Lateral thinking…

[Promoted from my Posterous ‘Overflow‘ blog…]

LATELY I have been wresting with a particular problem in the lab. I have been trying to put a rather complex DNA molecule down on a gold surface with the aim of having it perform the same chemistry on a surface as it does in solution.

Generally, when putting DNA down on a gold surface, we synthesise our DNA with a particular chemical modification, a thiol, on one end of the DNA strand. A thiol is essentially a sulphur atom, usually together with a hydrogen (-SH), and sulphur forms a strong bond with gold, so this is we want.

Unfortunately, we live in a very oxidizing world (basically, everything rusts), so my thiol gets oxidized to a rather less useful S=O. There are numerous other atoms that can reduce my thiol too, such as other thiols, or metals such as magnesium, zinc, copper etc.

This isn’t generally a problem as an oxidized thiol can be reduced back to -SH, making it ready to react with my gold surface.

Only, it turns out that my DNA adheres to the gold at too great a density. Like a mosh pit at a concert, the poor blighters are unable to move, and this results in them being unable to perform the particular reaction that they normally manage when not constrained.

So I modify my approach and use another layer between the gold and the DNA. This layer can be used to dictate how much of the gold surface is actually available to be bound. The chemistry is quite complicated, with several steps, all of which degrade quite rapidly, so it has me running around to make sure I get all the steps completed in time.

First a layer of long floppy carbon chains go down on the gold, and the ends of these molecules are reacted with another chemical that makes them able to react with yet another chemical, this latter chemical being capable of reacting with a thiol. Phew.

I have spent more time than I care to mention trying to get this approach up and running, all the while having to deal with the fiddly, slow and rather cumbersome thiol-based chemistry, which has a propensity to rust.

Then it occurs to me. The only reason I was using a thiol on my DNA in the first place was to stick my DNA directly to a gold surface. As I’ve already determined that we can’t do this (too dense), I really don’t know why I’ve spent time running around testing numerous crosslinking agents that can link the surface to my thiol-DNA.

Time to ditch the thiol and use something that connects DIRECTLY to the first layer of floppy carbon chains.

WHO responds to Sense About Science…

EARLIER this year, Sense About Science, a charity that seeks to promote good science and evidence in public debate, submitted a letter to the World Health Organisation (WHO) asking them to clarify WHO’s position on the inappropriate use of homoeopathy for five serious diseases: HIV, TB, malaria, influenza and infant diarrhoea. The use of homoeopathy as a treatment for such conditions is inappropriate because, basically, it doesn’t work, and the promotion of homoeopathy as a preventative medicine in the developing world is immoral and unethical.

In the letter they cited current examples of homoeopathy being promoted for these diseases, which include:

  • In Kenya, the largest homeopathic supplier, the Abha Light Foundation sells homeopathic medicines for malaria, diarrhoea and influenza. It now runs 20 health centres, 25 mobile clinics and five HIV/AIDS clinics.
  • In Tanzania, Jeremy Sherr and Sigsbert Rwegasira run three homeopathic clinics and claim to have government support to establish a school of homeopathy. Rwegasira claims to treat “no less than 100 malaria patients per day.” According to Sherr’s promotional material, “conventional medicine only supplies temporary relief, often at a great cost financially, and with many severe side effects”.
  • In Ethiopia, the Amma Resonance Healing Foundation, run by Peter Chappell, offers to treat AIDS patients with “resonance healing in the form of homeopathy”, as “an ideal alternative and complement for the treatment of HIV/AIDS in developing countries” because of “the very low costs of producing the remedy” and because it has “no side effects”.
  • In Ghana, the Senya/Tamale Homeopathy Project treats malaria patients with homeopathy.
  • In Botswana, the Maun Homeopathy Project offers homeopathic treatment in several locations and mobile clinics for HIV related complaints such as herpes and diarrhoea “for those people who are HIV+ but who are not taking anti-retroviral drugs”.

Sense About Sense WHO's response

Today the WHO issued a response stating that it DOES NOT recommend the use of homoeopathy for treating HIV, TB, malaria, influenza and infant diarrhoea, with each of the departments tasked with tackling each of these five serious diseases clearly expressing WHO’s position.

Visit Sense About Science to read a briefing document about homoeopathy, so that you can better understand why it is that scientists and medics do not support its use in serious diseases.

Illiberalism in rational causes…

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

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

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

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

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

Continue reading “Illiberalism in rational causes…”

Amalgam fillings are safe…

AMALGAM, a compound of mercury with another metal, has been used for fillings for 200 years. A ScienceDaily news article says, ‘Amalgam fillings are safe, but sceptics still claim controversy’.

Speaking at the 87th General Session of the International Association for Dental Research in Miami, Dr Rod Mackert, of the Medical College of Georgia, points out that someone would need 265 – 310 amalgam fillings before even slight symptoms of mercury toxicity could be felt. The reason being that when mercury is mixed with the other metals used in fillings (silver, tin and copper), the compound produced contains no free mercury. A poison is only a poison when it is at the right dose; a fact that has been appreciated for hundreds of years. You may absorb only 1 micrograms (1/1millionth of a gram) of mercury a day from a mouthful of fillings, yet consume around 6 micrograms from food, water and air, according to the US Environmental Protection Agency.

Continue reading “Amalgam fillings are safe…”

Bad Science excerpt: The Doctor Will Sue You Now

bad-scienceBen Goldacre has released the infamous chapter that was missing from the original ‘trade’ paperback edition of his book, ‘Bad Science’. He recently posted the chapter on his Bad Science blog, under a Creative Commons license; this means ‘You are free to copy it, paste it, bake it, reprint it, read it aloud, as long as you don’t change it – including this bit – so that people know that they can find more ideas for free at www.badscience.net

I have reposted the article in full, but you can just as well read it on Ben’s blog, or hell, you could even go spend a few quid and buy his book!

This is an extract from
BAD SCIENCE by Ben Goldacre
Published by Harper Perennial 2009.

The Doctor Will Sue You Now

This chapter did not appear in the original edition of this book, because for fifteen months leading up to September 2008 the vitamin-pill entrepreneur Matthias Rath was suing me personally, and the Guardian, for libel. This strategy brought only mixed success. For all that nutritionists may fantasise in public that any critic is somehow a pawn of big pharma, in private they would do well to remember that, like many my age who work in the public sector, I don’t own a flat. The Guardian generously paid for the lawyers, and in September 2008 Rath dropped his case, which had cost in excess of £500,000 to defend. Rath has paid £220,000 already, and the rest will hopefully follow.

Continue reading “Bad Science excerpt: The Doctor Will Sue You Now”

Letter to The Guardian…

A little long, didn’t fly, but better luck next time.

[Guardian, Tuesday 31st April] Cherill Hicks article, ‘Not to be sneezed at’, gave a timely and largely useful revision of therapies available to hay fever sufferers, but tripped up by suggesting that research on homeopathic treatments was ‘encouraging’.

It is still the consensus in the scientific literature that homeopathy does not perform any better than placebo, an issue which has been addressed by a comprehensive study by Aijing Shang MD and colleagues at the University of Berne, Switzerland. The study, published in The Lancet (2005), compared 110 homeopathy trials with 110 conventional medicine trials, and found that conventional medicines work, with little evidence to say the same of homeopathic medicines.

The positive findings of a few placebo-controlled trials of homeopathic medicines are cherry picked from a mountain of contradictory results, and are generally found to result from combinations of methodological deficiencies and biased reporting. The ‘encouraging’ results for treatment of hay fever with Galphimia glauca arise from a series of studies by a single homeopathy research group, and have been given unwarranted kudos in homeopathy circles due to the publication of a meta-analysis, which is an analytical over-view of combined results from numerous methodologically similar studies.

However, the meta-analysis only consists of seven trials (included in the Lancet study by Dr Shang and colleagues), and all come from the same research group; indeed, the group leader was a co-author on the meta-analysis itself. There are insufficient data from independently reproduced studies to corroborate the positive findings for Galphimia glauca as a treatment for hay fever, thus its status as a recommendable therapy is dubious.

Attention to detail…

[ratings]

Some MOST people would describe me as being a little moderately anally retentive; I have a rather punishing attention to detail, particularly so with the way I approach experiments. Something that really annoys me is when fellow scientists display a degree of slapdashness that borders on being negligent.

Many of us are publicly funded, and one of my aims in life is to communicate science to the public. I love science, both as a system within which I do research, and as a philosophy. If I am to wax lyrical about the rationality and worth of science, and the scientific method, to the public, and use it as a basis in arguments against irrationality, pseudo-science quackery and superstition, then I damned well better practice what I preach. As such I employ the skills and techniques I have learnt in a manner that takes account of these values; I design experiments with good controls, I vary the experimental variable whilst controlling the others. I use evidence-based methodologies that have been tried and tested, thus use minimal materials to achieve my ends in the minimal possible time.

It is not always possible to do this, especially in my current area where there are no protocols for what I’m doing as it’s never been done before. None the less, I form testable hypotheses, design experiments to test them and based upon the result, either modify, scrap or move on.

In your average science lab, based upon the very large number of science labs I have been to, I would have to say that the idea of sitting down and developing a testable hypothesis that makes predictions about outcomes, then designing experiments to test these is probably not what many researchers are doing. What they are doing is ham-fisting their way through protocols given to them by more senior players, which they follow blindly, often without knowing what each step in the protocol is doing at a physical level.

Many of these protocols have been adapted, cut-down and streamlined, which is often another way of describing that short-cuts, often rather slapdash ones, have been introduced. Now there is nothing wrong with this, per se, as long as the protocol is in the hands of a capable person who knows why the protocol has been revised in this way. But, the fact is you cannot instruct a junior member of research staff with protocols that have been cut-down in this way; the full anally-retentive protocol should be provided, or sought, and the researcher allowed to refine it once they’ve identified for themselves the pros and cons of keeping each step.

Continue reading “Attention to detail…”