treated as separate groups for much of the thesis, one group which is the stereotypical girl presented in the article, concerned with health and appearance and babies. The other is far more similar to the stereotypical boy. But she's as invisible in the article as she is in everyday life.
If we ignore her, maybe she'll go away? I hope not.

Towards the end, the author comes to the (obvious?) conclusion that

"In order to understand student's interest in science, we need to know more than their sex. We need to know what kinds of boys and girls they are"

however in the article, Professor Jenkins is quoted as saying

"We have had a generation or more now of promoting gender equality but the differences exist and I raise the question as to whether we should teach the two sexes separately for some of the time."

which seems to just ignore the earlier conclusion. Just because differences exist (for whatever reason) between the average boy and the average girl, doesn't mean dividing them into two groups without considering their individual preferences is a good idea. What about the individuals who don't fit the stereotypes? I wasn't even a feminist at 15, but I would have been furious at being put in a "science for girls" group.

Fortunately, so would my parents (and hopefully other girls' parents) and maybe enough of a fuss would have been made that it wouldn't have happened.

Teaching boys and girls separately (for some or all of their education) is a controversial idea, and there are probably good arguments on either side. But the arguments in favour tend to assume that the education will be "separate but equal" but unfortunately that is often not true. For example, in my further maths class there were two girls out of a class of over 20. If it had been a girls' school, would they have offered the subject at all? It's anecdotal evidence only, but in my experience many do not.

I'm not sure exactly what the statement above is trying to say. Maybe, giving him the benefit of the doubt, he wants separate classes so we can address the problem and give girls extra encouragement in physical sciences and boys more encouragement to learn about human biology etc. But it could be the opposite.

The bit about "a generation of promoting gender equality" makes me suspect that we are getting into biological determinism here and that he's saying that today boys and girls are treated exactly equally (does anyone actually believe this?), but differences still exist, therefore those differences must be entirely down to physical differences which we cannot change, and so we shouldn't try to do anything about them. He doesn't actually *say* that, but I suspect it. That would mean separate girl and boy classes where we don't even try to teach the girls any physics, because obviously their weak little brains couldn't cope with it, and they wouldn't like it anyway.

The other alternative is to allow the boys and girls who have atypical interests - and are brave enough to admit it and face the bullying (mostly for the boys) or social rejection (mostly for the girls)that might follow - to join the other group - but then what was the point of dividing them by gender at all?

Then of course is the question of whether it's a good idea to do this at all, and whether school should just be about studying the subjects you like and being allowed to drop the others. Especially if that means girls being allowed, and even encouraged, to drop the subjects that are most likely to lead to an interesting or highly-paid career in the future. How will this help close the gender pay gap?

Yes, the girls expressed an interest in health and medical issues - and medicine is definitely a career choice that could lead you to a fulfilling and well-paid job. But they won't ever get there if we encourage them to drop physical sciences in favour of learning about periods and babies. If you want to get into medical school, you don't need qualifications in human biology or psychology or whatever. You need an 'A' in chemistry, and maths and physics don't look bad either. The girl track is more likely to lead them into nursing, while the boys who got to learn about explosions and chemical weapons are the ones more likely to be qualified for a medical degree.

The problem isn't just with science teaching in schools, and by then it's really way too late to do anything about it. Sometimes I want to blame the girls themselves - I am angry with them for choosing "fluffy" subjects for themselves, for being afraid to try anything new, for having no confidence in their abilities at science/tech subjects even when the evidence suggests they're better than many of the boys, and most of all for policing each other and making it so difficult to be a different sort of girl. But I think the problem actually starts before that.

It starts way back when you get your first gendered toy from Argos, when your parents first dress you in a pretty princess dress or a blue sailor suit, when people start to behave differently towards the potential you before you've even been born. And I think that will be much more difficult to change.

not again

2006-03-09T15:27:00.000Z

Yet again, there's a 'new wave' of anti-abortion pro-lifers, the climate of opinion is changing, debate is being reopened etc etc. This time, though, it's different. It isn't a religious or moral thing:

"For the 45,000 British couples who seek fertility treatment annually, the 200,000 terminations that take place each year are a personal insult"

All 45000 of them are personally insulted? Did someone ask them all? This has to be the silliest prolife argument I've heard - to be against abortion because you consider it to be the same as killing a baby, at least that makes some sense. This is more like 'you have to eat up your vegetables because of the starving children in Africa', and preventing women with unwanted pregnancies from getting appropriate care does about as much to help infertile couples as eating your cabbage did to help those poor children.

There's also a big difference between being personally upset by the idea of abortion, and campaigning for it to be made illegal, which is what most prolife groups aim for. The two issues seem to be confused here, and I'm not sure which one she's talking about.

Also, people needing fertility treatment should be careful about supporting the prolife movement, which is generally strongly anti-IVF as well.

"Cristina Odone was editor of the Catholic Herald..."

which explains a lot.

I think this is too silly to spend much time on, but Holly at The F-word pulls it apart in much more detail if you want to read more.

badgers

2006-03-01T13:52:00.000Z

Do you want to help the badgers? Of course you want to help the badgers. Consider writing to your MP or directly to the animal welfare Secretary (see link above for details) before 10th March.

If you're not convinced that badgers are worth saving, there's also the evidence strongly suggesting that badger culls are counter-productive and appear to have actually increased the incidence of tuberculosis infection in cattle herds over the last 20 years (article for Nature subscribers only, unfortunately), making this a crime against logic, if nothing else.