27 April 2010


Just a little dump of some old stuff from my previous website. Enjoy!

I have been interested for some time in the field of Bioinformatics. On this page are a few of my modest contributions to the field. They are free for use in your research - all I ask is a citation. I'm currently working on a JAVA program to store and analyse genotypic information, and to parse SNP files. Hence the name ParSNiP. It has so far been programmed by Dr Charles Philpott, but I'm hoping to add a few more tweaks before making it generally available.

CALLELE (plus associated files)

A little program I wrote to convert non-integer allele sizes (such as the output from GenoTyper) into numbered alleles for direct use in LINKAGE software. It will allow you to totally slash the time it takes to analyse your linkage data. Using CALLELE, I can get from an allele table in GenoTyper to a LOD score in about 5 seconds. Contact me by leaving a comment on this thread, and I'll send you the code. It is neither big nor clever...


Not a program, but a format for the depiction of genetic pedigree data using standard ASCII text characters.

[_] Joe Bloggs Senior
(#) | Mary Bloggs
|-[#] Joe Bloggs Junior
|-(_) Shirley Bloggs

Basically, you use a proportional font (like Courier), and turn the pedigree on its side. Use square brackets [_] for a male, round brackets (_) for a female, and greater/less than signs <_> for sex-unknown. Put an underscore between the brackets for unaffected, and whatever you want (like a hash #) for affected. Each individual has his/her own line, and in general, older people are higher up than younger people (and younger generations are further to the right). You get the general idea?

26 April 2010

It's arrived! "Should Christians Embrace Evolution?"

Amazon have finally delivered this book that I am itching to review. It is published by Inter-Varsity Press as a compilation of articles written by creationists specifically for this collection, but (oddly) with copyright held by the individuals themselves.

Essentially it is a multi=pronged hatchet job on Dr Denis Alexander's "Creation or Evolution - Do We Have to Choose?". In Alexander's book (which I have not read fully), it is argued that creationism is based on flawed science and flawed theology - the former I agree with; the latter is debatable only in the sense that all theology is flawed, theology being a discipline that starts off with a massively improbable and unprovable premise, and goes downhill from there. Alexander argues that science is at least compatible with Christianity - a point that is accepted by the large majority of Christian commentators.

But not by a small rump of die-hard science deniers who have managed to set up a reasonably successful stall for their patent snake oil within the evangelical Protestant Christian sector. Evolutionary science has been under attack from religiously-motivated creationists since the publication of "On the Origin of Species" in 1859, and despite the fact that every creationist objection has been blasted out of the water, still the perky little gadflies pop up and fire off another round of nonsense. The most recent effort in this arena has been "Intelligent Design", a propaganda (for there is precious little science or theory) effort by the Seattle based creationist outfit "The Discovery Institute" to force the non-sequitur, "life is really complex, therefore god did it". These attacks have possessed all of the breathtaking inanity (to quote Judge Jones's perfect phrase) of olde tyme creationism, but without specifically pegging their pitch to a 6000-year-old Earth.

So, to some extent, "Should Christians Embrace Evolution?" is a refreshing return to form by the creationists - unashamedly simplistic in its naive analysis of the biblical texts and unashamedly young-earth literalist in its overall perspective, it's like stepping back in time about 200 years to the fire'n'brimstone, or teleporting to Ken Ham's Creation "Museum" outside Cincinatti.

Anyway, I have so far only read a few chapters, and so far the scholarship is very weak, the attacks on the scientific picture of origins are misguided, and the pretence at analysis paper-thin. Over the next few weeks I will review the chapters of this book from the perspective of science. I will also comment where appropriate on some of the wilder theological statements that crop up from time to time. Before that, perhaps a little quote from Chapter 1 (Alistair Donald) is in order: "a commitment to the supremacy of Scripture [sic] will not allow the embracing of any aspect of evolution that compromises the key themes of the biblical text."

There. You know the score. Stay tuned for more laughs...

23 April 2010

Should Christians eMbrace evkolution?

Aargh! I can't do this on the iPhone. It can wAit until I get a keyboard that can cope with fat fingers...

08 April 2010

Gene patents struck down: good news!

Hot on the heels of a breath of fresh legal air in the Simon Singh case, the case taken by the ACLU in the USA to overturn the patents on BRCA1 & BRCA2 has been successful (although may be appealed). The patents have been struck down.

Here's the link to the story in the New York Times.

[Actually, this judgement pre-dates the Simon Singh case, but never mind].

Many of us working in the field of Genetics have regarded the granting of patents for genes as inherently wrong - immoral, even. Finding a gene and linking it to a disease is a *discovery*, not an invention. Genes are products of nature - the normal everyday process of biological evolution. Myriad Genetics did not invent BRCA1 or BRCA2 - they have always been there (well, since we were yeast...). Showing a link between BRCA1/2 and breast & ovarian cancer is not an invention, but a discovery.

Some short-sighted people in biotech have claimed that this stifles research and investment in the sector - leaving aside the immorality and questionable legality of patenting genes, this argument is patently (thank you) bogus. What's more, the gold-rush for gene patents actually threatens the development of the therapeutic sector by siphoning off venture capital into dead-end enterprises.

There are families where breast and ovarian cancer appear to follow dominant inheritance with reduced penetrance - this much has been known for years. In the early 1990s, many of these families were shown to have defects in BRCA1 & BRCA2. Identifying the mutations in families allows screening and therapy to be targeted much more accurately. This is a mainstay of clinical genetics and is in routine practice.

The bottom line is that we do not need venture capital leveraged by gene identification (after all, we have had the full sequence for several years now) - what we need is an incentive for VC to go into the development of tools and therapies based on our knowledge of these genes and how they participate in biological systems. THAT is where the money should be made, and THAT is where we need to see the sectoral development.

So, biotech business people, please smell the coffee. Genes are discoveries. They should not be patentable, and it looks like this is the way the courts are going to look on these things from now on (and I hope Myriad's appeal fails). Use this as your impetus to target your R&D wisely. Yes, it means you have to talk in more intelligent language to your venture capitalists, and they (and you) are going to have to learn more about biology and medicine, but that's a GOOD thing, OK?

07 April 2010

Latest from Simon Singh

Message from Simon Singh: “A big step for me, a small step for libel reform, and what you can do to help today.”

Dear Friends

Sorry for the silence, but it has been a ridiculously hectic (and happy) time since last week’s victory at the Court of Appeal. However, I urgently wanted to get in touch to update you on the status of my case, the latest news on libel reform and what you can do today to push libel reform up the political agenda.
BCA v Singh

April Fool’s Day 2010 was a day to remember. The Court of Appeal gave a ruling in my libel case with the British Chiropractic Association. The ruling strongly backs my arguments and puts me in a much stronger position when my trial eventually takes place. At last, after two years of defending my article and my right to free speech, I seem to have the upper hand and can breathe a small sigh of relief.

Moreover, the judges made it clear that they did not want to see scientists and science journalists being hauled through the High Court. In particular, they endorsed the view that a so-called comment defence should be adequate for scientific and other articles on matters of public interest. As well as the legal technicalities, the three wise, charming and handsome judges quoted Milton on the persecution of Galileo and directed that the High Court should not become an “Orwellian Ministry of Truth”.
Libel Reform Campaign

This is a small step forward for libel reform, but there is still a huge battle to be fought over the issues of costs, libel tourism, public interest defence, balancing the burden of proof, restricting the ability of powerful corporations to bully individuals (e.g., bloggers, journalists, scientists) and so on.

The General Election was called yesterday and the manifestos will be published in the next week, so we need one last push to persuade the major parties to commit to libel reform. Although we have already achieved a huge amount (from editorials in all last week’s broadsheets to the Commons Select Committee recommending libel reform), we must keep up the pressure!

Both the Labour and Conservative parties have made encouraging sounds about libel reform, but now is the time for them to make commitments in their manifestos.
What you can do today to pressure politicians

I have spent over a million minutes and £100,000 defending my article and my right to free speech, so I am asking you to spend just one minute and no money at all persuading others to sign the petition for libel reform at www.libelreform.org/sign

The last time I made this request, we doubled the number of signatories from 17,000 to 35,000. Can we now double the number from almost 50,000 to 100,000?!

You could ask parents, siblings, colleagues or friends to sign up. You could email everyone in your address book. You could blog about it, mention it to your Facebook friends and twitter about it. In fact, I have pasted some possible tweets at the end of this email – it would be great if you could twitter one, some or all of them.

You could forward all or part of this email to people or just steer them to www.libelreform.org/sign . Or you could persuade people that English libel law needs radical reform by using some of the reasons listed at the end of this email.

Remember, we welcome signatories from around the world because English libel law has a damaging impact globally.

Please, please, please apply maximum pressure to the politicians by encouraging as many new signatories as possible. Please do not take my victory last week as a sign that the battle is over. My case is still ongoing and the campaign for libel reform is only just starting.

Thanks for all your support – it has been incredibly important for the campaign and a real morale booster personally over the last two years.

Simon Singh.

Ps. Please spread the word by sending out one, some or all of the following tweets

Pls RT English libel law silences debate, says UN Human Rights Committee. Sign up at www.libelreform.org & back #libelreform Pls RT English libel costs 140x more than Europe. We can't afford to defend our words. Sign up at www.libelreform.org & back #libelreform Pls RT Two ongoing libel cases involving health. The law should not crush scientific debate. Sign up at www.libelreform.org & back #libelreform Pls RT London is notorious for attracting libel tourists who come to UK to silence critics. Sign up at www.libelreform.org & back #libelreform

PPs. Reasons why we need radical libel reform:

(a) English libel laws have been condemned by the UN Human Rights Committee.

(b) These laws gag scientists, bloggers and journalists who want to discuss matters of genuine public interest (including public health!).

(c) Our laws give rise to libel tourism, whereby the rich and the powerful (Saudi billionaires, Russian oligarchs and overseas corporations) come to London to sue writers because English libel laws are so hostile to responsible journalism. (Again, it is exactly because English libel laws have this global impact that we welcome signatories to the petition from around the world.)

(d) Vested interests can use their resources to bully and intimidate those who seek to question them. The cost of a libel trial in England is 100 times more expensive than the European average and typically runs to over £1 million.

(e) Two separate ongoing libel cases involve myself and Peter Wilmshurst, and we are both raising concerns about medical treatments. We face losing £1 million each. In future, why would anyone else raise similar concerns when our libel laws are so brutal and expensive? Our libel laws mean that serious health matters are not necessarily reported, which means that the public is put at risk.

PPPs. I know that I will leave people out of this list, but I owe a huge thanks to:

1. The 10,000 people who joined the Facebook group “For Simon Singh and Free Speech - Against the BCA Libel Claim”, particularly those who joined when the rest of the world ignored the issue of libel.

2. The 300 people who packed Penderel’s Oak in May 2009 and who helped launch the Keep Libel Out of Science campaign, particularly the speakers: Nick Cohen, Dave Gorman, Evan Harris MP, Professor Brian Cox, Chris French, Tracey Brown (Sense About Science), Robert Dougans (Bryan Cave) and David Allen Green.

3. The 20,000 people who then joined the Keep Libel Out of Science campaign.

4. Jack of Kent and every other blogger who ranted and raved about libel reform when the mainstream media was turning a blind eye.

5. Everyone in the mainstream media who is now covering the various libel cases and the issue of libel reform.

6. Sense About Science, Index on Censorship and English PEN, who formed the Coalition for Libel Reform. And thanks to everyone who has contributed pro bono to the campaign in terms of design, technical support, chivvying support for the EDM and more.

7. The 46,000 people (i.e. you) who have signed the petition for libel reform, particularly those who have cajoled others to sign up at www.libelreform.org/sign

8. All the big names who have spoken out in favour of libel reform, from Professor Richard Dawkins to Derren Brown, from the Astronomer Royal to the Poet Laureate, from the Amazing Randi to Ricky Gervais. Particular thanks go to Dara O Briain, Stephen Fry, Tim Minchin and Robin Ince, who have gone out of their way to step up to the plate when the campaign has needed them. Immense thanks also to the 100+ big names who were the first to sign the petition to keep libel out of science and highlighted the need for libel reform.

9. Everyone who has emailed and twittered and told me in person that I am not going crazy, and who reassured me that I am doing the right thing by defending my article.

10. Thanks to Nick Clegg, leader of the Lib Dems, for promising to put libel reform in his manifesto. And thanks in advance to Jack Straw (Justice Secretary) and Dominic Grieve (Shadow Justice Secretary), because I know that the Labour and Conservative parties are going to commit to libel law reform. I cannot believe that they will allow more scientists, serious journalists, bloggers, biographers, human rights activists and others to go through the same hell that I have had to endure for last two years.

-Simon Singh

01 April 2010

Simon Singh wins libel appeal

Simon Singh has won his appeal for the right to a "fair comment" defence in his libel trial:

This is FANTASTIC news, as the previous ruling would have grossly prejudiced the case, and made it impossible to defend.

This is a victory not just for Simon Singh, but for free speech, the ordinary person, science, medicine and democracy itself.

The game is not over yet - unless the British Chiropractic Association back down (hint: if they know what's good for them, they will), this will proceed to court for a full trial.

Which they may lose.

And if there is any justice left (and this appeal seems to suggest there may well be), they will lose. Heavily. And they deserve to.

He may have a really bad haircut, but Simon Singh is a HERO!