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Tags epitaxy , homeopathy , raman , spectroscopy

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Old 24th August 2007, 03:48 AM   #201
wilsontown
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Quote:
I think we need to give special, extra thanks to JJM though.
I second that...
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Old 24th August 2007, 05:42 AM   #202
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Originally Posted by Professor Yaffle View Post
Can't contribute much to this discussion (though I have enjoyed reading it) - but I found a paper which defined envelope of differences for the purposes of their usage and I wondered if you could work out a definition from that?

http://www.riskmania.com/pdsdata/AMu...tRates-ch4.pdf

Quote:
Envelope of differences: the difference
between the position’s median Mark-to-
Future value and its potential future value at
the 97.5th or 2.5th percentile at each time step.

Actually, although I find the context incomprehensible, the mention of 97.5th and 2.5th percentiles sounds as if somebody is using standard deviations in there. 2.5th to 97.5th percentiles is ± 2 standard deviations from the mean.

At a wild, semi-educated guess, this definition might simply be that the "envelope" is produced by joining up all the -2SD points below the means and the +2SD points above the means. Makes some sort of reasonable sense to me.

We know that Roy has not done this, because if he had, it would be impossible for the lines to cross. And some of them do. Also, the resulting lines would not be individual spectra at all, still less "representative" spectra. While in fact all the "representative spectra" traces are lines on the "envelope of differences" figure.

So I still think he just chose a couple of traces for each preparation and called them "envelope of differences". And also "representative spectra".

How is it possible to be this incompetent? And for the scrutineering to be this incompetent?

I mean, if you're going to obfuscate and wiggle and wave your hands like this, deliberately misrepresenting your data, why not just make the data up while you're about it? Then you could make it credible, too. And we'd actually have to try to repeat the experiment to show you'd invented the results, and you could just accuse us of being rubbish at doing the experiment, and we'd be here till Kingdom Come.

It's beyond me.

Rolfe.
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Old 24th August 2007, 08:23 AM   #203
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Rolfe has exceeded their stored private messages quota and can not accept further messages until they clear some space.
Heads up!
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Old 24th August 2007, 09:10 AM   #204
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Fixed.

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Old 27th August 2007, 03:30 PM   #205
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OK, just for the record, here's the actual text that went in the envelope with the stamp stuck on it. It's not much changed from the draft above.

Wilsontown - do you think the people over at Bad Science would like to see it? I'd post it myself, but I never managed to register there and it's a while since the site has accepted unregistered comments.

Quote:
27th August 2007.

Dr. Peter Fisher,
Editor, Homeopathy,
The Royal London Homoeopathic Hospital,
60 Great Ormond Street,
London, WC1N 3HR.

Dear Sir,

We wish to draw to your attention serious anomalies and incongruities in the UV absorption data presented in the paper by Rao et al., published in your July 2007 issue [1].

In a study of this nature, which in effect is examining multiple samples of ethanol, the over-riding concern must be absolute uniformity in the source of the solvent. For the data to be valid, it is essential that every drop of ethanol used must be sourced from the same stock bottle. However, the authors fail to make any mention of this point, and it is clear from the results presented that the source of ethanol in this investigation was most certainly not uniform.

The most striking anomaly is the UV spectrum presented for "plain ethanol", a single trace repeated three times in figure 3. The provenance of this sample is not recorded. This trace reveals extremely high absorbance (greater than 0.8 absorbance units) at 250nm, falling off steeply towards 400nm but still above 0.4 units by 350nm, and demonstrating an absorbance peak of 0.65 units with a l-max of about 330nm. It is simply impossible to represent this trace as being ethanol of any recognised degree of purity. Spectroscopic grade ethanol has an absorbance of less than 0.05 units between 250 and 400nm [2], and even USP/NF pharmaceutical grade ethanol has an absorbance of less than 0.3 units at 250nm, falling off to less than 0.1 units by 270nm [3]. If the substance measured by the authors as "plain ethanol" was indeed ethanol at all, it is clear that it contained extremely high levels of impurities, possibly including acetone.

In contrast, the spectra of the samples which were diluted and succussed (Nat mur, Nux vomica and the "succussed ethanol" with no mother tincture), and which were presumably all supplied by Hahnemann Laboratories as detailed on page 178, demonstrate substantially lower levels of impurities. While still not being spectroscopic grade ethanol, these samples could well represent ordinary pharmaceutical grade ethanol. The authors claim these samples are "different", however the evidence presented for this is weak to nonexistent.

Figure 1 presents one trace each for Nat mur and Nux vomica, each at 6C, 12C and 30C potencies. The traces are said to be "representative", however with no information on repeatability or how the "representative" traces were selected, it is impossible to say whether there is any real difference between any of the six spectra.

Figure 2 purports to address this point, but then fails to present the necessary data. The legend declares that 10 samples of each of the six remedy preparations were analysed. The accepted way to present such data would be as mean absorbance ± standard deviation for each wavelength point, or at least for a representative selection of wavelength points. Statistical analysis could then be used to demonstrate whether or not there was a real difference between any of the remedies or potencies. However, the authors have instead chosen to present only two traces for each preparation, as "envelopes of differences". The derivation of these traces is not explained, although we surmise that "extreme" high and low traces for each preparation were chosen to provide an impression of the range of results obtained. This is not an appropriate method of handling data of this nature, as most of the information is lost and statistical analysis is rendered impossible.

A further difficulty with figure 2 is that the upper (open circles) trace in the top graph of fig 2a (30C Nat mur) appears to be a duplicate of the upper (filled circles) trace in the top graph of fig 2b (30C Nux vom). Comparison with other traces of the two remedies indicates that this trace is really one of Nux vom, which has been duplicated into the Nat mur graph in error.

Paucity of data, ambiguity of presentation and lack of statistical analysis prevent any conclusions being drawn from the information in figure 2.
Comparison of figure 2 with figure 1 reveals that all six traces presented in figure 1 are taken from figure 2, in each case the filled-circles traces. If indeed the traces in figure 2 represent the extreme range of results obtained, this is startling, as the traces in figure 1 are stated to be "representative". In addition, while it does appear that the Nux vom samples tended to demonstrate higher absorbances than the Nat mur samples (excluding the obvious mistake noted above), in two out of the three potencies the higher Nux vom trace from fig 2 has been chosen for inclusion in fig 1, thus exaggerating the apparent difference.

Figure 3 (b and c) again repeats the same six traces as figure 1, this time grouped by remedy. Presented in this way, it is clear that there is absolutely no difference between the three potencies of Nat mur, and that while variation between the Nux vom potencies is a little more pronounced, again all three appear to come from the same population. The same is true of the three potencies of "succussed ethanol" presented in fig 3a.

On simple visual inspection it does appear that there may be genuine differences between the three remedies (although no statistics are presented to allow this to be tested), with the Nat mur showing the lowest absorbtion and the Nux vom the highest, with the succussed ethanol lying somewhere between. Nevertheless, these differences are entirely consistent with small differences in purity of the ethanol stock used for preparation of the three remedies - small, that is, relative to the very high level of impurity evident in the "plain ethanol" sample presented alongside. This degree of variation in UV absorbance is entirely to be expected between different batches of pharmaceutical grade ethanol, which is not prepared with spectroscopic analysis in mind. The authors make no mention of having stipulated to Hahnemann Laboratories that all material sent to them should be prepared from the same stock bottle, and the data presented indicate that the different remedies, possibly prepared at different times, simply came from different bottles of ethanol.

We hope you will agree that these are very serious points, and it is regrettable they were not identified by your own scrutineering process. It is clear that the data presented are wholly inadequate to support the authors’ assertion that UV spectroscopy can differentiate between the two remedies, and between different potencies of the remedies. If the authors wish to test their assertion so that it can be substantiated it will be necessary to repeat the work from the beginning, ensuring that all samples used in the study are sourced from the same bottle of stock solvent, that all duplicate preparations for precision assessment are separately prepared de novo from the mother tinctures, and that sufficient data are generated to allow robust and valid statistical analysis of the results.

Yours faithfully,

Rolfe
JJM
Wilsontown
Pipirr

References:
1. Rao, M. L., Roy, R., Bell, I. R. & Hoover, R. (2007) The defining role of structure (including epitaxy) in the plausibility of homeopathy. Homeopathy 96, 175-182.
2. Sigma Aldrich catalogue, ACS spectrophotometric grade ethanol 95.0%, at www.sigmaaldrich.com/catalog/search/ProductDetail/SIAL/493511
3. Sigma Aldrich catalogue, USP/NF grade ethanol 190 proof, at www.sigmaaldrich.com/catalog/search/ProductDetail/ALDRICH/493538

Rolfe.
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Old 27th August 2007, 04:39 PM   #206
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Thanks, Rolfe, a job really well-done.
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Old 27th August 2007, 11:51 PM   #207
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I can post it for you, if you like, Rolfe. Do you want it in the blog (under the appropriate paper discussion), or in the forums, or both?
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Old 28th August 2007, 01:14 AM   #208
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I was thinking about the "journal club" part of the blog, under the discussion of the paper. Someone else had some interesting (and scathing) comments on the Raman spectroscopy there too. But wherever you think it's most appropriate, really.

Rolfe.
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Old 28th August 2007, 02:39 AM   #209
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Rolfe:

Again, congratulations on a job very well done. It will be very interesting to see what happens next...
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Old 28th August 2007, 03:01 AM   #210
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Originally Posted by Rolfe View Post
I was thinking about the "journal club" part of the blog, under the discussion of the paper. Someone else had some interesting (and scathing) comments on the Raman spectroscopy there too. But wherever you think it's most appropriate, really.

Rolfe.
I've posted it to the journal club.

http://www.badscience.net/?p=496#comment-16370
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Old 28th August 2007, 03:03 AM   #211
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Originally Posted by wilsontown View Post
Rolfe:

Again, congratulations on a job very well done. It will be very interesting to see what happens next...

If anything....

I've still to drop a copy off to Elsevier - I haven't written the "more in sorrow than in anger" covering letter yet. Tonight.

I don't suppose anyone will take a blind bit of notice. They don't want to test their hypotheses, all they want is "publications in a peer-reviewed journal" they can point to and say, look, there's real science behind this nonsense. This paper fulfils that need perfectly, and I imagine has been written for precisely that purpose.

However, at least we can say we've done our bit, and gone through the proper channels to draw attention to the abysmal academic standards of the thing.

Rolfe.
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Old 28th August 2007, 03:05 AM   #212
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Originally Posted by Professor Yaffle View Post
I've posted it to the journal club.

http://www.badscience.net/?p=496#comment-16370

Thanks a lot. I see the lambda character has come out as a lower-case l, but I imagine the intent is clear enough.

Rolfe.
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Old 28th August 2007, 04:09 AM   #213
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I don't suppose anyone will take a blind bit of notice.
You may well be right, but that in itself would tell us something about the standards employed at Homeopathy. Perhaps not anything we don't already know, admittedly.

As a suggestion: Rather than sending it to Peter Fisher as a letter, it might be worth submitting it to Homeopathy as an article, entitled 'Comment on “The defining role of structure (including epitaxy) in the plausibility of homeopathy”'. Then they would surely have to find an excuse not to publish it, which should be at least entertaining. The downside would be that Rao et al. would normally get a chance to respond, which would probably just further muddy the water.
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Old 28th August 2007, 04:53 AM   #214
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Ah well, it's in the hands of the postman now. But that doesn't mean we can't re-submit it in the form you suggest if he ignores the letter.

Hey, anyone know what happened to typondis? He she or it is now showing up as a "guest", and has not posted since about 5th August. The "guest" designation on H'pathy Forums usually means you've been banned, but not here as far as I know, and I see no record of any disciplinary action taken against this poster.

Rolfe.
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Old 28th August 2007, 01:26 PM   #215
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Originally Posted by Rolfe View Post
Hey, anyone know what happened to typondis? He she or it is now showing up as a "guest", and has not posted since about 5th August. The "guest" designation on H'pathy Forums usually means you've been banned, but not here as far as I know, and I see no record of any disciplinary action taken against this poster.

IIRC, Kumar asked to be voluntarily de-registered, and he shows up as a "guest".
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Old 28th August 2007, 02:58 PM   #216
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Originally Posted by Mojo View Post
IIRC, Kumar asked to be voluntarily de-registered, and he shows up as a "guest".

Hmmm. Joined 2nd August, made 19 posts, last post 5th August. Hardly seems worth it, does it?

And he accused me of being touchy!

Rolfe.
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Old 14th September 2007, 02:32 AM   #217
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Thought people might be interested to see this, over at Bad Science:

http://www.badscience.net/?p=528

I take it there's been no word from Peter Fisher as yet?
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Old 14th September 2007, 03:18 AM   #218
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Oh, that's good! So Peter may be getting some more correspondence? I've heard not a syllable about our letter, needless to say.

Rolfe.
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Old 14th September 2007, 05:53 AM   #219
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I just posted a copy of the letter on Philip Ball's blog. Seemed appropriate since Peter Fisher had already commented there. Maybe he should attend to his correspondence instead of adding comments to blogs?

Rolfe.
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Old 14th September 2007, 05:53 AM   #220
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Bringing up Rustum Roy, he's been in the news again for salt water fuels

http://www.ctv.ca/servlet/ArticleNew...0911/20070911/

Has this been discussed elsewhere? And do his findings have any merit to them WRT salt water? (I now have a very biased impression of his work after reading through these forums)

ETA : *I know this doesn't have to do with homeopathy, but it does seem to be another bomb that RR has dropped on us lately...
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Old 14th September 2007, 06:10 AM   #221
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Not on Rustum Roy's stuff, but I put together some brief comments on Martin Chaplin's paper in the same issue of Homeopathy. Might submit them for publication. Any comments welcome:

Martin F. Chaplin presents an interesting overview on the structure of water1. Disappointingly, though, it seems to contain no useful evidence of a ‘water memory’ effect that would be relevant to the efficacy or otherwise of homeopathic treatments. As is well known, the chance of a 12c dilution (a dilution factor of 1x1024) containing a single molecule of the ‘mother tincture’ used to prepare the remedy is on the order of 1 in 2 billion. So homeopaths require that water (or water/ethanol mixtures) somehow structurally ‘remember’ the mother tincture, and it is this structure that is responsible for any effect of homeopathic preparations. But Chaplin1 appears to be talking about an entirely different effect when he states that “If there is evidence that the history of a sample of water affects its properties, then the ‘memory of water’ concept is proven without the need for a rationale for its action” (p. 146). This apparently broad interpretation explains some of the examples given as “Evidence for the memory of water”, which otherwise appear to have little to do with homeopathic remedies, where the mother tincture must continue to influence water structure even when absent.

For example, Chaplin1 (p. 146) states that “human taste is quite capable of telling the difference between two glasses of water, processed in different ways (eg one fresh and one undrunk for several days)”. There is nothing mysterious about this. It is a result of impurities in the atmosphere (atmospheric gases, particulates, dead skin cells, etc.) becoming dissolved or suspended in the water. This appears to have nothing to do with how a mother tincture diluted out of existence has any effect on water structure. In the homeopathic context, what would be really interesting is if it were possible to taste the difference, say, between two 30c dilutions made from different mother tinctures prepared under identical conditions. Chaplin also refers to the Vybíral and Voráček paper in the special issue of Homeopathy2, stating that the authors “have shown that water changes its properties with time and its previous history”1 (p. 146). There is no doubt that this is an interesting paper, but the authors specifically conclude that their results are a consequence of ions dissolved in the water, as the effect they observe is not present when deionised water is used. Again, it is unclear how this is relevant to cases where mother tinctures are diluted out of existence. What Chaplin seems to be talking about in his paper is how impurities might affect water structure, as illustrated when he states “The water used for dilution is not pure relative to the putative concentration of the ‘active’ ingredient, with even the purest water considered grossly contaminated compared with the theoretical homeopathic dilution levels. This contamination may well have a major influence, and itself be influenced by the structuring in the water it encounters”1 (p. 148). Since the concentration of the mother tincture will always be dwarfed by the concentration of impurities, it is difficult to see why the mother tincture should have an effect more important than the impurities on the water structure. Homeopathic remedies are not ‘just water’: they will contain significant amounts of impurities. But how this would make them different from any sample of water is not clear.

I am in agreement with Chaplin when he states that “simply proving that water does have a memory does not prove that homeopathic medicines work”. The best evidence as to whether homeopathic medicines work or not is to be found in randomised placebo-controlled trials of the medicines. A recent meta-analysis3 has demonstrated that the best-conducted trials show no effect for homeopathic remedies beyond placebo. The structure of water is certainly a fascinating subject, but, in terms of an explanation for homeopathy, it is not relevant as all the best evidence shows that there is nothing to explain.

1. Chaplin, M.F. The memory of water: an overview. Homeopathy 2007; 96: 143-150

2. Vybíral, B. and Voráček, P. Long term structural effects in water: autothixotropy of water and its hysteresis. Homeopathy 2007; 96: 183–188.

3. Shang, A., Huwiler-Müntener, K., Nartey, L., Jüni, P., Dörig, S., Sterne, J.A.C., Pewsner, D., Egger, M. Are the clinical effects of homoeopathy placebo effects? Comparitive study of placebo-controlled trials of homoeopathy and allopathy. Lancet 2005; 366: 726-732.
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Old 14th September 2007, 07:13 AM   #222
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I would tend to lay off the reference to Shang. It's a red rag to a bull, with homoeopaths. The entire thrust of that issue seems to be, the hell with whether or not there is any therapeutic effect, let's just look at whether the remedies could have any odd properties. I'd frame any criticism within those parameters.

The thing I've never been able to get any of them to take on board is, if there really was a genuine effect there, who would be most interested? Medical types would be quite interested, sure, but that's nothing to the attention they'd get from physicists and chemists. Basic sciences would be falling over themselves to be the first to characterise the phenomenon and get the Nobel Prize.

Instead, all we have is this small handful of kooks and weirdos, who can't produce work good enough to get published in any non-woo journal. Conclusions?

Rolfe.
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Old 14th September 2007, 07:20 AM   #223
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Rolfe:

You're right, of course. I'm in two minds as to whether to include the Shang reference myself. The main reason why I think it would be worth including is that the work is published in Homeopathy, so if it's entirely irrelevant to homeopathy, what's it doing there? The point is that water is pretty cool stuff, but if you want to use it to explain homeopathy, there isn't actually anything to explain. You're howling at the moon. I appreciate that Shang et al. hasn't made the homeopaths admit defeat yet, so my bringing it up is unlikely to make much difference.

Quote:
Conclusions?
Indeed...
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Old 14th September 2007, 07:23 AM   #224
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Oh, and good job on posting the letter at Philip Ball's blog. That's a good place for it to be.
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Old 14th September 2007, 09:17 AM   #225
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Originally Posted by Baron Samedi View Post
Bringing up Rustum Roy, he's been in the news again for salt water fuels

http://www.ctv.ca/servlet/ArticleNew...0911/20070911/

Has this been discussed elsewhere? And do his findings have any merit to them WRT salt water? (I now have a very biased impression of his work after reading through these forums)

ETA : *I know this doesn't have to do with homeopathy, but it does seem to be another bomb that RR has dropped on us lately...

I have no ideaTM.

I think you should start another thread on this, it's quite intriguing.

Rolfe.
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Old 14th September 2007, 09:24 AM   #226
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Originally Posted by Baron Samedi View Post
Bringing up Rustum Roy, he's been in the news again for salt water fuels

http://www.ctv.ca/servlet/ArticleNew...0911/20070911/

Has this been discussed elsewhere? And do his findings have any merit to them WRT salt water? (I now have a very biased impression of his work after reading through these forums)

ETA : *I know this doesn't have to do with homeopathy, but it does seem to be another bomb that RR has dropped on us lately...
This is quite beyond the pale. It is one thing to be incompetent at research in an area that is new to him; but he has no excuse not to know the thermodynamics.

RR has always been a loose cannon. Tenty-five years ago, when complaints about cuts in Federal research funding were rising, he called us "welfare queens in white coats." Of course, the money he got was not "welfare." [Note, I think welfare is called "the dole" in the UK. Also, Mythical "welfare queens" were women who had lots of kids in order to get more welfare to support their "lavish lifestyles."]
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Old 14th September 2007, 09:29 AM   #227
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The salt water... thing is being discussed here:

http://forums.randi.org/showthread.php?t=92954
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Old 14th September 2007, 09:39 AM   #228
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Ah, found the right thread

http://forums.randi.org/showthread.php?t=92954

However, I will say this here. According to the recent story, RR states,

Quote:
The discovery is "the most remarkable in water science in 100 years," Roy said.
I thought that this thread was the most amazing thing in water science ever... *ponders*

ETA - darn my slow typing skills... thanks Pipirr!
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Old 23rd October 2007, 07:07 AM   #229
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Folks, time for an update on the Rao et al. paper.

In the latest edition of Homeopathy, Rao et al. publish an erratum.

I reproduce it in full, here, and for added excitement, behind a spoiler tag:


ERRATUM

Erratum to: Rao ML, Roy R, Bell IR, Hoover R. The defining role of structure (including epitaxy) in the plausibility of homeopathy.
Homeopathy 96 (2007):175–182

We regret that incorrect details were given for Reference 22 of the above paper. The correct reference details are as follows:

22. Rao ML, Roy R, Bell I. Characterization of the structure of ultra dilute sols with remarkable biological properties. Mater Lett. (in press).


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Old 23rd October 2007, 07:38 AM   #230
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Have you had any reply to the letter y'all sent to the editors of Homeopathy? If not, have you considered trying to take it to a different audience? It was too good to go to waste.

Linda
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Old 23rd October 2007, 09:03 AM   #231
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I'll wager that this is wholly non-reproducible...
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Old 23rd October 2007, 10:11 AM   #232
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Originally Posted by Pipirr View Post
Folks, time for an update on the Rao et al. paper.

In the latest edition of Homeopathy, Rao et al. publish an erratum.

I reproduce it in full, here, and for added excitement, behind a spoiler tag:


ERRATUM

Erratum to: Rao ML, Roy R, Bell IR, Hoover R. The defining role of structure (including epitaxy) in the plausibility of homeopathy.
Homeopathy 96 (2007):175–182

We regret that incorrect details were given for Reference 22 of the above paper. The correct reference details are as follows:

22. Rao ML, Roy R, Bell I. Characterization of the structure of ultra dilute sols with remarkable biological properties. Mater Lett. (in press).



If only that was the only error....

I thought maybe they'd at least realised about the error in the figure that we pointed out, if nothing else.

I've spread the letter as far over the Net as I reasonably can. Wilsontown submitted it electronically as a letter to the editor, to complement my reliance on postage stamps.

What else could we try?

Rolfe.
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Old 23rd October 2007, 10:48 AM   #233
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Originally Posted by Rolfe View Post
I've spread the letter as far over the Net as I reasonably can. Wilsontown submitted it electronically as a letter to the editor, to complement my reliance on postage stamps.
Ah, I see. I thought you had held off on spreading it around until you heard from them (don't know why I thought that).

Quote:
What else could we try?

Rolfe.
Did you send it to Randi?

Linda
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Old 23rd October 2007, 11:44 AM   #234
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See if it's wanted over at BadScience, Improbable Science (David Colquhoun), Swift, Respectful Insolence, etc. etc...?
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Old 23rd October 2007, 01:09 PM   #235
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See http://www.badscience.net/?p=528 and http://www.badscience.net//?p=496#comment-16370
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Old 12th November 2007, 05:04 AM   #236
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Folks:

According to the fancy Elsevier electronic submissions website, the status of the letter is "Decision in Process". I'll keep you all posted as to what actually happens to it.

It is a journal submission (even if to a pseudojournal), and these always take a long time to process, to be fair.
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Old 13th November 2007, 03:03 AM   #237
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This very morning I was told that the letter has been accepted for publication in Homeopathy. It won't actually appear until the January issue, but they have actually accepted it.

Cool, eh? Wonder what the response of the authors will be?
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Old 13th November 2007, 04:01 AM   #238
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Originally Posted by wilsontown View Post
This very morning I was told that the letter has been accepted for publication in Homeopathy. It won't actually appear until the January issue, but they have actually accepted it.

Cool, eh? Wonder what the response of the authors will be?
Good work.
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Old 13th November 2007, 05:38 AM   #239
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Originally Posted by wilsontown View Post
Cool, eh? Wonder what the response of the authors will be?
I don't know what Rao et al. will think of this, but I hope that they do respond to it.

What an interesting development
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Old 13th November 2007, 08:37 AM   #240
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In our letter (Post #205, this thread) we mention the possible presence of acetone in the "pure ethanol" spectrum. The reason for that guess comes from the absorbance peak at 324 nm, and the fact that acetone-denatured alcohol is a common solvent. It is called Specially Denatured Alcohol 23A. You can see some literature on it by googling "sda 23a". Although I have not found a UV-Vis spectrum for SDA 23A, this liquid does not appear even to be pure SDA because there is still too much absorption on either side of the 324nm peak.
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