Monday, February 28, 2011

Anticancer

(Summarising some of David Servan-Schreiber's book Anticancer, 2nd edition, 2011.)

Why are cancer rates increasing so quickly? What can we do to stop the spread, both as individuals and as a society?

Curing cancer: the long route

The World Health Organisation runs the world's biggest cancer epidemiology lab (IARC, in Lyon, France). They publish the standard reference work on carcinogensis, and in recent years have done a lot of work on genetic and epigenetic factors in cancer. They found the first gene that increases the risk of lung cancer in smokers (see Nature, April 2008), for example.

Their work involves finding tiny needles in huge haystacks. The new generation of sequencing machines can process an entire genome within a week. Then billions of data points from populations of cancer sufferers must be correlated with environmental factors like smoking, diet, pollution, etc.

In their latest experiments IARC scientists are using GATE to adjust their statistical models based on previously published research results. In 2010 they found a gene that associates with head and neck cancer this way. The method can boost the productivity of cancer research by exploiting the gigabytes of published research, government studies and patent applications that cover cancer and its causes.

One of the best things for me about working with GATE in recent years has been this stuff on carcinogenesis with the genetic epidemiology team in Lyon. As part of the LarKC project we developed a simple text processing system to boost probabilities in their models of gene-disease association. It is quite a buzz to be able to say that we've contributed to finding a new proven susceptibility that associates with a particular genetic marker. Knowledge of this type of susceptibility promises to contribute significantly to the development of targeted pharmaceuticals for cancer treatments in the long term.

This is, though, only part of the story -- just as one of the main consequences of our increased understanding of genetics has demonstrated the need to understand the biological and environmental context of gene expression (or epigenetics), so an understanding of cancer must also lead beyond the purely pharmaceutical. Let's look at the other side of the coin: what is it that causes cancer in the first place?

Polar bears

As pure as the driven snow? Unfortunately not:

Polar bears live far from civilization... Yet of all the animals in the world, the polar bear is the most contaminated by toxic chemicals, to the point where its immune system and its reproductive capacities are threatened... The pollutants we pour into our rivers and streams all end up in the sea... The polar bear is at the top of the food chain that is contaminated from one end to the other... There is another mammal that reigns at the top of its food chain and its habitat is, moreover, distinctly less protected than the polar bear's: the human being.

And it is here that we find two huge causes of cancer: first, the food we eat, and second the artificial pollutants that permeate both our environment and our food. As many as 85% of all cancers are caused by environmental factors (the food we eat, the air we breath, the stresses and strains of modern life). For example, a large Danish study

... found that the genes of biological parents who died of cancer before fifty had no influence on an adoptee’s risk of developing cancer. On the other hand, death from cancer before the age of fifty of an adoptive parent (who passes on habits but not genes) increased the rate of mortality from cancer fivefold among the adoptees. This study shows that lifestyle is fundamentally involved in vulnerability to cancer. All research on cancer concurs: genetic factors contribute to at most 15% of mortalities from cancer.

In other words, there is a clear potential for preventing cancer by adjusting our lifestyles, and the same comment applies to increasing our chances of surviving the disease once diagnoses. In the short term there is an increasing body of work that can guide individuals, families and communities to methods for decreasing their cancer risks and for improving the prognosis once diagnosed, and Servan-Schreiber's book is an excellent summary.

In the longer term, we must change our modes of transport, our agriculture and our industrial processes, if we are serious about making a lasting difference to cancer rates.

Curing cancer 2: short cuts

It is in this sense that cures for cancer already exist: we don't need to wait for scientific miracles or technological breakthroughs (that may or may not come) -- we can prevent many cancers and remit many existing cancers by changing practices that we already understand very well (perhaps starting with your next meal!). It seems that

... by upsetting the balance in our diets we have created optimal conditions in our bodies for the development of cancer. If we accept that cancer growth is stimulated to a large extent by toxins from the environment, then in order to combat cancer, we have to begin by detoxifying what we eat. Facing this overwhelming body of evidence, here are simple recommendations to slow the spread of cancer:

  1. Eat sugar and white flour sparingly: replace them with agave nectar, acacia honey or coconut sugar for sweetening; multigrain flour for pastas and breads, or sourdough.
  2. Reduce consumption of red meat and avoid processed pork products. The World Cancer Research Fund recommends limiting consumption to no more than 500 g (18 oz) of red meat and pork products every week – in other words, at most four or five steaks. Their ideal recommended goal is 300 g (11 oz) or less.
  3. Avoid all hydrogenated vegetable fats – ‘trans fats’ – (also found in croissants and pastries that are not made with butter) and all animal fats loaded with omega-6s. Olive oil and canola oil are excellent vegetable fats that doesn’t promote inflammation. Butter (not margarine) and cheese that are well-balanced in omega-3s may not contribute to inflammation either.

(Lower cost options are also discussed.)

Servan-Schreiber's book is one of those rare texts that combines a rigourous and detailed apprehension of the scientific literature with a clear, simple and practical messages about how we can live better. If you read one book this year....!


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Thursday, February 24, 2011

Talk or Technology?

Talk or technology -- which is most expensive? Talk, it seems.

I spent the weekend with a friend of mine who runs one of the bigger semantics companies (he's a peddlar of used meanings, I like to tell him -- a kind of wholesale supplier of double entendres). He's very active in the community, and he follows the fate of all the other startups and joint ventures that have sprung up over the last decade or so, and the machinations of their customers, the tech savvy media and the analyst firms and so on. Several months ago he told me a story about Corporation X (let's call them Turnip for no particularly good reason), Startup Y (let's call them Cabbage) and a certain popular text processing framework, which, if you're sitting comfortably, I shall relay for your general delectation and personal improvement.

Now, Turnip are a megacorp, biggest publisher of one sort or another, and supplier of diverse databases and data streams to the jobbing information worker. In common with pretty much every other publisher out there (except Cory Doctorow) Turnip can see the writing on the digitally revoluntionary wall, and are casting around for ways to make their offerings more exciting than the competition. (Whether they can make their expensive, closed and stuffy stuff seem more attractive than the new free and open world is not something I'd bet the house on, but there you go.) One obvious route is to use text analysis to hook their text corpora up to conceptual models and bung the results into a semantic repository. Hey presto, all sorts of new and nifty search and browsing behaviours suddenly become possible. So publishers have been pretty keen customers of both the GATE team and my friend's company in recent years.

Turnip realised the importance of text processing in their collective future some time ago, and, after reporting work based on GATE up until a few years back, decided to take the function in-house. They bought Cabbage, one of the most active text analysis startups of the time. We assumed that they were going to use Cabbage tech to replace the stuff they'd done with GATE...

Fast forward to the present, and my friend was chatting to one of the people who run the publishing side of things at Turnip. Surprise surprise: the Cabbage stuff is nowhere to be seen, and they're still using the old and trusty Volkswagen Beetle of text processing.

Well who'd have thought it.

So, coming back to the question of talk vs. technology, we can conclude that the good people at Cabbage, who were big enough talkers to see themselves bought for a large chunk of readies by Turnip, had the right approach. Sad old technologists like me and mine just don't cut the mustard in the self-promotion stakes.

In fact, I've seen this pattern in a number of contexts. The people best at telling you about why you need them are generally too busy doing just that to really get to grips with all that inconvenient science and engineering that needs doing to actually make a practical difference. Therefore I have formulated Cunningham's Law: the quality of the work varies in inverse proportion to the quality of the slideware. (Next time you're unlucky enough to be bored to tears by one of my talks, please bear this in mind.)

To finish, a hint, free of charge, for those who have text processing problems to solve but would prefer not to spend large sums of money on cabbage and the like. You need open systems, you need to measure from the word go, and you need a process that incorporates robust mechanisms for task definition, quality assurance and control and system evolution. And you need a pool of available users and developers, training materials, etc. etc. So mosey on over to http://gate.ac.uk/ :-)

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