http://www.nytimes.com/interactive/2008/05/05/science/20080506_DISEASE.html

Every time I see something like this I am struck with the anxious feeling that there is so much to glean from visualization of complex data sets, yet we are so primitive in our ability to generate these on a large scale and flexibly ask questions. For instance it's really instructive to see here that all cancers cluster together genetically and represent an island in the larger network of diseases. But I'd like to now ask, to what extent are genes a factor in each of these diseases (vs. all environmental and developmental influences). The number of genes involved that the circle sizes represent give a proxy, but are misleading, and probably roughly inverse when it comes to the question I asked.

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I'm guessing many/most of you know about the recent Scientific American special issue on cancer. If not, it's worth checking out. In particular, Way Gibbs' article is superb (though it appears to be a straight re-print?)

Although we should all be pleased that there is some attention being focused on cancer's complexity, I disagree with their treatment of cancer evolution:

http://rafefurst.wordpress.com/2008/08/22/cancer-as-evolution-part-2/

I also wrote a letter to the editors expressing my concern on this front.

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http://www.webmd.com/melanoma-skin-cancer/news/20080814/moisturizers-up-skin-cancer-in-mice

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Thanks to Carlo Maley, John Pepper, Brian Reid, Sabrina Spencer, Tom Vincent, Stephanie Forrest and Henry Heng, there is now a fairly comprehensive Wikipedia entry on cancer as somatic evolution:

http://en.wikipedia.org/wiki/Somatic_evolution_in_cancer

Of course, you are all encouraged to contribute and maintain this page, grow branches off of it, etc.

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An experimental treatment which injected a man with billions of his cloned CD4 T cells has "cured" the man's skin cancer which included tumors in multiple organs. (NEJM) Mainstream media article found here, http://www.guardian.co.uk/science/2008/jun/19/cancer.science

This approach appears to be very promising, as moderate changes in immune function (stress, etc.) do not appear to have much effect on cancer. But, with extreme immunoboost described above the tumor cells are destroyed. Conversely in extreme immunosuppression (HIV/AIDS) we see a marked increase in Kaposi's Sarcoma (also a skin cancer) and other tumors.

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A friend pointed me to this project recently:

http://www.hhmi.org/news/foldit20080508.html
http://www.fold.it/portal/adobe_main/

Independent of whether you think protein folding prediction will help us understand cancer better, what do you think of the idea of harnessing crowdsourcing for complex computational problems which would be fruitful? And what might those applications be for cancer?

For a glimpse of the power of game-style crowdsourcing, check out the work of Louis von Ahn:

http://video.google.com/videoplay?docid=-8246463980976635143

I particularly like the labeling of images application as it illustrates the stark differences between what computers are good and and what humans are good at and it leverages the best of both to solve a practical problem.

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While (Mental/Psychological) Stress is linked to Metabolic Syndrome (Heart Disease, Diabetes, etc) , Reproductive and Immune System problems, a host of other maladies, and more generally a shorter lifespan, there appears to be no link between stress and cancer.

There exists little evidence linking stress to a greater incidence of cancer or a greater chance of relapse (out of remission.) Even research on the effects of positive mental states ("fighting spirit) and social interaction (to reduce stress) have mixed results.

What do we make of this? Why can stress negatively impact almost everything in our daily lives, but has no apparent affect on cancer?

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In an earlier post, I argued that the gene concept is in bad need of a makeover. It turns out that Evelyn Fox Keller and David Harel feel the same way and have made an actual start of it in a paper titled Beyond the Gene. In the paper they propose a new lexicon:

* dene - “Like the gene, our notion of dene is intended to capture the essence of genetic transmission, but, rather than being confined to denoting a discrete chunk of DNA, it is far richer and more expressive.”
* bene - “As with denes, our notion of bene will also be extremely rich, making it possible to express complex modal and temporal characteristics of the organism’s behavior over time, characteristics that go far beyond simple statements about, e.g., protein synthesis or transcription.”
* genitor (aka genetic functor) - “…a genitor relates a particular dene to a particular bene, stating that whenever the organism’s DNA is seen to satisfy the property expressed by the dene, it’s behavior satisfies the property expressed by the bene.” And later, “…A genitor, with its dene and bene, connects the static with the dynamic. It carries no expectation that its truth can be predicted on the basis of purely structural information.”

[ for the rest of the blog post go here:

http://rafefurst.wordpress.com/2008/05/29/beyond-the-gene/

]

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After formally and informally polling everyone currently on here, it seems like the best way to achieve critical mass of activity is to make it public.

There were two valid concerns, one of which was that some people would be fearful of speaking their mind if it were public. If you for whatever reason wish to have any of your writing or involvement removed before we make this public, feel free to let me know privately or otherwise and I am happy to do so.

The other concern was the signal-to-noise ratio, but given the relative lack of signal so far, we can cross that bridge when the time comes. I don't personally see too many trolls and flamebaiters interested in cancer complexity, but who knows :-)

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I posted the following open letter to the Gotham Prize today:

http://rafefurst.wordpress.com/2008/04/12/open-letter-to-gotham-prize/

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