Wednesday, February 24, 2010

Welcome to the genetic revolution

San Diego

I leave today for London. But as I woke this morning at 5.30am, I remembered that I had one last job to do before leaving. The bay was inky black and the street lights around the harbour were still twinkling. There, on my bedside table was an empty plastic sample tube.

I rubbed my eyes, sat up and got to work spitting in the tube. The instructions told me, “do not eat, drink, smoke, chew anything, brush your teeth or rinse your mouth for at least 60 minutes prior to collecting your saliva”. A couple of mouthfuls was all it took to reach the fill line, then I screwed on the blue cap and a clear preserving fluid ran into it. I shook it a bit, put the tube into a bag and Fedexed it off to a local company called Pathway Genomics. Welcome to the genetic revolution. Please deposit your DNA on the way in.


Pathway has been set up in competition to some of the consumer genomics companies launched a year or two ago. 23andme, Navigenics and deCODEme. It offers a surprising number of different tests, for $399. Navigenics cost $999, and 23andme costs $499. deCODEme is also quite pricey but this company is bankrupt at present and has been bought up. The fate of its consumer genetics division remains unclear. Another company, Counsyl, has also started up just offering to test for carrier genes of rare conditions ($349), which makes Pathway look like pretty good value.


Of course when taking this test this morning there were all sorts of things going through my mind. Excitement at discovery and fear of finding out something bad. Of course, genes are not destiny. But they do tell you something about what might make you sick, and most of us like to go through life without having to think about this sort of thing. And when I visited the lab yesterday, I was told that I could actually register so that if there was anything I didn't want to know about, I could chose not to have these results shown to me (or Pathway's genetic counsellors that review their customers' data).

None of us are perfect, something that becomes increasingly evident as we age. Genetic information means that I'll have the best information possible to understand how to look after this body through, I hope, many more decades alive on this planet. What would be better for me, an hour doing cardiovascular training or yoga or swimming? Maybe my health and genetic profile will give me some clues about how best to look after myself.

I'd also be interested in any clues to my ancestry (also promised as part of the test), and on which migratory path they took around the globe. The tests will also tell me if I am a carrier of any genetic mutations that can cause genetic disorders, and also whether my genes are likely to cause any adverse responses to drugs that are given for medical conditions.

I'm particularly thrilled about discovering one very trivial piece of information, whether I have a fast or slow caffeine metabolism. If you have a slow caffeine metabolism it means that caffeine hangs around your body far longer and it is much more likely to give you a heart attack.

Tuesday, February 23, 2010

Libel reform

* Picture creditRobert Sharp / English PEN

An important case was heard today, Tuesday 23rd February, at the Royal Courts of Justice in the United Kingdom.

It was the case of Simon Singh v the British Chiropractic Association. This case has turned into a focal point for the broader issue of libel reform.

Libel reform is an issue that a lot of people should be interested in...

  • Got kids? Don't think you are free to discuss what you think of childcare ideas with other parents on the web. Link
  • Rely on new medicines and drugs? Don't think that academics are free to raise any doubts they have about their efficacy or safety. Link
  • Got a business or reputation to protect? Don't think that Britain's restrictive and archaic libel laws protect you. They don't, unless you happen to have enormously deep pockets. The cost also constrains newspapers from publishing the truth. Link.
  • Think that because you live abroad, British libel laws don't affect you? Think again. If you publish or speak in the UK, British laws apply to you--no matter how few copies of your words are read here. Link. Also see Wikipedia on Libel Tourism.
Indeed, Britain's libel laws are causing so much trouble overseas several US states have introduced laws to protect American citizens from enforcement of legal settlements in foreign jurisdictions such as Britain. A federal law is before US Congress.

Libel reform affects everyone. We need laws designed for the 21st century. Laws that consider both freedom of speech and access to the law.

If you agree.......please sign the petition, and ask your friends to sign it too. 100,000 signatures are needed.

Who writes Science and Technology at the Economist?

  • Update June 2014: this post is getting a little out of date. Please refer to this page. 

  • Updated July 2012: Although I no longer work in the Science and Technology section, this post is pretty popular so I thought I would update the names to reflect the current situation in the science department.

N.L. Chicago, July 2012.

Monday, February 22, 2010

Science in the courtroom

San Diego

The AAAS meeting in San Diego has been something of a blur. The highlight so far has been a session called The Brain on Trial, which was an attempt to reproduce the courtroom discussion surrounding the admissibility of evidence from an MRI scan of the brain in a court case. Judge Luis A. Rodriguez, from the Superior Court of California in the County of Orange, presided over the session. There were lawyers for the prosecution and the defense, and two expert witnesses in neuroscience.

This session was the AAAS at its best. Well thought out, and well planned. The scenario was a trial in to the murder of a woman called Jane Owens by a former lover Will Johnson. Will Johnson is on trial for first degree murder, however the defense would like to argue that he has a lesion on his brain that makes him incapable of forming an intent to kill--and therefore could not have planned to murder Jane Owens.

Theoretically, lesions of the type that Mr Johnson has (in the cortex, which is the planning region of the brain) could lead to a failure to form an intent to kill, it equally might leave him completely or mostly normal. In addition, one would expect that such a failure in ability to plan would be reflected in his everyday life as well, from getting up in the morning to put on his pants, to making his dinner at night.

The difficulty that arises with the evidence of a lesion that no scientific data exist that would help a juror decide how likely this lesion was a factor in the murder. Indeed, many people have lesions in their brain and walk around entirely unaware of them.

The prosecution didn't want it admitted in evidence, and argued it would be likely to confuse, mislead and take a great deal of court time to discuss. The defense wanted it included, arguing it was evidence. The scientific experts provided different views of the evidence, according to which side they represented, but both would agree that the lesion was far from proof that Mr Johnson could not have formed an intent to kill.

The judge took the not-unreasonable view that it was up to the jury to decide. But of course the prosecution then used this evidence to suggest there was "reasonable doubt". It was fascinating to watch, and the audience voting (as jurors) suggested that such evidence would sway them from a conviction for first-degree murder.

This was a hypothetical example, and any court case would (one would hope) not end up hanging on a dodgy MRI scan (and with an absence of psychological evidence of past or current mental problems). But the entire session was a graphic window into how science can be used in the courtroom.

Whether or not scientists believe that their research is reliable evidence of anything, it may well appear in the courtroom.

Wednesday, February 10, 2010

Forest footprint disclosure

Last Wednesday, the Forest Footprint Disclosure (FDD) project unwrapped its first report in London. This new organisation, funded in part by the British government, aims to highlight the amount of forest destruction involved in big business. A "forest footprint" indicates the extent to which corporations are relying on unsustainable practices, such as rainforest destruction, to do business.

On the face of it, one might wonder why Fortune 500 companies would be willing to investigate, and then reveal, the extent to which the products they buy are from unsustainable, or even downright illegal, sources. And, true enough only 35 companies participated in the FFD this first year.

It turns out, though, that some companies are interested in doing this. One reason is the reputation risk that may come with their brand, whether it is Clarke's shoes, Dove or Kit Kat, companies have a great deal of money banked on a brand, and they know what damage can be done when the NGOs get nasty.

Another reason, partly related to this, is that dealing with unsustainable ways, or with practices that are likely to bring in bad PR (like cutting virgin rainforest), is also something that asset managers want to know. This sort of project helps investors identify how an organisation’s activities and supply chains contribute to deforestation, and how this links with their forest footprint and their value. FFD says it is backed by 34 financial institutions with $3.5 trillion in collective assets under management.

At the end of the day, companies need to know the provenance of the products they buy. They need to know whether what they sell is legal and sustainable. The issue of child labour harmed parts of the clothing industry, and so there is the possibility that rainforest destruction could become a similar kind of problem. Pictures of dead orangutans are powerful, and shareholders don't like it. It will be interesting to see what comes of this. Indices do affect companies. Access to Medicines index, I hear, is already leading companies to change their policies towards drug access.

On a final word, for now, on the FDD. It brought together some quite interesting people from both sides of the fence. From the corporate world and the green NGOs. This conversation, which I caught part of, was overheard...

Paper industry man: Why did you call for a 12-month moratorium on cutting forests?

Green NGO man: We didn't, we called for a 12-month moratorium on cutting virgin rainforest for paper?

Paper industry: But we don't cut virgin rainforest for paper.

Green NGO: What about [unclear name of place in Asia]?

Paper industry: That's degraded land.

Green NGO: We don't think so.

Paper industry: Well why don't I locate the satellite images so we can sit down and show you.

Green NGO: Fine, but you'll also need to look at where the concessions are.

Paper industry: Well we only take out what we call wood residues from these areas.

Green NGO: Well we call it virgin rainforest.

Friday, February 05, 2010

One-third less hungry

It never ceases to amaze me that some pieces of research are necessary. In the latest report from the Annals of Unsurprising Research, comes a study that shows that preventing humans from fishing is good for the other fish-eating animals. A study published in Proceedings of the Royal Society says that breeding African penguins spent one-third less time looking for food within three months of closing a 20-km zone to purse-seine fisheries around a major colony, while birds in a comparable colony 50km away increased their foraging effort.

Quantifying this sort of thing is probably helpful, but is it really that surprising?