Illiberalism in rational causes…

The blogdom of skeptics has been in uproar over the ruling of Mr Justice Eady in the libel case Simon Singh vs British Chiropractic Association (BCA). The case has already been covered extensively, by The Lay Scientist (background | verdict) and Jack-of-Kent (background | verdict).

In Simon Singh’s book, ‘Trick or treatment: alternative medicine on trial’ (review by The Times here), he systematically addresses the pseudoscience of numerous alternative healthcare measures, including Chiropractry, about whom he said:

“The British Chiropractic Association claims that their members can help treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying, even though there is not a jot of evidence. This organisation is the respectable face of the chiropractic profession and yet it happily promotes bogus treatments.”

The ruling hinged on Simon Singh’s use of the word ‘bogus’, which means counterfeit or fake, spurious, or bad. Unfortunately, when you start thinking about it meaning ‘counterfeit’ then this infers some degree of fraudulent use, or deliberate misuse, which is how the judge chose to rule in this case. Mr Justice Eady decided (evidently prior to the hearing had commenced) that the definition would be taken as consciously and deliberately dishonest. In this case it rules in the favour of the BCA where, by the judge’s own reasoning, Simon Singh has libelled them by labelling them deliberately dishonest. It seems strange that a judge can make any objective ruling on the definition of such a word in this case; Mr Justice Eady has effectively ‘cherry-picked’ the evidence by looking at the word ‘bogus’ within a paragraph, without including the evidential support of context from the chapter as a whole.

As I have discovered through word battles myself, different people lean towards different definitions of words when multiple definitions are available. An example might be ‘tautology’, which in one vein can be a rhetorical definition of ‘using different words to say the same thing twice’, yet can also have a meaning in logic of ‘a statement that is necessarily true’. What distinguishes the uses is the context in which they are used, and this seemed to be apparent in this case.

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Basic research…


TODAY ‘The Scientist’ reported that the UK government is going to bail out biotech, investing £750 million ($1.1 billion) to bolster this and other ailing commercial science and technology sectors. This isn’t a bad thing, per se, but at what cost?

Well perhaps it comes at the cost of ‘basic research’:

Government funding for basic research, however, will receive no additional funds. Buried deep on page 130 of the new budget, the government called on the public research councils, including the MRC and the Biotechnology and Biological Sciences Research Council, to reallocate £106 million ($154 million) of their pre-existing budgets to support key areas with predicted economic potential — a plan which leaves some science lobby groups less than happy.

They’re going to move money around, rather than putting more into the areas of basic scientific research. In contrast, the US government’s economic stimulus package has fed money into the National Institute of Health (NIH) and National Science Foundation (NSF), between whom most of my US scientist friends are funded in their basic scientific research.

But what do we mean by ‘basic scientific research’? The term, synonymous with fundamental or pure research, is first and foremost a quest for knowledge; it has no specific end goal or commercialisation, i.e. a practical application cannot be envisaged. We might also consider research that may yield a commercial application after 10 -50 years to be basic research too (I put my own current technologies work in this bracket). Applied research, in contrast, is work that is aimed directly at a specific commercial end, such as development of a particular drug.

So what’s the problem in the UK, why are we bothered?

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Three cups of tea….


A Pakistani friend of mine recently lent me a book called ‘Three Cups of Tea’. At the time I had absolutely no idea how famous this book now is, it’s been on the New York Times best sellers list for 109 weeks. Reading it has been a formative experience.

It is the story of Greg Mortenson who, in 1993, after a failed attempt on K2, wandered accidentally into a small Baltistani village in the Karakoram mountains. The name of the village was Korphe (Kor-fay), and his experience here would change his and, by dint of this, tens of thousands of people’s lives in this impoverished region of the North-West frontier of Pakistan. The kindness of the Korphe villagers, their willingness to give Greg so much, when they themselves had so little, truly humbled him; thus prior to his departure, upon seeing how the children of the village were forced to write their lessons in the soil with sticks, he promised to build them a school.

The book describes how Greg returned to California, broke and living out of his car, to raise the $12,000 required to build the school. From humble beginnings, to patronage by the late multimillionaire scientist Dr Jean Hoerni and the formation of the Central Asia Institute (CAI), Greg has directed the building of 80 schools, women’s community centres and student hostels in North-West Pakistan and Afghanistan. This could only have been achieved with a very loyal team of local contacts that Greg has a natural faculty to draw towards him. The schools are built by the people of the villages with the full support of the village communities.

The emphasis of CAI schools is on the education of girls, an idea captured by the maxim, ‘If you educate a man, you educate an individual; but if you educate a woman, you educate a nation’ (Mahatma Gandhi). This lasting and indelible educational structure is at the core of improving healthcare and welfare of villagers, but furthermore, will reduce the number of illiterate and uneducated people who would otherwise provide cannon fodder for radicalism by fundamentalist clerics; a mother is less likely to give her blessing to her son’s jihad, a strong social requirement, if she is educated and literate.

The byline of the book is, ‘One man’s mission to promote peace…one school at a time’. It is a noble cause and one that I will happily support. I highly recommend that everyone read ‘Three cups of tea’. If you enjoy the book, also read some of the CAI publications (Journey of Hope), which provide updates and fantastic photography of the current and ongoing projects.

Writing about reading…

READING about writing has been a pass time for some time, but writing about reading is a first. Those who know me know that I am a passionate reader; I’ll read from an eclectic range of genres, though of course I have my favourites. But I don’t really want to write about what I read, rather, I’d like to write about how I read.

My entire life, well, teenage onwards, I have carried a rucksack or satchel wherever I go. In this bag I always have certain essentials: a notebook, pens, journals, papers and a book (or two). More recently I also carry an iTouch and mactop, and perhaps more bizarrely, a torch and a whole array of iPod, camera and mic adaptor cables. You see, on the one hand I love technology; I am an unashamed technocrat, though perhaps less so than the eminent Stephen Fry. On the other, I lament the loss of handwriting, and very much enjoy putting pen to paper, hence the notebook. One thing I can never be without, however, is some reading material.

I almost always have more reading material than I would ever have time to duly read and digest, but carry it none the less, hoping I may just absorb the material by prolonged contact. This is certainly nothing unusual, most academics and students I know have been guilty of carrying papers around for weeks, without ever actually doing more than skimming them.

Books though, what a slave to them I am, and what guilt they engender by the mere fact that I haven’t read all of them yet! The process of preparing to read a book is described quite nicely in a recent article by Mandy Brown at A List Apart; the article is not exclusively about this subject, being more to do with the process of presenting web writing in an accessible and readable manner, but she none the less echoes any sentiments I could offer:

Think of your first encounter with a book. You look at the cover to get a sense of it, then perhaps flip to the back or the flaps to skim the publisher’s copy. Opening the book, you might glance at the title page, or quickly run your eyes over the table of contents. Maybe you peek into the back to check the page count, or casually assess the weight of the book in your hand. If it’s a hardcover, you might take the dust jacket off, lest it get in the way.

Most readers engage in at least one and usually several of these behaviors—they’re a kind of pre-reading ritual, part of the culture of books. And yet they serve an important purpose as well, in that they ease the transition between looking and reading. They help the reader establish interest, and they serve as an invitation to reading, setting the stage for the act that follows.

I spend a lot of time looking, holding and admiring books. People say, “Don’t judge a book by its cover”; I’m not sure which people, but people say this. Now I don’t think anyone would say that a book is crap based solely on how it looks, but they’ll certainly pass it by. Time is so limited now, so precious. If we’re going to invest our much prized spare time by reading the labour of one author, amongst so many others, then there has to be a draw. In the absence of the Times Literary Supplement, New York Book Review or some other trusted review of current literature, how else do we pick out books if not by them grabbing our eyes?

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Hidden in plain sight…

So it seems that the Democratic Republic of the Congo is finally back in the lime light, and about time. In the past couple of years the coverage of the atrocities that have been ongoing there have meritted only the most glancing coverage in the world press, not least of which has been the coverage of the murder of Congolese Gorillas in Virunga National Park.

There are well over 4 million people estimated dead as a result of the rebel insurrection since 1998, with a further 1,200 per day dying, this is a stupefying statistic. Comically Gordon Brown has announced recently that DR Congo must not become another Rwanda, referring of course to the 1994 genocide that was largely ignored by the Western world until it was too late.

Firstly I would say, too little, too late Mr Brown and Mr Blair, you were all too busy pouring money and lives into fighting over oil in Iraq to pay any real attention, and we all know the UN is now a powerless entity after Bush rode roughshod over it to get to Iraq; indeed, the UN have been accused of merely being “tourists” in the DR Congo, despite it being their largest peacekeeping mission.

Secondly, the current news coverage describing the current increased fighting in the Eastern DR Congo would make it seem to some people that the conflict in DR Congo is somehow a recent thing! Whilst peace accords and on paper stability were announced around 2003, and again in January this year, the conflict has been allowed to brood for so long that we now once again find Rwandan Hutu rebels are able to re-enact violence towards Tutsis living in DR Congo, not to mention the numerous other ethnic groups living there.

As I have written before when reviewing Slavoj Žižek’s “Violence“, Žižek believes that we have a ‘will to ignorance’; Four million dead is beyond any mental boundary scale that we are able to deal with, nothing in our evolutionary development prepares us for dealing with numbers on these scales, thus we can’t approach a true reflection of emotion and outrage that smaller numbers would engender. Perhaps now, with renewed interest the West really will take note?

BBC’s Q&A on the subject.


I went to see the film Appaloosa last night, starring Ed Harris, Viggo Mortenssen, Jeremy Irons, Tim Spall and Renée Zellweger; directed by Ed Harris.

Whilst many will dismiss it as yet another Western, I will add it to one of the many recent Westerns (including 3-10 to Yuma and Cold Mountain) that demonstrate how the genre is benefiting from improved photography, timing and attention to detail in both language and physical accoutrements. Appaloosa makes fantastic use of photography, costume and lighting. The pace of the story was excellent, permitting time for good character development, particularly in the form of the friendship between Harris’s and Mortensen’s eminently likeable characters as gunmen and law men.

Harris and Mortensen have great on screen chemistry, and Jeremy Irons plays the suitably self-righteous “baddy” very well; I was however less impressed by Zelleger’s acting role in the film. Zellweger has demonstrated her ability to perform in the genre (c.f. Cold Mountain), yet I’m beginning to wonder if she can deploy any speech patterns or facial expressions that aren’t Bridgit Jones come Beatrix Potter. Perhaps she should watch herself in Cold Mountain and remind herself of the suitably sour and beguiling face she managed there in portrayal of her character, Ruby.

Appaloosa is, by all accounts, a faithfully rendition of the book by Robert B. Parker, about a town called Appaloosa (after the Nez Perce American Indian breed of horse). I’ve never read any western fiction strangely enough, favouring non-fictional accounts of the history of the American west instead, thus I haven’t read the book; I have ordered Parker’s sequel to Appaloosa, Resolution, which sees the roles of Everett Hitch (Mortenssen’s character) and Virgil Cole (Harris’s haracter) reversed in a town called Resolution; we’ll see how it goes.

Viruses in the genes


THERE was a recent article in NewScientist suggesting that viruses are the unsung heroes of evolution. Whilst that is somewhat of a sensationalist position, there is a great degree of truth in it. Many anti-evolutionists seem convinced that it is mathematically impossible that genetic variation and mutation can be a sufficient substrate upon which natural selection can act.

What they forget is that whilst a mathematical proof is always the truth, it is a truth that is dependent upon whether the mathematical model accurately reflects the physical problem. Mathematics is limited to the validity of the assumptions that underpin the statement of the problem, thus in the fixing of certain variables it’s important to distinguish between getting the maths right and getting the problem right.

The variation seen in a species, upon which natural selection can act given circumstances that favour one variation over another, is encoded by alleles; this is the name given to different “versions” of the same gene, thus for eye colour, different alleles may be: brown, blue, green etc. Some alleles are dominant, some are recessive; the dominant ones win and get used, the recessive ones lose  and don’t get used. The dominant and recessive alleles are both part of your genetic make up, and this is called your genotype. The dominant alleles result in a physical attributes in the organism, such as brown eyes, and these physical attributes are known as the phenotype.

It is true to say that whilst all phenotype is derived from the genotype, not all genotype results in phenotype. Dominant traits, because they are aspects of the genotype that are reflected in the phenotype, are traits that can be acted upon by natural selection; however recessive traits are effectively hidden from natural selection unless the DNA that codes for the recessive alleles is physically linked to a piece of DNA that results in some other dominant trait that can be selected for or against. This recessivity maintains a store of genetic diversity.
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Well the new student residents are moved in, over a very long, but thankfully very sunny weekend! The sheer force of humanity entering the site over the weekend was overwhelming, the different personalities of bouncy, excited people was quite a heady mix. I have a team of sub-wardens working for me and they worked tirelessly to welcome all the new students and get them set up, I was very impressed. It’s good fun though, handling 6-10 questions at the same time, running around, making on the spot decisions. It’s nothing I don’t do in the lab on a day to day basis, but it’s far more fun when it’s to help people.

The whole weekend of events went perfectly, with the final Welcome Meeting (big dinner, a bit of a welcome address by me, then a chill out tent) last night coming off with excellent attendance, giving me a very positive view of the people we have in this year; most of them seem like a good bunch.

The task now is to get them organised to form a JCR and start organising things for themselves, so my task this week is to organise the JCR forming “Jarbeque” – that’s a “jar party” come BBQ – for this Saturday.

Then I might take a rest and get back to my philosophical digressions.

On science in society


AT this time, as the Large Hadron collider (LHC) comes online, and we hear tales of the doomsayers (and here) who would stifle curiosity, free enquiry and discovery, I think to my own area of science and the great efforts we have to go to defend the science that gives, and has given, so much to society. The LHC beam line has thus far met all expectations, and when it starts the actual collisions in the next few months there is absolutely nothing to suggest that it will cause the end of the world. Science is under attack like never before; media sensationalisation, poor science education, the barrier between those “in the know” and those not, and the rise of religious fundamentalism are largely to blame.

There comes a point when you really must accept the advice of experts, because you can’t expect to be an expert on everything about which you hold an opinion, this would be an unreasonable and untenable position. You trust that a cardiac surgeon knows how to perform your quadruple by-pass surgery; you trust that aeronautic engineers have really created an aeroplane that will fly; and you trust that if you buy a phone, you are in fact going to be able to call someone with it. So if the LHC scientists say that the comparatively low energy bombardments (yes, large for human experiments, but nothing compared to what the Earth experiences from the Sun) are not going to cause cataclysmic damage to the Earth, then you have to trust that they are sensible, rational, careful and intelligent people who know what they’re about, and believe that what they are doing is good for our society.

Many people go through life imagining worldly attributes into a world that is inherently, and obviously, physical in nature. A world that does not in fact conform to any such imaginings, except in the heads and societies of those who enjoy protection from the crueller and more selective attributes of the physical world; a protection afforded to them by scientists, technologists and engineers, people whom they presume to lecture, deride and slander in the errors of our ways. This is largely because the pursuit of knowledge in the physical world has resulted in knowledge that contradicts the inherited fantasy of some social groups. All I would say is that it is not sensible to hold an opinion in the face of overwhelming evidence to the contrary; wisdom comes from noticing when ones opinions are disproved by evidence.
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I used to attend creative writing classes, if anything to attempt to undo the damage wrought by years of technical writing. Technical writing robs you of certain freedoms: to make mistakes as you write, to use active verbs, present tense, embellishing adjectives and superlatives. Technical writing is precise, well crafted, but passive and impersonal. It is utilitarian and functional “nuts and bolts”, to the “heart and minds” of popular prose.

Exercise (warming up the mind and fingers): write anything within 5 minutes (from an old class):

Small vortices caught dust on the desert floor, swirling them into the face of the oncoming Touareg, peppering his face, mapping his sweat with a glittering foundation.

A haze of flies danced in the grains of sand, a mesmerising display of light and dark. The nomad, oblivious to this battle between light and dark, trudged his way along the fading track of his leader, hating every step, but enjoying the thought of sweet water at journey’s end.

Upon his mind, stripped bare by days of relentless heat, was the Bedouin girl he’d seen at the bazaar. Her face a mystery, only her crystal green eyes telling of heretical beauty.

Such thoughts open holes for hope to fill, but if not filled allow despair to flow in hope’s stead. Such thoughts are wasted, when the day is hot and you are robbed of your life energy.