Wednesday 27 February 2008

The first earthquake of spring

Last night, the largest earthquake since 1984 struck Britain. There I was, sleeping, like any good scientist should be at that time of the day (unless they're writing a PhD) when I was woken by the bed shaking. Sometimes this is because of the enthusiastic couple who live in the flat upstairs, but this was different. The room shook for probably 20 to 30 seconds, accompanied by a low rumbling, and I realised it was probably an earthquake. I checked the time so I could look at the BGS website [pdf] this morning: it was 1am.

This morning I discovered that it was a magnitude 5.2 quake, with the epicentre near Market Rasen, Lincolnshire. 5.2 is a pretty hefty magnitude, and it's fortunate that the focus was 10 km deep; if it had been much shallower it could have caused a lot of damage. There was only one injury, a man in Wombwell, near Barnsley, who was hit by a falling chimney pot. As the man's father said 'of all the things to happen-an earthquake!'

If you felt the earthquake, the BGS have a questionaire to fill in. It only takes a few minutes, and they use the information to do science.

As far as the Earth's crust goes, the UK is pretty stable, but earthquakes are not that rare. They just tend to be small. The BGS has a list of earthquakes for the last 30 days here. You'll notice that there has been aftershock, magnitude 1.8, from the Market Rasen quake.


The BGS now reckon that the depth of the main earthquake was more than 18 km. There have now been three aftershocks, with the largest at a magnitude of 2.2.

Tuesday 26 February 2008

Antidepressant manufacturers sound a bit like homeopaths

The papers today are full of the news of the meta-analysis of clinical trials of anti-depressant drugs (including Prozac) that shows such drugs only have a clinically significant effect for a very small subset of the most depressed patients. The authors also concluded that the larger effect compared to placebo for the most depressed patients was caused by those patients responding less well to placebo, not to the SSRI drugs being more effective for those patients. [I should add that if you are prescribed such drugs, you shouldn't stop taking them unless you are advised to by your GP].

Obviously, this is not good news for the companies who make these drugs. GlaxoSmithKline, who make Seroxat, said that the conclusions were at odds "with the very positive benefits seen in actual clinical practice" and that "This one study should not be used to cause unnecessary alarm". What the study is suggesting is that the benefits of the drugs seen in clinical practice may be partly related to the placebo effect, and that those benefits not related to the placebo effect are small and usually not clinically significant. That's the point that GSK need to address. But they don't, and not only that but they disingenuously describe a meta-analysis of 47 trials as 'one study'.

Eli Lilly (makers of Prozac) said that "Extensive scientific and medical experience has demonstrated that [Prozac] is an effective anti-depressant". This just ignores the evidence from the meta-analysis that says the opposite.

When I read these responses, I couldn't help but be reminded of the responses of homeopaths to the evidence from double-blinded, randomised, placebo-controlled trials that homeopathy doesn't work. They simply ignore that evidence and say that they know it works, through clinical experience or anecdotes.

It's disappointing, but perhaps not surprising, to see drug companies falling back on these unscientific statements. After all, homeopathy transparently doesn't work, but plenty of people still use it. Perhaps the companies are hoping for a similar outcome for their anti-depressants. The point here is not that these anti-depressant drugs are useless: clearly they do 'work', especially for the most depressed patients. The point is that for most people taking them, they don't work particularly well.

Tuesday 19 February 2008

Netcetera fold like a cheap suit

The mighty Quackometer blog has been pulled by its hosts, Netcetera, apparently because of ludicrous legal threats made by one Joseph Chikuele Obi. This follows a previous attempt by the Society of Homeopaths to get the website shut down.

Encouragingly, it seems that this will have no effect at all, as the Quackometer will shortly re-appear hosted by Positive Internet, who host Bad Science, amongst others.

Obviously, there ought to be some protection against genuinely defamatory material on the web, but there also ought to be some protection for bloggers against the sheer frivolity that has characterised the threats against the Quackometer. The Quackometer has provided a useful service by exposing quackery of all kinds, and it's a shame that its author, Dr Andy Lewis, has been subjected to such nonsense.


Happily, the Quackometer is now back online and causing trouble for quacks and frauds, courtesy of Positive Internet. You can read all about the saga here.

Monday 18 February 2008

The uses for terrorist atrocities

I couldn't help but be struck by the Guardian front page last week, that included two stories related to the 7th July terrorist bombings on the London transport system in 2005.

The first story outlined how the Saudi Arabian government, being investigated under corruption allegations linked to the sale of military equipment by BAE systems, allegedly threatened that intelligence co-operation would be compromised unless the investigation was called off. This would threaten another 7/7 and lead directly to the "loss of British lives on British streets". Any government with a spine would have told the Saudis where to go, given threats made in an attempt to halt an ongoing criminal investigation would be a criminal offence. Disgracefully, our government caved in and ordered an end to the investigation. This just can't be right.

The second story featured George Bush, who claimed that the 7/7 bombings could justify torture.

"To the critics, I ask them this: when we, within the law, interrogate and get information that protects ourselves and possibly others in other nations to prevent attacks, which attack would they have hoped that we wouldn't have prevented? And so, the United States will act within the law. We'll make sure professionals have the tools necessary to do their job within the law ".

On being asked about whether Guantanamo Bay, Abu Ghraib and extraordinary rendition send the wrong signal to the world, Bush said "It should send the signal that America is going to respect law, but is going to take actions necessary to protect ourselves, and find information that may protect others -- unless, of course, people say, well, there's no threat, they're just making up the threat, these people aren't problematic. But I don't see how you can say that in Great Britain, after people came and blew up bombs in subways. I suspect the families of those victims understand the nature of killers".

So there you have it. America will respect the law, by using techniques such as waterboarding that are transparently illegal. Families of the 7/7 victims will support torture, because they understand the nature of killers. But what if they understand the nature of torturers too? Again, this just can't be right, can it?

The terrorist attacks of 7/7, in which 52 innocent people were killed, are now being used to justify torture and corrupt arms sales to dictatorial regimes. Nice.

Thursday 14 February 2008

Bad geology: another pseudojournal

Generally, my own field of geology is not somewhere you find a lot of pseudo-science. So it's nice to be able to comment on some, via the folk at Answers Research Journal. Thanks to Michelle for the heads-up. The journal contains a paper on 'catastrophic granite formation', an attempt to show that granites can form very quickly, quick enough to be consistent with what creationists call 'flood geology', the theory that most of the geology we see was formed in the Genesis flood.

The author is one Andrew Snelling, proud holder of a doctorate in geology from the University of Sydney. It seems that Snelling is happy to use the conventional geological column when working as a consulting geologist, but happy to disregard it when propagandising in favour of creationism.

The 'journal' claims to be "a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework". This raises some questions. Who are the reviewers for the journal, and who reviewed this article? In geology it is standard practice for reviewers to be acknowledged in published papers; reviewers usually identify themselves to authors, unless there are strong reasons not to do so. No reviewers are identified in the article: in fact there are no acknowledgments at all. In the instructions for authors [PDF], prospective authors are asked to suggest at least three referees. The guidelines state that comments will be solicited by at least three reviewers. I wonder if only reviewers nominated by the authors are used? Certainly it's hard to imagine mainstream geoscientists agreeing to review for the journal, or agreeing to the publication of any articles on 'flood geology'.

Why is the journal restricted to "research from the perspective of the recent Creation and the global Flood within a biblical framework"? The instructions for authors suggest that work will be rejected if it is not "formulated within a young earth-young universe framework". This would be like, for example, a physics journal refusing to accept papers that were not formulated within a string-theory framework. No real scientific journal would restrict itself to publication of work that addresses a single hypothesis, because that wouldn't be science.

The journal is claimed to be a "technical journal", but there's a lot of language in the article that suggests otherwise. For example, in the introduction, Snelling writes that "Each recognizably distinctive granite mass, the boundary of which can be traced on the ground, is marked as a separate geologic unit called a pluton on a geologic map". In a section headed 'Magma Principles', Snelling writes that "The molten material which flows from volcanoes is known as lava and cools to form volcanic rocks. So lavas must be molten rocks; that is, they were originally rocks that melted deep inside the earth underneath volcanoes. When deep inside the earth, these molten rock materials are called magmas because they are slightly different in composition and physical properties due to the steam and gases they have dissolved in them that erupt separately from the lavas through volcanoes". There's nothing in particular wrong with these statements, but they read much more like excerpts from a GCSE level textbook than prose from a technical journal. This sort of basic information is never included in real geological journals: the assumption is that those who read them are already familiar with the basics. The article reads much more like a piece written for a general audience.

What of the actual science? It's actually not too bad in the main. The issues surrounding the production and emplacement of granite are quite well set out. The point of the article is that granites could be created and emplaced within a timescale of 6000-7000 years. This seems like a reasonable conclusion, at least in some cases, though I'm not convinced that it applies to every intrusive granite body on the planet. The problem is that Snelling then jumps to the conclusion that this is consistent with the Genesis account of creation. At this point, the article is no longer talking about science, but is trying to provide evidence for an answer that has already been decided on. The argument that the earth is a lot older than 7000 years does not depend on granites taking more than 7000 years to form and become emplaced. It relies on pretty much everything we know about geology, but particularly on radioisotopic dating. How does Snelling get around this? He simply states that isotopic dating is in gross error because it fails to account for the acceleration of decay. This is a load of rubbish, as you can see here.

The dead giveaway, though, is the section devoted to 'Evidence from radiohalos'. A radiohalo is supposedly a zone of crystal damage surrounding a crystal that contains radioactive substances, for example zircon crystals that are relatively common in granites. Snelling claims to be able to identify radiohalos associated with decay of three polonium isotopes. The argument is that the isotopes of polonium have very short half lives: 3.1 minutes (218Po), 164 microseconds (214Po), and 138 days (210Po). Therefore cooling of the granite has to be rapid, because otherwise the polonium would decay too rapidly to form halos. Not to put too fine a point on it, this is drivel. There's a useful summary of why it's drivel here.

Snelling has come to an initially reasonable conclusion about the potential rapidity of formation of some granite bodies, and then extrapolated wildly to suggest that this is the case for all igneous rocks, and that most of what we know about geology is wrong. Still, he is happy to ignore that conclusion in his consultancy work and publications in real scientific journals. Like Homeopathy, Answers in Genesis is a pseudojournal: it's designed to look superficially like it is publishing real science "from a different perspective", but it is not. It is a creationist propaganda organ, and it is publishing creationist propaganda.

Friday 8 February 2008

Sinai again...

Back in one piece from Egypt, once again. This time I wasn't really collecting any new data. Instead I was helping a field trip to the study area for the industrial sponsors of the project. The trip went well, I think: it's such a great area that it would be difficult to make it uninteresting.

I'm going back in a few weeks with another field trip, so it's also good practice.

"City view" at the Maadi Towers Sofitel, Cairo.

Strange weather. It was cold, cloudy, windy and occasionally rainy. This is Gebel Hammam Faraun lurking through the weather from Wadi Wasit.

The bakery at Abu Zenima.

Thursday 7 February 2008

Eagleton to get booted?

Just read this Guardian article, where it is suggested that Terry Eagleton may be forced to leave the University of Manchester on reaching the age of 65. The article approaches this from the angle of Eagleton's 'feud' with Martin Amis. While both these characters are employees of the University of Manchester, and therefore technically colleagues of mine, you're not likely to see them hanging around the School of Earth, Atmospheric and Environmental Sciences. In the case of Amis, you're not that likely to see him in Manchester, given his contracted 28 hours a year (at £80,000).

While the 'feud' was moderately entertaining, I'm more interested in how all of this fits in with the university's 2015 plan. This is highly ambitious, and sees the university as one of the world's top 25 by 2015. One of the targets is, apparently arbitrarily, to employ five nobel laureates by 2015. I'm a little cynical, and wonder if the university was taking a bit of a gamble on Amis winning the Nobel in the near future. Certainly, Amis is a high-profile addition to the university, but could that £80,000 a year have been better spent than on 28 hours work and some (not entirely positive) publicity?

Eagleton, whether you agree with him or not, also enjoys a high profile. Surely it can't be smart for the university to force him out at 65. I get the impression that universities in other countries will look askance at an institution that discards a professor decribed as "the best internationally known literary critic this country currently can boast" in such a cavalier fashion. Certainly, the work of my department is enhanced by the presence of eminent scientists who are long past the retirement age.

While 5 Nobel laureates would be a nice headline figure, it's not at all clear to me that it will improve the research and teaching at the university, especially if those nobel laureates only work 28 hours a year.

Wednesday 6 February 2008

Memory of water: what have we acheived?

After the journal Homeopathy published a special issue on the concept of water memory, a number of sceptically inclined people, including me, concluded that the research presented was mostly of poor quality, and didn't tell us anything useful about the plausibility of homeopathy. A number of letters to the editor were submitted to the journal, and eventually published. A useful summary of the letters, and the responses to them, can be found here.

This is all very well, but have we actually acheived anything by taking this course of action? Reading Peter Fisher's editorial comment on the memory of water debate, you could be forgiven for thinking not. Fisher says that there a number of themes have emerged:

"1. Water, prepared by the homeopathic method of successive dilution and succussion, exhibits anomalous properties which can be detected by a range of chemical and physical methods.
2. Trace amounts of contaminants including silica and dissolved gases are important in determining those properties.
3. These properties exhibit surprising temporal evolution.
4. The findings suggest organisation at a mesoscopic scale. No author disputes that, on the microscopic scale, water structure is extremely short lived.
5. So far there is no satisfactory or uniting theoretical explanation of these observations".

I don't think that any of these points are really true, and in any case they haven't been adequately demonstrated. Certainly the papers by Rao et al. and Vybiral & Voracek fail to show any such thing, as the sceptical responses demonstrate. The other experimental papers, by Louis Rey and Elia et al., are equally poor and essentially show no repeatable and statistically robust results. Overall, the experimental papers show nothing at all, and certainly nothing relevant to homeopathy. But Peter Fisher can still talk as if these papers are merely controversial, rather than flat-out wrong.

Meanwhile, the Quackometer [unavailable at time of writing: google cache version here] has discovered a newsletter of the newly formed Homeopathy Research Institute that references the now severely deaded Rao et al. paper, as well as the infamous Benveniste paper in Nature that started all the memory of water nonsense, has been thoroughly debunked [PDF], and yet refuses to die. It seems that no research is too discredited to be cited in favour of homeopathy.

If you actually bothered to check out the claims made by, for example, the Homeopathy Research Institute, you can easily find material de-bunking them. But how many people will do this? I think that publishing the various letters critical of the Homeopathy memory of water issue was at least an interesting experiment, and it seems worthwhile to try and deny anti-science a scientific platform, but I wonder how much actual difference it will make to the purveyors of nonsense.