Mental Indigestion

by Jim Caryl

Month: August, 2009

A cure in the toxin…

Coley [from Starnes, 1992, Nature 357: 11-12]THE year is 1892, and in a small ward of the Memorial Hospital in New York City, a male patient lies dying. He has a large sarcoma (a type of cancerous tumour) that originated on his right arm, and been feverish for 12 hours. His fever isn’t due to the cancer though – it’s a result of an infection his physician gave him. The physician’s name is William B. Coley, and he recently administered an injection of ‘Coley’s toxins’, a potent mix of bacterial toxins that may cure the man of his cancer, but equally may also kill him.

William Coley had for some time observed that his patients experienced a regression in their cancer as a result of infection with a bacterial pathogen. Indeed, Coley had read publications that supported this observation, most notably with sarcoma patients suffering from erysipelas infection – an acute skin infection caused by Streptococcus bacteria. Based on these observations Coley engaged in a system of treatment that would have modern day ethics committees in apoplexy – he set about deliberately inducing erysipelas in his cancer patients.

There was no guarantee that erysipelas would take hold, or that it wouldn’t actually kill the patient. However, by all accounts Coley achieved some definitive results that led to him to further develop his treatment. He set upon the idea of killing the Streptococcus by heat-treatment, and collecting the bacterial extract to inject into the patient – an approach akin to early forms of vaccination – however, the results weren’t so impressive. It wasn’t until he combined the extract of his heat-killed Streptococcus with extract of another heat-killed bacteria, Serratia marcescans (another common cause of wound infections) that he noted reproducible clinical successes. This toxic brew of bacteria extracts was called ‘Coley’s toxins’.

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Wordle of the month…

See what I’ve been writing about in August, though expect a Bank-Holiday post tomorrow.

Wordle of the month - August 2009


Mimicry: survival or flattery?…

This post was chosen as an Editor's Selection for ResearchBlogging.orgIF you hadn’t guessed already, I’m busy trying to write a paper at the moment. This being the case, I have managed to successfully postpone this onerous task by spending time reading other people’s papers. I’m now going to spend a little more time explaining one of them you, my lovely readers.

Many years ago, when I was a grad student, I found myself at an otherwise rather dull conference on nucleic acid research; but fortunately it was not a complete wash-out, a chance conversation with a grad student who happened to be presenting a poster on the adjacent board to mine introduced me to the world of molecular mimicry.

Hoverfly (via David Packman, what is mimicry and why is it important in the natural world? Mimicry is the imitation of one species by another, with the most well known purpose being to avoid being eaten. Most people will have encountered hoverflies, and may in the first instance have mistaken them for a wasp or a bee; from an evolutionary perspective, predators such as birds have also learnt to associate these warning (aposematic) colours with a stinging or poisonous prey, and so the Hoverfly gets to fly another day.

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Anatomy of (preparing to write) a scientific paper…

IT IS probable that most readers won’t know how much effort it takes to get the results of a scientific investigation in to press. After months and months of work, copious experiments, repetitions, frustrations, banging head against the wall, we enter the next phase – the paper. The effort of will, the to-ing and fro-ing from author to author, author to editor, author to reviewer, author to author, author to reviewer, through revisions and heartache, all so that 99.9% of the working population will never read it, never even know that it exists.

07.00 – Eager with anticipation I hit the computer. I then hit it again, and this time it starts. I’m at work and I’m using one of the institute’s computers. Last night I painstakingly arranged the four lab books I think I need, together with copious scraps of paper bearing notes and ideas for sentences, comments, discussion points. I’m ready to go.

All. I. Need. to. do. is. write. this. paper.

07.05 – [Waiting for computer] Cup of tea.

07.20 – Computer has finished loading. Quickly check emails.

13.00 – Lunchtime and all I’ve got to show for it is five open browser windows, each containing 12 tabs of web pages; an email-driven surf safari gone wrong, and haven’t written a word. Ok, quick lunch and then get down to it.

14.03 – Right: ‘Based on these observations we propose a model of incremental recognition layered specificity in the assembly of…

[Knocking at door] Lab mate: ‘Can you remind me how to use the Fluorescence spectrometer….?’

16.20 – ‘Based on these observations we propose a model of incremental recognition layered specificity in the for assembly of…

[Knocking at door] Lab mate: “Fancy a coffee?”

16.45‘Based on these observations we propose a model of layered specificity in the assembly of nucleosomal control complexes…

[Prof. walks in and sits down] Prof.: “The group in Bristol want the details of that construct we sent them, they’ve lost it, and they also want the other construct from last year, whatever it’s called, I mentioned it to them and they like the idea. I’m off shortly so could you get them away today?”

[Frantic searching through a year’s worth of meetings notes to identify what Prof means by ‘other construct’, then search archive freezer – once the lab manager has been found and the archive freezer key located. Realise that the sample was from July last year when I went on holiday, thus is poorly labelled as I was too excited to get out of the lab. Thirty minutes of cross-checking and I have the sample. Run to get items into last mail collection across campus in the mail centre.]

18.00 – ‘Based on these observations we propose a model of layered specificity incremental recognition in the assembly of nucleosomal control complexes…

[Decide to try working on a figure instead]

20.00 – Figure sorted. ‘Based on these observations we propose a model of layered specificity incremental recognition in the assembly of nucleosomal control complexes…


22.00 ‘Based on these observations we suggest that the nucleosome assembles stochastically.

[Save. Shut down computer. Walk home]

22.30 – Realise that your plan to continue writing was foiled by forgetting the crucial lab note book. It’s either another figure, or bed. Decide on bed, but worth just checking emails/news/blogs briefly on laptop.

02.30Drearily close laptop. Collapse in to bed.

[Start the whole sorry affair again tomorrow].

Like this article? Please consider submitting it to Open Lab 2009:

Open Lab 2009

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Ground-breaking research, reported by The Onion.

My take on Science Online London 2009…


Faraday lecture theatreI HAD good reasons for attending Science Online London 2009, not least of which was to meet – in person – some of the people whose blogs I’ve been reading for some time; and furthermore, how could I turn down an opportunity to spend a day at the Royal Institution of Great Britain. It is always interesting to discover the many cross-overs I shared with other delegates, shared experiences, desires and goals; in one case I found that I’d been working quite literally on top of a fellow blogger (Paolo!) at the same university for five years without once bumping in to him!

However, I am also a professional scientist, so I had a vested interest in some of the more technical discussions in the meeting; I am also passionate about science communication, thus with a varied programme covering the new media applications for science communication, it was bound to be good.

[More below the fold]

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In London…

I will get down to the task of giving my informed opinion on this weekend’s Science Online London 2009, though it has to be said I’m pretty sure I missed 30% of it; it wasn’t until mid-afternoon on Saturday that I actually capitulated and became a twitterer. I joined the live-feed, jumping in at the deep end and being swept away in a wave of information, though not the Google wave, which came later. With nary a grasp of the twitter culture, nomenclature nor software I started monitoring the virtual debate whilst also taking notes on a lecture by Dave Munger (aka 50% of Cognitive Daily) being given through the virtual venue of Second Life.

So while I get to grips with twitter, read through the notes of the conference (courtesy of The Mind Wobbles – a piece of prodigiously talented live-blogging), and read the #solo09 twitter-feed, I’ll leave you with some evidence of a different kind –

The one where Jim (finally) also becomes ‘a tourist’.

South Kensington Subway Buckingham Palace The Treasury

Bali bomb memorial The cenotaph Parade ground of the Guard House

The Thames and Houses of Parliament IMG_4467_950 The London Eye

Flat White, Berwick St, Soho Princi, Waldour St, Soho Gorgeous Princi food - yes, that is a water fountain and infinity pool behind

The Royal Institution of Great Britain The Natural History Museum The Natural History Museum (Darwin now in his rightful place at the top of the stairs)

The Minerals and Vault Prince Albert's instument exhibit, Museum of Science & Industry Deck chairs on the Serpentine, Hyde Park

Science Online London: Day n-1…

I ARRIVED in London today ahead of tomorrow’s Science Onine 2009 meeting. Having a bizarrely uneventful travelling experience, both to and within London, was a great start. London in August seems to have a special kind of heat, hot and stuffy in a way that only large cities can be, but then you descend into the lower tube lines to discover yet a new flavour of heat, slow cooked.

I remember walking through the tube tunnels as a child and being deeply flustered, owing in part to having just seen ‘An American Werewolf in London’, and we all know what happens when you encounter a Werewolf in a tube tunnel don’t we? This time however I was too occupied thinking about the pressure differentials through the tube network as I enjoyed the tremendous cooling winds as you ascend the levels. Perspectives change.

The Albert Hall today

I’m staying next to the Albert Hall at Imperial College’s Beit Hall, with the above scene (taken today) available within 1 minute of leaving my room; a pretty good location really, near Knightsbridge, and opposite Hyde Park.

I have memorised the Piccadilly Line, so it will be my linear feature for navigating London this weekend. I got myself to Piccadilly Circus, and from there to The Royal Institution, and then on to Soho where I made a bee-line for Flat White (to finally renew my love for the antipodean ‘Flattie’ coffee), and get some food at Princi, a most excellent Italian delicatessen, owned by London’s Armani of bread.

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On teaching lab skills…


I HAVE been applying for jobs in recent weeks, far and wide. The flavour of jobs that I’ve been looking at are teaching positions, some lectureships, and others senior tutor positions. One of the aspects of my jobs that I’ve enjoyed over the years is teaching people, especially teaching people how to do molecular cloning and protein biochemistry. I’ve looked after many final year project students, summer students, grad students and junior postdocs over the years, and enjoyed access to a diverse array of projects, seemingly linked by the need to clone, manipulate DNA in weird and wonderful ways and engineer protein.

Ever tried sticking a 5 nm gold nanoparticle onto a protein using an engineered cysteine? I have. Don’t ask.

As a grad student I spent many years demonstrating, which is a job that you can either throw yourself in to, or alternatively turn up, grunt a few times at the undergrads and take your money; I was of the former persuasion, though I certainly had plenty of the latter in my time as an undergrad.

It was always great fun having control of a bench of undergrads for a full year as you dragged them kicking and screaming through procedures and experiments, the like of which many of them will ever have to do again (even as research scientists). However, what sticks in my memory most of all were those times when the little darlings didn’t quite click with what they were supposed to be doing; there were sometimes truly spectacular lapses in common sense.

One incident took place during a microbiology skills practical. The class were to be learning about oil-immersion microscopy. They were told how the refraction of light through a glass sample slide prevents the use of higher resolution magnifications, but one way round this is to use oil with the same refractive index as glass. By using an oil layer between the lens and the slide, the refraction is lost and we can achieve higher magnification.

“Sir….?” (yes, they were freshers, still in ‘school-mode’)

“Jim. Yes? What’s the problem?”

“It doesn’t work, the samples are all fuzzy”

“Have you focussed them correctly?”

“The microscope won’t focus at all, it’s broken.”

“….so tell me again what you did exactly.”

It turned out they had taken oil-immersion rather literally and, having removed the high magnification lens from the microscope and filled it to the top with oil, they’d screwed the lens back onto the microscope and now had some problems.

“….! Erm, the oil goes on the top of the cover slip, on the glass slide you’re looking at, NOT in the microscope itself.”

As I said, great memories. Next time I’ll tell you about the group of lads who eagerly, and with great attention, streaked E. coli out to single colonies – directly onto the bench top (even though there were a stack of agar plates for them to use). The mind beggars.

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.