Why should I make the data available to you

[BPSDB] In many comments on the CRU hack I’ve seen it alleged that Professor Phil Jones of the University of East Anglia Climate Research Unit denied his data to another researcher with the words, “Why should I make the data available to you, when your aim is to try and find something wrong with it?”

Whenever I’ve seen it quoted, it’s implied that  Jones made the comment in one of the emails. I finally got around to looking for it, in the file FOIA.zip I downloaded soon after the hack was made public – and it ain’t there. Not perhaps surprising, as it really doesn’t sound like the sort of thing an academic would say, except jokingly or sarcastically.

Indeed, the words are there. In August 2007, a fellow researcher warns Jones that the words are being attributed to him by someone else. In October 2009, another colleague sends Jones a copy of the text of an article in the National Review of 23 September 2009. In this Patrick Michaels quotes Warwick Hughes as alleging that Phil Jones said, “We have 25 years or so invested in the work. Why should I make the data available to you, when your aim is to try and find something wrong with it?”.

So it doesn’t appear to be evidence that Jones actually wrote it.  Given the unreliability and political commitment of all the links in this chain, and that this was one of the main pieces of evidence for the supposed ‘conspiracy’, I think there is even less evidence of wrong-doing.

Conspiracy theories have a tendency to spawn new conspiracies: here’s a climate ‘sceptic’ who thinks the CRU staff may have leaked the emails themselves to make ‘sceptics’ look stupid. If so, they’ve succeeded.

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Fake medicine and AIDS denial are ‘charitable’

[BPSDB] Richard Wilson wrote this about a registered charity that is actively promoting AIDS denial.

This reminded me that, last year, I wrote to the same Charity Commission to complain about Frontline Homeopathy, which collects funds to promote homeopathy as “as an effective, low cost primary health care system” in developing countries. I got this reply. The Commission’s criterion is ‘charitable’, which apparently has nothing to do with ‘true’ or ‘effective’.

Thank you for your request.

The Commission’s policy on registering charities who pursue practices which constitute alternative and complimentary medicine was made following our Decision on the application for registered charity status from the National Federation of Spiritual Healers. Please see the link below for more details (you may need to scroll down to see the specific case and our findings).

www.charitycommission.gov.uk/tcc/issueguidesum.asp

I trust you will find this useful.

Perhaps this is matter for another campaign by bloggers?

“Deep Waters Trust” out of its depth

Darwin in Shrewsbury [BPSDB] You might think that if creationists want to criticise the theory of evolution by natural selection, as understood and used by the overwhelming majority of biologists, then they would try to understand the theory. Especially as the series of meetings in Shrewsbury, Darwin’s birthplace, was billed as “an assessment of the evidence for design which has emerged through the advances in science since publication of his [Darwin’s] On the Origin of Species in 1859”.

I have already commented on the fact that there didn’t appear to be any books explaining evolution on the bookstall at the Meyer meeting. Perhaps the organisers were afraid that if they understood evolution they may come to be convinced by it.

That the Shrewsbury Deep Waters Trust misunderstands the theory is clear from the press release put out before the meeting. Obviously, to understand the theory properly, and how it agrees with the evidence, you need to read a lot more than I can write here.

1. Because we are based in his birthplace we see a need for a different approach to Darwin from the extreme positions of devotion and hostility that are commonly adopted: while we don”t accept the conclusions of modern neo-Darwinians about evolution we respect Charles Darwin himself – both for his theory of Natural Selection and for his honesty in acknowledging the possibility that evolution might be proved false. There is evidence in his writings and those of his contemporaries that shows where he believed his theories were in need of confirmation by future research.

Scientists are not “devoted” to Darwin, although admittedly there appears to be a lot of hostility to him in some quarters. The commemoration honours a great scientist – but scientist is the word.  All scientists expect that their theories (if important) will be tested and questioned in the future. This questioning and testing is called “research”. In the case of Darwin’s theory – evolution by natural selection – the theory was vitally important and had implications over a wide range of science.  It could have been disproved by discoveries, not only in natural history and paleontology (the study of fossils) but also by discoveries in geology and astronomy and even physics. And, especially, by discoveries in the new science of genetics which was just beginning, unknown to Darwin, during his lifetime.

All this evidence has tested the theory to the maximum, and it has survived, improved, since Darwin’s day. It’s the only theory that matches the vast amount of evidence that has been collected. And it is still being tested.

2. Christians believe that God, not random mutations, is responsible for the design that underlies the world we live in. Particular recent evidence of design of which Darwin was not aware is in DNA – the genetic code: it is a language, containing information that controls the formation and operation of cells. It exists independently of the material from which the cells are made.

It may come as a surprise to the Deep Waters Trust that evolutionary scientists, even the most atheistic ones, do not believe that “random mutations” are responsible for design, or the appearance of design, in living organisms. Darwin’s insight was the selection of particular organisms by the environment – those that reproduce most successfully in the environment – enabling their genetic material to persist and become predominant. This is called “natural selection”. Darwin knew nothing about the genetic mechanism, of course, but the fact that it is consistent with evolution in all respects is one of the successes of Darwin’s theory.

3. Evolution involves progress “up” the evolutionary tree, each step requiring the addition of information to the genetic code.

No, it doesn’t! This is a serious misunderstanding. Evolution is about adaptation, not progress. The outcome of evolution, as it has happened, is that there are some complex organisms (a few of which think they rule the world), but simple organisms are just as evolved. Think of the bacteria – they live and exist much as the earliest of their kind, but they have evolved to live in all sorts of ecological niches.  There is possibly a larger mass of bacteria on the planet than of all other organisms put together. And loss of function is common in evolution – think of flightless birds.

Random processes do not produce meaningful information. Some Christians believe God used evolution to bring about his purposes, producing more complex designs progressively by stages. Others believe the DNA evidence is better interpreted as demonstrating a gradual loss of information as species change through Natural Selection. (Loss of genetic information produces greater variety in sub-species, but not the ability to change from a simpler species into a more complex one.) The ancestors of today’s species would have been fewer, more elaborate, forms containing all the genetic information from which present day life has descended.

Creationists abuse the idea of “information” and “complexity” (which seem to be interchangeable to them) by using the words in different ways so that you think they are talking about the same thing when, really, they are changing the meaning as they go along. In fact, there does not seem to be any generally accepted definition of either “information” and “complexity” that applies in understanding evolution. Dr Stephen Meyer, in his lecture, used the Shannon definition of information (as was clear from the slides he displayed). This definition specifically relates to understanding the transmission of information down a predefined communications channel. What relationship it has to evolution needs to be demonstrated. Dr Meyer’s use of it seemed to be mainly to give an apparently scientific appearance to a non-scientific argument.

4. The debate is sometimes portrayed in terms of a conflict between science and religion, where science suggests that life has evolved as a result of random processes, while religion claims God has brought it about deliberately.

Some believe both these views can be held at the same time; others that they are mutually exclusive, and that only with “blind” faith – faith despite evidence to the contrary – can one claim that both are true. We believe there is a third position that needs to be explored: the possibility that the scientific evidence is best interpreted as confirming design, not randomness.

No, as I said before, no scientific theory holds that life evolved purely as a result of random processes. That makes a difference.

To make ID (or creationism) scientific, what you have to do is show that it makes specific predictions about the evidence (fossils, genetic makeup of species, or whatever) that are different from (the real) theory of evolution by natural selection. And then show that the actual evidence agrees with ID (or creationism) and not with evolutionary theory. This is the challenge to the Discovery Institute or anyone else. And ID and creationism have always failed this challenge.

5. We believe there is not one debate but two: one debate about interpretations of the scientific evidence – what has come to be known as Intelligent Design versus random processes – and another between two faith positions: an originally good world which has been in decline as a consequence of human wrongdoing, or an originally simple and amoral world which has been evolving into something more complex and better.

These are both false dichotomies – a logical error. Are there really only two possible positions in each argument? I can think  of many positions in each case. I won’t bore you with mine, except to say that my position is emphatically not a “faith” position, as I would change it if any convincing contrary evidence was presented.

Stephen Meyer’s book

Dr Meyer’s book has now been published. I shall not be buying a copy, as his lecture suggested that there was nothing in it that is both significantly new and interesting. Other people, better qualified than I am to do so, will no doubt be reviewing it in time, and I shall look forward to reading their reviews.

Dr Meyer’s main theme in the lecture was a bit like the following argument. Suppose he had claimed that it was impossible to create a baby, because it is highly improbable that all the chemical components of a baby could come together in the right combinations.  We would surely argue that he is wrong, because babies are not made by the process of assembling all the chemicals at once. In fact, a baby is assembled slowly by processes in which the baby’s genes interact with his environment (including the mother’s womb and the outside environment). Similarly, the evolved biosphere is a product of continual processes of interaction between the organisms’ genetic materials and their environments.

Update

The Deep Waters Trust seems to have gone into hibernation since the event. There is no sign of the recordings promised from the February event. The aims of the charity are given as “The advancement of education in the public arena of the relationship of belief in a creator god based on the Holy Bible and scientific discovery, philosophy, theory and investigation”.

See also

Creationism in Darwin’s birthplace

Not quite so honest to Darwin (or anyone else)

More about Stephen Meyer’s lecture on Intelligent Design

Other creationists who crashed the Darwin party

Follow-up to Homeopathy Awareness Week

[BPSDB] There was no follow-up to the letter published prominently in the Guardian on 13 June 2009, on which I have commented before. I have followed this up with a letter to the paper’s Readers’ Editor. I actually wrote on two different issues, so this is an extract from the letter.

On Saturday 13 June you published prominently a letter from three physicians (Dr Lewith et al). This consisted of an unfounded claim (see http://apgaylard.wordpress.com/2009/06/15/false-positives/) about evidence for the effectiveness of homeopathy, in which the signatories appear to have a direct financial interest.

I expect that there were many letters (including my own) in rebuttal of this claim, but none appeared in the paper. It appears to me that homeopaths and their supporters get an easy ride in the paper (outside of Dr Ben Goldacre’s columns) despite the fact that it is to medicine pretty much what astrology is to astronomy.

For information, this is the public information on the involvement of the three signatories with homeopathy:

Dr George Lewith

Dr Michael Dixon

Dr Peter Fisher

They all use the weasel word “integrative” or “integrated”, which has come  to be a warning sign for serious bullshit whenever it is associated with the word “medicine”. Homeopathy is fake medicine. It imitates the protocols and procedures of medicine (but not necessarily the ethics), while the theory behind it, and the remedies themselves, are as empty of real content as the magic in the Harry Potter books.

Homeopathy Awareness Week: The facts of life

[BPSDB] Here’s a description of the process for producing a homeopathic remedy, as described on Wikipedia:

…homeopaths use a process called “dynamisation” or “potentisation” whereby the remedy is diluted with alcohol or distilled water and then vigorously shaken by ten hard strikes against an elastic body in a process called “succussion”. … During the process of potentisation, homeopaths believe that the vital energy of the diluted substance is activated and its energy released by vigorous shaking of the substance.

… A 2C dilution requires a substance to be diluted to one part in one hundred, and then some of that diluted solution diluted by a further factor of one hundred. This works out to one part of the original solution mixed into 9,999 parts (100 × 100 -1) of the diluent. A 6C dilution repeats this process six times, ending up with the original material diluted by a factor of 100-6 = 10-12. Higher dilutions follow the same pattern. In homeopathy, a solution that is more dilute is described as having a higher potency, and more dilute substances are considered by homeopaths to be stronger and deeper-acting remedies. The end product is often so diluted that it is indistinguishable from the dilutant (pure water, sugar or alcohol).

Now for some real science, what you learn in chemistry at school. A ‘mole’ of any substance – for water 1 mole is 18 grams – contains approximately 6 × 1023 molecules of the substance, that’s 6 followed by twenty-three zeros (6 × 1023 is called the Avogadro constant).

That seems an awfully large number of molecules, but if you carry out the homeopathic dilution you soon reduce the concentration of the substance to effectively nothing. Suppose you start the homeopathic preparation with about a tenth of a mole of the active ingredient in 100 ml, by the time you have a 12C remedy (diluting by 100 twelve times) there is only, on average, approximately one molecule in every 100 ml. Homeopaths typically use 30C or even 200C solutions. Once you get to those dilutions, there is absolutely no chance of finding any of the original remedy in a sample. Such a homeopathic remedy consists only of the inert basis substances (water, alcohol, sugar, chalk etc.) that are used for making the dose or pill, like the placebos that clinicians use in tests.

Kate Chatfield of the Society of Homeopaths was asked by a House of Lords Select Committee:

“Is it possible to distinguish between homeopathic drugs after they have been diluted? Is there any means of distinguishing one from the other?”

She replied:

“Only by the label.”

Exactly.

Nevertheless, homeopaths still claim that the dilution process somehow makes a “remedy” more effective, even hinting at danger if the “strong” remedies fall into untrained hands. How this happens appears to be magic, the same way magic happens in the Harry Potter books. A few more scientifically-minded homeopaths have tried to come up with a pseudoscientific explanation called “memory of water”, but they have yet to put even a proper theory to this name, let alone find any evidence that it exists.

For the sake of argument, let’s just assume that the homeopaths are right, and that succussion does turn the material that you started with into an effective “remedy”. By the homeopathic “principle” that “like cures like”, the homeopathic solution should produce the symptoms of the disease that the “remedy” is used to treat.

In practice, even the very purest available water contains parts per trillion or parts per billion of numerous impurities. These chemical substances are in the water because the world we live in is made out of chemicals (they are not necessarily man-made pollution). Typical impurities would be common ions like sodium, chloride (that is, salt), calcium, magnesium,  iron and sulphate. There are likely tens of thousands of impurities in the form of molecules and ions at this level or lower. We don’t expect homeopathic “remedies” to be prepared with water this pure, which is expensive water used for chemical analysis and other experiments in labs requiring high accuracy. We happily drink water with higher levels of impurities than this – at those levels they have no significant affect on the human body.

So, even if a homeopathic “remedy” is prepared with the very purest available water, there may still be something like 1012 (1,000,000,000,000) molecules each of numerous impurities in a 30C or a 200C remedy and this level cannot be reduced. Of those molecules, some molecules of each impurity have been through the whole dilution/succussion cycle, so the impurities have been “potentised” too. So a homeopathic “remedy” ought actually to deliver the effect of many thousands of uncontrolled chemical substances. Fortunately it doesn’t – imagine drinking potentised Epsom salts. That’s because the whole idea of “potentising” is nonsense.

Even worse, if homeopathy were true, it would be potentially one of the most polluting industrial processes. Suppose the homeopath dilutes a commercial 6C “remedy” to 30C for a patient, each time diluting 1 ml to 100ml. Each stage generates 99ml of by-product, each more “potentised” than the next. That’s 24 × 99 ml, almost two and a half litres of stuff that supposedly will induce symptoms, and more than enough for treating the most hypochondriac of patients. It’s even worse for a 200C remedy – you would have almost 20 litres to dispose of.  How much of this strong magic water is flushed away and finds itself back in our water supply?  Fortunately, you could drink a lot of 200C and the only symptom you would get is a strong desire to pee.

The homeopathic manufacturer Helios has a catalogue that is good for a laugh. It consists mainly of lower “potencies” that your friendly local homeopath can make into “remedies” for you. Helios’s Excrementum can, for example, presumably does actually contain a small amount of dog shit. Sooner you than me. Marc Abrahams has more about this.

Yes. Be aware  of homeopathy. It’s homeopathetic nonsense.

I want to do something really dangerous

[BPSDB]There is this piece of flimflam on the web site of Neal’s Yard (the unethical selling company):

In more severe, acute situations the 200th potency (200C) may be administered once – this should not be repeated. Unless you have some knowledge and experience of Homoeopathy it is best to leave administration of 200th potency remedies to a qualified practitioner and remedies of higher potency than 200C should never be taken without first seeking the advice of a qualified homoeopath.

Surely, though, homeopaths like to claim that homeopathy is absolutely safe if done properly – the one thing that homeopaths and the reality-based community agree on?

In the real world, we know perfectly well that a properly prepared 200C homeopathic remedy is exactly the same as a 30C or 400C remedy of the same remedy or any other remedy – it contains absolutely nothing of the original substance used to prepare it. (Even if it was prepared with the purest available water, however, it will still contain trace amounts of tens of thousands of other chemical substances that pass through our bodies every day.)

I’m sure this must have been done before, but I’d be happy to take any 200C or higher “potency” remedy under controlled conditions to find out why it is a risky business as Neals Yard claims. Presumably, I should start to experience symptoms related to the remedy (under the principle of “like cures like”).

“Under controlled conditions” would mean that I wouldn’t know what remedy I was taking, but someone would have to ensure that the homeopath didn’t cheat. Perhaps this could be made more of a scientific trial by having a sufficiently large number of us, none of whom knows which is having a homeopathic remedy and which is having an inert pill or water. And the samples would be blinded before administration – in other words, the person who prepared the samples would also not know who was getting what.

Perhaps homeopaths will object to this on the ground that it would be unethical to administer a strong remedy to someone who is not sick, but I’m a willing volunteer, and will endure great danger in the cause of science…

If anyone is willing to collaborate on this, please contact me.

Added 19 June: jdc325 pointed out that there is a 2004 video of a meeting of Australian sceptics taking an overdose of homeopathic sleeping pills.  The pharmacy assistants (around 3m40s into the video) gave dumb advice which was good for a laugh.

Other creationists who crashed the Darwin party

[BPSDB]The “Shrewsbury Deep Waters Trust” were not the only creationists to take advantage of the Darwin celebrations in Shrewsbury. During March/April the Christadelphians sent leaflets throughout the town and set up a stall in the town centre advertising meetings – although they were not very efficient about it, as the leaflet came through my own door after the meetings had taken place.

The leaflet was produced by the Shrewsbury Christadelphians, although it seems likely that similar materials have been distributed elsewhere. What interested me was the quotation on the cover.

Darwin Question leaflet

Darwin Question leaflet

I asked the local Christadelphians, at their email address, for the source of the quotation, but I haven’t yet had a reply after five weeks.

I have searched on the web, where all Darwin’s writings are available, and have not been able to find it there. As far as I can tell, Darwin did not write a volume called “My life and Letters”. His son Francis put together a collection called “Life and Letters”. This contains one sentence that may be what the Christadelphians are referring to. This reads: “When we descend to details, we can prove that no one species has changed [i.e. we cannot prove that a single species has changed]; nor can we prove that the supposed changes are beneficial, which is the groundwork of the theory.”

If you do a search for the exact words, though, you will find it quoted widely on creationist websites, with the same erroneous citation. Quite likely, the Christadelphians simply lifted it from one of these. It is an example of what is often called called “quote mining” – selecting from the words of people who are perceived to be “authorities” in such a way as to change the apparent meaning in a favourable way. Creationists often use this trick to make it seem as if scientists are expressing doubt about evolutionary theory, or pointing out a problem with the theory that does not actually exist. In this case, I doubt if the Christadelphians are being consciously dishonest – it probably never occurred to them that something that is so widely quoted by their brethren could be wrong.

“Quote mining” is so prevalent that TalkOrigins, one of the best web resources on evolution, has a project devoted to it: you can find the misquotation I am referring to discussed here.

Selecting Darwin on this matter is misleading too: Darwin is not an “authority” on evolution as the Bible is an authority to Christadelphians. Darwin originated the theory of evolution of natural selection which continues to be the basis for a vast research project. Discoveries in genetics now mean that we can trace the evolutionary descent of huge numbers of species – which Darwin could not do in the state of knowledge that existed in his time.

Incidentally, the history of the Christadelphians makes interesting reading. They comprise a tiny sect that tries to uphold to an extreme the literal accuracy of the Bible. Not surprisingly, it has fractured into even tinier fragments as its members fail to agree on differences of doctrine that most of probably couldn’t even see. A probably inevitable consequence of believing that you know the absolute truth is that eventually you must believe that only you (and your followers) know the absolute truth.