What’s wrong with this photo?

April 23, 2010

The wonderful @medtek pointed us to this website where some homeopaths are talking about their campaign to exploit exploit the people of Haiti with their highly ritualised placebo.

They provide this nice picture,

taken from the homeopathy clinic, the inference being that it is showing many people queuing up outside the homeopathy clinic to get treatment.

Now, the image isn’t the greatest quality (I took it as was from the above website – fair use claimed, etc etc) – but, (please download it yourself and take a closer look…_

if all those people are queuing up for homeopathic treatment, why are they mostly facing the other way?

EDIT: I have just figured out what is going on here. This is, homeopathically speaking, a *very* powerful crowd. The dilution of the 5 or so people looking the right way with the hundreds (?) of people looking the other way clearly potentiates their effect.

EDIT EDIT: Also it has been pointed out that this photo is taken from outside the medical clinic – presumably the one outside which they set up shop. Everyone still looking the other way. Strange. Article infers that those people were waiting for homeo, and comment 1 certainly makes that assumption.

Boobquake vs Boobcano.

April 21, 2010

Weapons of mass distraction.

Brief seismological news –  Iranian Cleric Hojatoleslam Kazem Sedighi blames earthquakes on exposed flesh – he recently decreed that:

“Many women who do not dress modestly … lead young men astray, corrupt their chastity and spread adultery in society, which increases earthquakes,”

Now, other than the fact that this is about as likely as Deepak Chopra causing an earthquake via the power of meditation, this is clearly a rather misogynistic assertion.  This has rightly ticked off many people, but a couple of skeptical ladies, Jen McCreight & Rebecca Watson, have taken his comments to heart, and lo! The scientific experiment that is Boobquake is born.

  • Hypothesis: Exposed female flesh causes earthquakes.
  • Methods: Get as many ladies as possible to wear something revealing on a given day & monitor for seismic activity.
  • If we get increased seismic activity on that day – Boobs cause earthquakes. Got that?

Given that various geological organisations constantly monitor seismic activity – that part of the experiment is taken care of. So how do you get lots of people involved? Why, Facebook of course! At the time of writing, the facebook event for “boobquake” has over 16,000 confirmed guests. About six hours ago it was only 10,000.

So boobquake is go.

However, a friend of mine has pointed out a potential flaw in boobquake.

The people of Iceland, what with their financial woes and their volcano, have had an inordinate amount of press attention recently. Amongst other things, they have recently (March 25) elected to ban stripping and lap dancing clubs, thus preventing women from dressing immodestly.

And on the 14th of April – Eyjafjallajökull erupts. Coincidence?

Clearly not. Whilst the earthquake god dislikes boobs, the volcano god is clearly appeased by them.

Women of the Earth – your choice is simple:

  1. Cover up, stop earthquakes, but cause volcanoes.
  2. Show some cleavage, cause earthquakes, but put a stop to volcanoes.

Choose wisely.

My favourite… Homeopathic remedy

April 17, 2010

Celebrating the end of WHAW.
(world Homeopathy awareness week, of course)

You may not be aware of it, but we have just survived world homeopathy awareness week (WHAW), the amazing non-event that was marked by ever-so-slightly elevated levels of pro-homeo spam on twitter, and a plethora of pithy science blogs that carefully pointed out that there was no evidence that homeopathy works, or indeed, how it might conceivably work. This was topped off by a Dilbert cartoon that handily lampooned both homeopathy and astrology.


Homeopaths might want take note of the current plight of UK chiropractors – who this week, finally folded in their attempts to sue Simon Singh for libel. In suing Simon Singh, the British Chiropractic Association (BCA) stuck their collective heads above the parapet of public ignorance/apathy, and were struck down by a combination of artillery fire from organisations like Index on Censorship, English Pen and the “Keep libel laws out of science” campaign, and some precision snipping from science/skeptical bloggers such as Zeno and Simon Perry. As a result of all this:

  1. the libel laws look set to change,
  2. the BCA lost,
  3. the BCA will be paying a proportion Simon Singh’s costs.
  4. ~25% of all chiropractors are currently under investigation for making unsubstantiated claims on their websites

Given this, one would hope that other “unreality enthusiasts” (© Dr_Aust_PhD) might keep their heads down for a while – but oh no. Not the homeopaths. Despite the 1023 campaign drawing attention to homeopathy, and STFC report into homeopathy concluding that homeopathy is not deserving of NHS funding, the homeopaths continue to draw attention to themselves – by having an “awareness week”.

Of all the “remedies” that homeopaths use1, from the light of Venus, to fragments of the Berlin wall, Natrum Mur has to be one of the most ridiculous, from a scientific point of view. According to this webpage, Natrum Mur is used for:

Homeopaths give this remedy for emotional problems, such as anxiety and depression, that are caused by suppressed grief and other emotions.

Natrum mur. is also used to treat conditions with a watery discharge, such as colds, and phlegm or profuse, clear mucus. Complaints that are generally worse with heat and that are often brought on by stuffy heat or exposure to hot sun are helped by this remedy. These include: migraines with zigzag lines in front of the eyes; eyestrain with aching eyes; headaches that come on after menstruation; and cold sores.

It is also good for mouth problems, for example, gingivitis (inflamed gums), dry, cracked lips, mouth ulcers, and bad breath (halitosis).

Skin complaints, for example, warts, dry cuticles, hangnails, boils, and painful acne are helped by Natrum mur. It is also effective for goiter; anemia; indigestion; constipation with dry, hard stools; bleeding anal fissures; backache; and delayed urine flow.

In women, Natrum mur. is given for absent menstruation induced by shock or grief; irregular menstruation; and a general feeling of being unwell both before and after menstruation. It is also good for a dry or sore vagina, vaginal discharge, and vaginismus (vaginal pain during sexual intercourse).

When ill, people who need this remedy are chilly but dislike heat.

Clearly a highly potent remedy with a wide range of clinical applications. *cough*

But what, I hear you ask, is was in Natrum Mur? It is some exotic herb, a distillation of fermented sheep eyes? No.

It’s table salt. Sodium chloride. The same stuff you put on your chips. The main flavouring in “ready salted” crisps. Salt.

Incidentally, the first crystal structure ever determined was NaCl, which earned Sir W.H. Bragg and his son Sir W.L. Bragg the Nobel prize for physics in 1915.

Salt is an important part of our diet, but problems generally stem from having too much of the stuff. The food standard agency recommend that an adult eat no more that 6g of salt per day. Aficionados of Avogadro’s constant will be able to tell you that this is 6/(22.99+35.453) X 6×1023 = 6.15×1022 molecules of salt – which is “some” salt.

More than “some” salt may cause you problems – hypertension, cardiovascular disease, renal stones, osteoporosis, stomach cancer to name but a few. Now, given that homeopaths follow the law of similars, which states that “like cures like,” one might expect these diseases/pathologies would be the same that homeopaths might claim to cure with Natrum Mur. Curiously, these are all absent from the list.

Salt is also used to balance electrolytes in saline solutions for fluid replacement, and washing wounds with salt water has an antiseptic effect (killing bacteria by “osmotic shock“).

But then we all contain “some” salt  – according to Wikipedia (yes, I know!) the human body has about 0.15% by mass of both chlorine and sodium – this will all be present as sodium and chloride ions. However, if you could extract all this as sodium chloride from an average 70kg person, you’d end up with about 150g of salt.

So, given that we contain ~150g of salt, and we consume/excrete 6g of salt per day, how is adding the memory of salt going to make a blind bit of difference to “anxiety and depression”, “migraines with zigzag lines in front of the eyes” etc?

My favourite homeopathic remedy is Natrum Mur – because for me, it really drives home the inane, reality-deprived nature of homeopathy.

1 – of course, homeopathic remedies above a potency of 12C don’t actually contain anything.


My favourite… protein structure.

April 15, 2010

A bit of deadly but beautiful biology…

Crystal structures are intricate models of great complexity and beauty. Some of them may simply just resemble 3 dimensional squiggles that happen to bring the right combination of molecular groups together in space to allow some funky chemistry to happen, or some highly specific binding event. Some other them, however, look like pieces of art…

Bacteria are scavengers – tiny little single celled organisms whose raison d’etre is to proliferate, thrive and survive. (This is also your raison d’etre, but humans have developed all sorts of clever distractions to make us think that life is something more that just an advanced way of passing genetic information from generation to generation.) In order for bacteria to do this, they need lots of  chemicals – both to metabolise for energy and to serve as building blocks for components they need to fulfil their task.

It just so happens that nature has provided bountiful supplies of those chemicals almost everywhere you look – Us.

Human (and indeed all animal) cells are essentially bags of chemicals – exactly the chemicals that are so highly prized by bacteria. Which is why the bacteria have devised many cunning ways of extracting those chemicals from the bags in which they reside – one of the more formidable weapons in the bacterial arsenal is that of the “pore forming toxin” or PFT.

Pore forming toxins do exactly what they say on the tin – they form pores in cell membrane. In the short term, these pores will lead to nutrients flowing out of the cell – where the bacteria can get hold of them. In the long term, loss of membrane integrity often leads to the death of the cell – important cellular processes stop due to lack of important chemicals, and the concomitant influx of water into the cell makes it swell uncontrollably and burst – even more goodies for the bug to get hold of!

PFTs are interesting proteins to work with – partly because they are schizophrenic. They have a happy and often easy to handle soluble form, where then generally exist as single molecules (monomers) and act as normal soluble proteins. Then they have a hydrophobic (water “hating”) pore form, where they exist as large complexes (multiple proteins join together) to form the active pore. The pore mode is generally a pain in the backside to work with, as they aggregate and precipitate very easily. As a result of this, many crystal structures of PFT tend to capture them in the soluble state. However, there is one very notable exception to this rule.

In 1996, Song et al crystallised α-hemolysin (grr, US spelling) and managed to isolate it in the pore conformation. And it’s a beaut.

Sometimes crystal structures need months of evaluation and further experiments to determine the implications of the structure and develop a full picture of how the protein accomplishes it’s biological role.

Fig1: alpha-hemolysin's stalk is perfectly designed to span the plasma mebmrane of eukaryotes

In the case of α-hemolysin, one look is all you need – it is (hopefully) very obvious how structure relates to function.

To get a better sense of the 3D-nature of this beasty, I’ve knocked up a quick animated gif – view here (give it a while – it’s a bit jerky to start with)

7 monomers (each a different colour in the figures) come together in a ring – each monomer donates 2 -beta- hairpins – these form the ‘stalk’ that protrudes from the bottom of the structure. This stalk is hydrophobic/lipophilic, and is 2.8nm long. The cell membrane it’s designed to punch though? Made of lipids and ~2.5nm deep. So the stalk of the protein has just the right dimensions  and chemical composition to span the membrane of your cells.

Fig 2: Looking down alpha-hemolysin's pore...

In figure 1, what you can’t see is the pore – running from top to bottom of the stucture – figure 2 shows this better. It’s identical to figure 1 but rotated 90º top-towards you.

You can see that right though the middle of the structure is a hole – the pore through which the nutrients flow out, and water flows in.

The 7-fold rotational symmetry (a bit of a rarity) also adds to the curious attraction of this molecule.

Anyway – ever since I first stumbled across this structure in 2000, it’s been my favourite, even though my own attempts to replicate it failed. ( or did they? – work still in progress 😉 )

In my humble opinion, this structure is one of the best example of how the structure of a protein is related to its function, and also how well adapted bacteria are to explioting host biology.

EDIT – Since I did this, the wonderful guys at proteopedia have been in touch via the medium of twitter (@proteopedia) about using this as a basis for a page on α-hemolysin. If you’re interested, follow them on twitter and have a look around the proteopedia wiki. Good page to start with is ‘the ribosome

Homeopathic Piggy Poo – Updated.

April 11, 2010

A quick note on another homeopathy paper doing the rounds.

Before you read this, take a look at the paper, published in pro-homeo journal, Homeopathy, and then read this blog post at moteprime.org.

As noted in the moteprime piece, this paper is one of the better attempts at conducting a homeopathic RCT. The basic methodology seems pretty sound, and the conclusions are largely borne out by the reported results.

In addition to what Sean at moteprime mentions, I have a couple of remarks about this paper.

EDIT 22.09.10 – two things have been brought to my attention recently:

1) The significance of antibodies in colostrum is not widely appreciated. See 6).

2) Adam (comment 1) has pointed out that treating the piglets as individual, independent data points is not valid, as teat sharing and close proximity within a litter would accentuate the spread of scours within said litter. As a result of this the reported p-value of 0.0001 is extremely optimistic. The N number of 525 piglets is also invalid, as the data should really be taken on a sow-by-sow basis – it was the sows that were treated, after all. So in reality, N=52. The statistical power of this study is not nearly as impressive as what the authors lead the reader into believing.

(Yes – I am kicking myself that I got sucked in and missed this – If I get a chance I might do the numbers on this…)

3) Despite hypothesising that E.coli was to blame, and an E.coli nosode would cure them, no E.coli was detected in the faeces of the pigs –  suggesting that maybe another agent was to blame (Clostridia, coliform, viral infection…). Therefore the logic of using an E.coli nosode would appear to break down – but then, I suppose if one only considers symptoms and not causes…

4) Having determined that E.coli were not present in the faeces, the authors state:

Because treatment with Coli30C had worked before, and E. coli diarrhoea generally can be distinguished based on day of appearance and colour, this was not further investigated.

Coli30C (a similar homeopathy nosode remedy of E.coli) working before is not referenced at that point. It is however mentioned in the introduction: (my emphasis)

Homeopathic treatment of E. coli has been studied by Velkers and others (10) in commercial broilers. In that study, broilers were infected with E. coli and treated afterwards with an antibiotic or with different combinations of homeopathic remedies, including a nosode of Coli30C. None of the homeopathically treated groups differed significantly from the controls. In another experiment E. coli nosodes were administrated to calves suffering from scours(11).  Here, the nosode treated group did not differ significantly from the control group, but the study was underpowered, due to small numbers of diseased animals in the treatment and control group. Many experiments in the homeopathic field have failed to prove an effect of the treatment. Reasons for that could lie in the methodology of medicine testing as applied in regular medical science, which partly contradicts with the homeopathic philosophy (12).

So previous studies have clearly not shown that Coli30C works. But this must be because regular medical science “contradicts with the homeopathic philosophy” – right?

So having established that Coli30C doesn’t work, and regular medical science contradicts homeopathic philosophy, the authors go on to test homeopathic Coli30K using regular medical science.

5) Another potential source problem is that the exposure of the sows to the diarrhoea causing agent prior to or during is not measured or controlled for. It’s almost as if no consideration was made for variation in the natural immunity of the pigs.

But this isn’t tested, checked, acknowledged or controlled for… there will also genetic factors which may make pigs more/less susceptible to E.coli, but these aren’t checked for either.

6) Amounts of colostrum ingested by individual pigs also has an effect – this is mentioned in the conclusions, but not randomised/controlled for.

Antibodies raised against local pathogens (i.e. those to which the piglets are most likely to get exposed to) are passed from sow to piglet. The amount of colostrum produced by sows and imbibed by piglets is correlated with scours.

7) Birth weight of piglets is also a major risk factor, and this is not randomised/controlled in the trial.

NB) With points 5, 6 & 7 – one might expect these to have a normal distribution through-out the herd of pigs, but unless this is tested for, acknowledged or controlled, they exist as caveats for the conclusions of the paper.

Note also that the authors state – “Independent repetition on different farms with standard preventive treatment against E. coli, is required.” – a caveat which is curiously missing from many pro-homeopathy blogposts about this study.

So, in conclusion, better than many efforts, but still important questions remain unanswered.

My snoring causes M7.2 Earthquake in California.

April 9, 2010

A quick note on causality and earthquacks. (with a tip-o’the-hat to @batarista)

On Sunday the 4th of April 2010, at 3:40 in the afternoon, the residents of Baja California experienced the effects of a magnitude 7.2 earthquake. One might have assumed that this was down to plate tectonics – the North America plate moving past the Pacific plate, as indeed the US geological survey said in their earthquake summary.

However, they are wrong. It has emerged, via the medium of twitter, that this was not the case. It turns out that alt-med guru and transcendental navel-gazer Deepak Chopra has the answer. Indeed, he is the answer.

Not long after the quake he tweeted:

Had a powerful meditation just now — caused an earthquake in Southern California

It just so happened that at the same time (23:40, BST) I was sound asleep. And if my wife’s constant complaints are anything to go by, probably snoring.

Therefore I proclaim that Deepak Chopra is wrong. It was my snoring that caused the earthquack. I would like to take this opportunity to apologise to those who suffered any ill-effects as a result of this unintentional side-effect of my snoring. Sorry.

PS if Deepak Chopra disagrees with me, let him prove that he was the cause of the earthquack…