13 April 2013
Express delivery
02 December 2011
History fatigue
I've just watched an episode of Anthony Horowitz's second world war police drama sequence Foyle's War, in which the eponymous Foyle tells his son that he (the son) is suffering from "combat fatigue".
My immediate assumption was that this was an anachronism. At a guess, I'd have fairly confidently said that the term dated from the 1960s. Not that I am viscerally opposed to anachronisms; it just surprised me in a fiction known for its diligent research.
Looking up combat fatigue, however, I discover that I couldn't be more wrong.
The OED seems to locate "combat fatigue" (“n. a nervous disorder resulting from prolonged or severe battle experience”) 1943 – firmly in Foyle's time. There are references to it in US medical journals from the mid to late 1940s, even though the earliest PubMed hits are from 1945.
Google Labs' Ngram shows a peak frequency at 1948. It also shows occurrences from as early as 1860, but a quick sampling suggests that this is a red herring – a dozen spot checks all yield either usage such as “At present we have no drugs that combat fatigue of the central nervous system directly”* or retrospective reference from later dates.
On a lazy search, then, it seems that this description dates from about twenty years earlier than I had assumed.
* Psychiatric bulletin of the New York State hospitals: Volume 2, Page 311, 1917)
21 October 2011
Acid drop (...and subverted Friday crab blogging...)
Personal nostalgia alert ... and an apology to Dr C for dragging his Friday Crab Blogging series into disrepute.Danny was with Maryjane's best friend, Brenda Williams. In retrospect, that was the first night of the rest of their lives together which is a romantic thought; but at the time it was just an uncomfortable coincidence – I probably had the dubious distinction of being Brenda's last fling before Danny. "Fling", on second thoughts, overdignifies our encounter. It was very short, taking place in the half hour break between Physics and Double Maths. It was conducted in some discomfort, amidst the disorganised clutter of the sports equipment storage hut. And it ended with Brenda observing, as she gazed out to sea and adjusted her clothing, “yes ... well ... I'd rather have eaten a carrot”.
12 October 2011
Conversation overheard
1st woman: “So how's your Seamus, now?”
2nd woman: “Oh, he's sore bad, so he is. They say he could have died, God bless him. They're keeping him in the hospital, so they are.”
1st woman: “Sure and what is it that's wrong with him?”
2nd woman: “Oh, it's a food poisoning thing – it's chlamydia difficult, they're calling it. Well, it's difficult for him, I'm telling you...
22 August 2011
Bringing technology to life
Biomimetic electromechanical prostheses are delivering the first generation of active replacement parts, but between biological inspiration and industrial delivery comes a lot of data analysis. [more]
Case in point
A collection of case studies from recent science literature highlight the importance of statistics...
- Beating the drought: using GenStat to investigate drought tolerance in chick peas.
- Reading the future: multivariate data analysis of brain patterns using IDL gives improved prognosis for improved reading in dyslexia sufferers.
- Committing fluicide: OriginPro analyses the viricidal potential of hydrophobic polycations.
- Fishy business: Statistica analysis of otolith microchemistry data illuminates population relationships amongst Atlantic herring.
- Wears the diamonds?: Multiple linear regression in SPSS offers a way to better prediction of wear rates in industrial cutting tools.
- Learning from past mistakes: Pursuing future geopolitics through historical data with Wolfram Mathematica.
09 June 2011
A healthy approach to data analysis
As this appears, by a happy piece of synchronicity from my point of view, the Wellcome Collection in the UK has on show an exhibition called Dirt: the filthy reality of everyday life. One exhibit in particular is of pivotal relevance to data analytic epidemiology: Dr John Snow’s so called "ghost map". In 1854, using what would today be described as data visualisation, Dr Snow plotted cases of cholera on a map of Soho, London. From the results he deduced that a water pump, was the source of infection. This was particularly impressive because water was not, at the time, suspected as a transmission vector and the pathogenic germ theory of disease had not become generally accepted. The local council decision to disable the pump was therefore, in the circumstances, a seminal act of faith in datacentric deduction over conventional wisdom.
Seemingly unlikely causation chains are often discovered by more sophisticated variations on Snow’s theme, emerging through statistical winnowing of gathered data. More than most data analytic areas, epidemiology can benefit from pooled work by numerous users at the sharp end of their practice as well as high level overviews, and data analysis is vital across that whole range. Those who have me in preparing this article include theatre nurses, general practice managers, country vets and hospital porters.
In a more recent high profile example, again involving cholera, an outbreak in Haiti after the devastating earthquake seems to have been traced¹ to a tragic “confluence of circumstances” arising from the aid effort itself. Identification of the apparent initial import vector didn’t require any sophisticated analysis in this case, but patterns of spatial spread within the country subsequent to that were a different matter. In an unfunded study of data from census and hospitalisation records (using Madonna software, widely used software from the University of California at Berkeley) Tuite and others² were able to model transmission in a way which “Despite limited surveillance data ... closely reproduces reported disease patterns”. [more]
- Cravioto, A., et al. Final Report of the Independent Panel of Experts on the Cholera Outbreak in Haiti. 2011, New York: United Nations News Service Section.
- Tuite, A.R., et al., Cholera Epidemic in Haiti, 2010: Using a Transmission Model to Explain Spatial Spread of Disease and Identify Optimal Control Interventions. Annals of internal medicine, 2011. 154(8).
I would like to thank Dr Brian Corden for invaluable help in assessing an item which, as a result of his advice, was not eventually used. He thus saved me from making a fool of myself through lack of confidence in my own judgment
03 December 2010
Bus stop
I met a very interesting person, today.
It was seven in the morning, and the air was bitterly cold as I arrived at the bus stop. My bus was due in ten minutes. The man already standing there with no hat told me that he had been waiting for half an hour, he had given up on the bus he'd come for and was now looking forward to the next.
We got chatting, as people do when they stand for any length of time together in the dark and the cold. We compared notes on this and that, and eventually got around to what we do.
He is a doctor, a GP working in a practice at the other end of two bus routes. That already puts him above me in the scale of things; the world needs doctors more than it needs mathematicians. But as we talked, there was more. He is Senegalese. He trained at the University of California medical school at Davis. He runs a free clinic in Senegal.
Hang on ... wind back a bit ... if he runs a free clinic in West Africa, what is he doing at a bus stop on the western edge of Europe?
He is, I learned, one of several doctors at the clinic. Since free clinics generate no income, and since this one is unfunded, money has to come from somewhere to pay its running costs and to feed the families of the staff (medical and otherwise). So, the doctors take it in turns to take contracts in developed economies. The income from these contracts goes to maintain the clinic, its staff, and their dependents. My bus stop companion is in his sixties and half way through a two year contract, a year away from his family whom he misses desperately and with another year to go.
That this system is able to work depends, of course, on the same asymmetry which makes it necessary: the yawning gulf between first and third world economies. This doctor, and his colleagues, live and work at one end of an economic gravity well where money is scarce so costs and incomes are low. They have found a way to exploit that same gradient, using it to make a first world salary run a clinic, pay operating costs (including salaries), and provide pension provision for old age.
I've seen a fair amount of quiet heroism in the face of third world poverty and health needs. In the field, I've carried bedpans or washed bandages or ... but then I've always scuttled back to my comfortable first world billet. I've supported campaigns to fund third world medicine ... but never for even a day to the extent that this man and his partners do, across whole lifetimes. Any of them could stay permanently in our more comfortable settings, bring their families with them, reap the rewards of the hard work which gained them the qualifications and expertise which they now possess ... but they don't.
I didn't get around to asking where the pump priming finance came from, to put him through a US medical school in the first place. Wherever it came from, though, it wasn't used to buy his way out of hardship; it has been ploughed back over a lifetime into his roots.
Four of the charity links at the top left of this page point to organisations concerned with the third world; two of them are medical; one is dedicated to helping communities meet long term health issues and thus escape a cycle which they can't afford to break on their own. If you have money which you are inclined to donate, any one of those charities (and many more besides) would be a worthy recipient – but, after my bus stop conversation, Health Poverty Action (formerly Health Unlimited) is the one that will get any extra that I have available this festive season. And if you want to combine a lifeline with present giving, they have a selection of ideas starting from as little as US$8/€6/£5 (a contribution to child health monitoring) running up by easy increments ($16/€12/£10, $24/€18/£15...) through a set of surgical instruments ($160/€120/£100) to the top whack installation of a life saving water system ($630/€470/£400).
06 February 2010
Locked in, locked out
Most new research doesn't make it to the general news media. This week's publication of a paper describing two-way communication with patients who had been believed to be in a persistent vegetative state, via functional magnetic resonance imaging, is an exception: it captures the imagination and horrifies to an irresistible extent.
As part of the spill-over from that story I overheard, on a passing radio in a crowded place, fragments of an account by someone who had been in this locked-in state for more than two years. (I can't, unfortunately, locate a reference for the radio programme.) As I listened to the bits I could hear, I was most struck not by the science or technology involved but by the calm, rational phrasing of the interviewee.
I am a person who considers myself able to cope well with isolation. I have, on occasion, spent weeks or even months on end without human company and (so far as I know; perhaps I delude myself and others think differently) suffered no ill effects. But I cannot imagine that, after two years in which I was fully aware of the world but unable to communicate with it, I would still be in any sense sane – never mind able to construct rational discussion of the experience. I know, from experience, that human beings are incredibly tough ... but thinking about this situation raises my amazement at the degree of that toughness by several orders of magnitude.
-
M M Monti et al., "Willful Modulation of Brain Activity in Disorders of Consciousness" in New England Journal of Medicine, 2010: p. NEJMoa0905370. Available from: http://content.nejm.org/cgi/reprint/NEJMoa0905370v1.pdf. (accessed 2010-02-05)
27 September 2009
More soul searching
My “soul searching” post of Sept 17th prompted a whole set of interesting and valid comments, from a variety of viewpoints. All of which I've been mulling over with further soul searching. Replying to all of them, or even properly to one of them, would take more time than I can envisage ... so I'll pull just two of them and do my best in the few minutes available.
First up, Dr C (for whom I have nothing but respect and admiration) who said:
“As for animal experiments, many drugs and treatments would never come to light without experimentation on animals.”
I agree. And it's a powerful argument. I don't pretend to know what is right or wrong for others to decide, and I certainly do not judge others for deciding as Dr C suggests. I can only say that I would not (in the generalised abstract) decide that way myself.
“One might make an analogy to the use of animals in farming and transportation. Certainly dragging a heavy plow around a field is not a horse's idea of fun. In fact, there would not be horse whips if this were true (or if horses ran races on a whim).”
That is true; we can indeed make that analogy. However (again, for myself and not for anyone else) ... speaking philosophically ... since I see the horse as conceptually indistinguishable from me from Dr C, and since I would not harness Dr C up and make him haul a plough around a field nor carry me at speed while I whipped him (nor allow him to do the same to me), I could not use a horse in that way either. So the analogy still leaves Dr C and I on opposite sides of the same divide.
“I think that we can make an argument for the use of research animals based on moral principals accepted by the majority.”
Once again, I agree. And, as a society, we do. But the individual has a duty to act morally according to her/his conscience, and to decide when that requires dissent from the majority. If I do not recognise the conceptual difference between human and laboratory rat, then I cannot morally or ethically use a rat where I cannot morally or ethically use a human.
“This leaves begging what I mean by "humanely".”
Indeed ... another can of worms. (No, I won't follow a byway into the philosophy of worm rights at this juncture!)
To Geoff Powell I have no right to say very much. His viewpoint seems to be the same as mine, but I hang my head at the thought of claiming his lifetime of adherence in support of my easy, facile abstraction.
On the other hand, Geoff's point that a significant proportion of modern illnesses are iatrogenic is a valid one which sits alongside Dr C's reminder that our use of antibiotics has led to multiple resistance in the bacteria which they combat. However, the proposition that we have more disease now than we had before "modern medicine" is not one which seems defensible to me. Would I swap 2009 for 1909? No, I'm afraid I would not – which, of course, causes yet more anguished soul searching and self accusations of hypocrisy
Later additions:
On the iatrogenic issue, I agree with Ray Girvan that the putative link between polio vaccine and HIV is spurious. The MMR/autism controversy seems likely to go the same way on a balance of probabilities, although as yet it's less clear cut. Those specifics don't, though, invalidate the assertion that intervention does introduce a significant level of new problems (nor, incidentally, does iatrogenicity affect Geoff Powell's expressed preference for declining animal research based treatments). A quick search of medical literature published in the last twelve months for example, throws up almost a hundred papers mentioning iatrogenic hepatitis B or C. As I registered above, however, I do not think that a fair observer can claim an overall balance against medicine on functional grounds; my soul searching remains moral/ethical/philosophical.
On another front, in a side correspondence Matthew Revell raised the philosophical question of validity in an experiment where conceptual equivalence is denied. That's another road I haven't world enough or time to pursue here, but an intellectually intriguing one which is occupying a fair chunk of my mental "spare processing cycles time".
-
M Khurram et al, "Nephrogenic systemic fibrosis: a serious iatrogenic disease of renal failure patients", in Scandinavian Journal of Urological Nephrology. 2007; 41:565–56.
02 September 2009
Two historical fictions
I've neglected books lately. There have been several good ones, which I've intended to mention ... but then time and a half slipped by... (Ray Girvan used to have a link to my books tag but I notice that he has tactfully removed it to spare my blushes.) One of them I really must address because it's one of the most impressive fictions I've ever read ... watch this space, “real soon now”. The rest, since time is finite, will have to drift away.
I will, however, briefly mention a young adult novel which I read on the recommendation of The conscience pudding – Jennifer Donnelly's “lovely, plaintive book”, A northern light. I won't review it here; Watoosa has done that for me. I'll just add a couple of comments. First, to register a small reservation (as she does in her current post) about the tendency of fiction in general, and young fiction in particular, to "prettify" or idealise the past – there are some social aspects of Mattie's world which are more generous than true. At the same time, I nevertheless am impressed by the way difference between “then” and “now” is soaked into the fabric of the book in a way which brings it home to the intended audience. Chrissie, a 16 year old of my acquaintance, was deeply affected by the description of life only a hundred years ago and embarked on a library search to fill out her understanding of social development in the century between. (Aside: this book is an example of the irritating practice, mentioned by Watoosa, of changing titles as they cross the Atlantic: in Britain it is for some reason known as A gathering light which somewhat misses the original point.)
Also a hundred years ago is the story within a story of Salvador Carriscant, a surgeon in the early 20th century, told in retrospect by the narrator of William Boyd's A blue afternoon. The descriptions of surgical and medical knowledge (or, from our viewpoint, lack of it) didn't actually tell me anything I didn't already intellectually know, but they did for the first time bring many things home to me in visceral (literally!) and vivid context just as A northern light did for Chrissie. Two days after reading this, serendipitously, I found Unreal Nature's post on surgery and poetry and the ensuing discussion in its comments.
- Jennifer Donnelly, A northern light. 2004, San Diego: Harcourt. 0152053107 or 978-0152053109 (published in the UK as A gathering light. 2003, London: Bloomsbury. 0747570639)
- William Boyd, The blue afternoon. 1993, London: Penguin. 0140238255 (pbk)
28 August 2009
Analysis is the mother of invention

Invention isn't what it used to be. When I made the decision (at age 11, or thereabouts) to be freelance scientist, I had a lot of role models in mind but prominent among them was the anarchic spirit of absent-minded inventor Professor Branestawm[1]. It was still easy to find real inventors like him, then; I knew one, and was taught by a couple more as an undergraduate. Nowadays, while part of him still lurks in many outwardly staid scientists, they would never acknowledge him. His demise was inevitable, but was finally assured by the arrival of computerised data analysis.
Invention comes in two basic types: ‘let’s try this and see what we get’, and ‘this is what we want, so how are we going to get it?’ Branestawm, surprisingly for a scatterbrained professor archetype, was of the second kind: he started from an idea for an invention, and pursued likely paths to its realisation. Modern equivalents are easy to find, from James Dyson who envisaged a better way of picking up dust and made it happen, to Altair moon lander architect John Connelly. Shifting from physics to pharma, the search for an H1N1 vaccine (proceeding apace as I write this) is in the same category, but there are also many examples of the first type: batteries of agents tried in combination and in various situations until a therapeutic effect is identified. For the most part, of course, invention programmes are mixtures of the two approaches, especially when seeking a nonpatented way to compete with an existing solution. Regardless of approach, invention is (like all post-Branestawm science) highly dependent upon data analysis. [more...]
This one benefited in different but equally significant ways from conversations with Julie Heywood, Jim Putnam and (as always) Ray Girvan. They may well disagree with me about the use I have made of their input, but it is no less valuable for that. There was no mechanism or opportunity for acknowledging this benefit in the article itself, so I do it here.
- Norman Hunter (ill: W Heath Robinson), The Incredible Adventures of Professor Branestawm. 1933, London: John Lane.
27 August 2009
Healthcare
With a lot going on (the new academic year looms, and all the other commitments which get packed into the summer break are, of course, still incomplete!) I seem to have posted very little recently. And to have even been remiss in responding to interesting posts by others. This will have to be a very quick token effort over a rushed breakfast...
That doesn't mean I'm not reading and listening to the world. In my immediate blog circle, see "Slow pleasures", for instance. I've enjoyed Ray Girvan's piece on fossil ink (in both JSBlog ad The apothecary's drawer), Julie Heywood's prolific and always thought provoking (too prolific and thought provoking to keep up with even in quiet times!) output at Unreal nature, and Dr C.
In the mainstream media, one of the strands is the US health care funding controversy. I am reluctant to get too involved in this one because it's an area where entrenched views, knee jerk responses and anecdote drown out reasoned argument. All my own experiences of the US medical system have been frightening, while those everywhere else have been good; that is, of course, anecdotal, and I know with my rational mind that it cannot possibly be representative. It's mainly on the nature of the argument that I feel competent to comment.
Somewhere in the past few weeks I heard a BBC Today programme discussion between US and UK individuals of the perceived differences between US and UK systems. Both tried hard to put aside their preconceptions and discuss it dispassionately. I noted that the US participant managed this slightly better than his UK counterpart – particularly interesting because he was from the Cato Institute, which tends to what is, in UK terms, a rightward libertarian outlook with which the British NHS (National Health Service) is, of course, at odds.
This is, of course, at heart, currently an internal US debate over proposed changes there. One of the more bizarre and shrill strands within that debate has been use of UK and Canadian system scare stories to suggest that national funding systems produce charnel houses where people die needlessly. One which I heard suggested that Edward Kennedy would not have been treated if he had been a Briton. The propagators of such stories seem entirely untroubled by the fact that private medicine exists in the UK just as it does in the US for those who can afford it. So do private and corporate medical insurance. The NHS is an addition, not a replacement.
To risk a personal comment ... I (for what it's worth) second Jim Putnam's TTMF plea that "Caring must become a human right. We are, every one of us, a part of one another."
That's it, folks ... breakfast is over, time to rush off ... busy, busy, busy...
06 August 2009
Today is Hiroshima Day
Why do I insist on mentioning this, each year?
Not because I particularly wish to warn against nuclear weapons. That moment is long past.
Nor because I wish to continue emphasising a particular act of war (amongst many) from sixty four years ago.
Because it is an occasion to remember that we have gone on creating and using ever more effective ways to kill civilians. A good occasion to think about napalm, perhaps. Or the many Iraqi civilian deaths (something like a hundred thousand so far) which we ignore as we note on our television screens only the relatively tiny numbers of our own military losses. Or those in the ongoing mess which is Palestine.
And perhaps also the deaths by negligence while we pour funding into means of killing. Like the nearly ten million children under age five who die every year from causes which we could prevent by diverting just a small fraction of our military spending.
That's why I insist on mentioning Hiroshima Day.
01 August 2009
Love in the time of swine flu (2)
In my last post, I said that I expected to be deluged by angry knee jerk criticisms to my interest in a Simon Says item. I wasn't disappointed, but I also received some very thoughtful ones – two of which arrived as comments to the post.
06 June 2009
British Chiropractors Association vs. Simon Singh
Today I received an email from Greg Parker (scientist, inventor, astronomer, university professor, businessman, not necessarily in that or any other particular order) urging me to sign a petition. "Rarely do I feel moved to support anything along these lines - but this one I feel is a very clear exception."
The petition is in support of Simon Singh, whom the British Chiropractors Association (BCA) sued for libel after he wrote a critical article ("Beware the spinal trap") in The Guardian in April last year.
I'll say, at this point, in case I seem to be undermining Singh's appeal, that I did sign the petition. Furthermore, I am only writing this post because I want to play a small part in further publicising that petition.
I am cautious about signing petitions; I want to know exactly what the background is, and to what exactly I am signing up. In this case, I wanted to know exactly what had been said in the original article. I am well disposed towards Simon Singh, and also disposed to support individuals sued by bodies, but this isn't about my personal sympathies.
If I sign just because I like someone (in this case someone I have never met), or on the basis of unverified third hand information, it doesn't really serve truth or justice in any way. It certainly isn't scientific, science being (and this is after all Singh's and his supporters' central point) evidence based. I frequently discover, on investigation of a petition that seems reasonable, that I really don't agree with it at all.
I don't believe that you should follow me in signing the petition until you, too, have satisfied yourself that you agree with it. Because it's a libel case, the original article is not easily available – it has been withdrawn from The Guardian's web site, in particular. I spent some considerable time schlepping fruitlessly around looking in obvious places for a copy. There are copies out there, though. Here are some links which work at the time of writing:
- An exact copy (apart from addition of an explanatory header) of the original Guardian web page, posted by Svetlana Pertsovich
- A copy of the text itself, at the Confessions of a quackbuster blog.
- An annotated version of the text at Gimpy's blog.
Be aware that those are all posted by supporters of Simon Singh. The web is even more able to mutate material than is print, as well as more able to protect against censorship. But, for myself, I'm satisfied that they are honest reproductions of the original.
I've more to say, but it's not perhaps appropriate to place it in this post. I urge you to read the article and then consider the petition.
10 July 2008
Doctor, doctor, I think I'm a computer...
The title, as I’m sure you have already recognised, is from a well-known strand in schooldays humour. This particular example came from a medical student, and I’ll keep the punch line until later.
From the submicroscopic level to international social policy, medicine has become a scientific computing dominated domain. Electronic data handling approaches are centrally responsible for increases in reach, effectiveness and efficiency, though also for dramatic growth in health programme delivery costs.
The highest persistent profile belongs to genetic areas, which could not exist without a mature substrate of computing technologies upon which to build. This doesn’t just mean computerised study leading to fundamental knowledge about genetics, but more traditionally pragmatic correlational studies such as the linkage between leptin expression and DNA methylation or MMP-13 activity in chondrocytes[1] (pointing to potential osteoarthritis therapies), or between gene variants at a particular chromosome locus and incidence of asthma[2]. Then there is the ascendancy of in silico methods for biological chemistry at the molecular level; computing is now so much a part of biology as to be inseparable from it and medicine, a consultant at a large hospital told me briskly over a cellomics display, ‘is only applied biology’.
[more, including the punchline for that joke...]
1. Iliopoulos, D., K.N. Malizos, and A. Tsezou, Epigenetic regulation of leptin affects MMP-13 expression in osteoarthritic chondrocytes: possible molecular target for osteoarthritis therapeutic intervention. Ann Rheum Dis, 2007. 66(12): p. 1616-1621
2. Konstantinidis, A.K., et al., Genetic association studies of interleukin-13 receptor {alpha}1 subunit gene polymorphisms in asthma and atopy. Eur. Respir. J., 2007. 30(1): p. 40-47