My Daughter’s DNA, Google Sky, and Reinventing Academic Publishing

Here’s a summary of some way-cool things that have passed my way lately, especially following SciFoo.

Last week’s issue of The Economist had a great piece about some of the practical implications of personal genomics, not least for health insurance. It begins with this anecdotal account:

“If you can make a good soufflé, you can sequence DNA.” That assertion sounds preposterous, but Hugh Rienhoff should know. When his daughter was born about three years ago, she suffered from a mysterious disability that stunted her muscle development. After many frustrated visits to specialists, Dr Rienhoff, a clinical geneticist and former venture capitalist, decided to sequence a specific part of her genome himself. He discovered that her condition, which most resembled a rare genetic disorder known as Beals’s syndrome, was probably due to a new genetic mutation. “Without a lab and for just a few hundred dollars, you can contract or outsource almost all the steps,” he explains.

What a well-connected and highly motivated scientist in California can do today the rest of the world will be able to do tomorrow. Indeed, a number of firms are already offering tests for specific ailments (or predispositions to ailments) directly to the public, cutting out the medical middle-man. Dr Rienhoff, for his part, will soon launch, a not-for-profit venture intended to help others to unravel the mysteries of their family’s genes in the way that he unravelled those of his own.

Hugh was at SciFoo and held a session about this (which I managed to miss, but he told me about it later). I think it’s an amazing story, mixing DIY biology with personal genetics and a great human story — a kind of Lorenzo’s Oil for the 21st Century. But while you wait for the movie to come out, check out Hugh’s site, where he’s trying to help parents and patients in similar situations. I think he’s doing something truly amazing here and I wish him every success.

Google Sky

Speaking of SciFoo alumni, Carol Christian from the Space Telescope Science Institute, who attended with colleague Alberto Conti, was kind enough to email about their work (which they weren’t quite ready to reveal at SciFoo) on Google Earth’s new sky features. But Ian, our resident physics geek, has long since beaten to me to posting about that.

Reinventing Academic Publishing

Meanwhile elsewhere, Jim Hendler (of Semantic Web fame) has posted some post-SciFoo thoughts on reinventing academic publishing. I strongly agree with one of Jim’s main points, which is that (as I would put it) getting “social software” right is 90% “social” and only 10% “software”. For example, MediaWiki is great, but Wikipedia took off primarily because of the idea and the community around it, not the quality of the code. Conversely, wikitorials failed because there was no community and because it’s a terrible use for a wiki. Jim also makes a great point about scientists’ inherent conservatism (which I deal with on a daily basis in our various web projects):

While scientists have gloried in the disruptive effect that the Web is having on publishers and libraries, with many fields strongly pushing open publication models, we are much more resistant to letting it be a disruptive force in the practice of our disciplines.

If we don’t think through the social issues of usage, the technologies alone will not have any significant impact, and will go largely unused.

One option, and I’d like to see more effort expanded in this area, is that this is a case where innovation needs to come “from the top.” Eventually, as these young scientists become the leaders of our fields they would bring these new technologies with them, but with the world in its current shape, we can’t afford to wait that long. Rather, we need to find ways to bring more senior scientists into contact with the positive side of these technologies.

It’s great to read a Semantic Web visionary opining so insightfully about Web 2.0, not least because I (unlike some) see these two approaches as mainly complementary, not competitive.

On that note, Ian (who, when he’s not blogging about Google Sky, runs Connotea, our social bookmarking service) has another great post , this time on his Nature Network blog, about some intriguing work that Connotea user Benjamin Good has done to unify folksonomy- and ontology-based approaches. From the info page:

[EntityDescriber] is a mechanism for intersecting the Semantic Web with the normal Web. It lets Connotea users (though we may extend it to other systems such as annotate (tag) resources on the Web with terms from existing controlled vocabularies such as MeSH, the Gene Ontology, the Atom ontology, and the Person ontology.

I have no idea how well this will work, but it’s a great thing to try.

Less interestingly, but still relevant, I have a piece about Web 2.0 in science in the latest issue of CT Watch. More important, it’s part of a special issue on “The Coming Revolution in Scholarly Communications & Cyberinfrastructure” and the other authors are far more knowledgeable and august than me, so do check out their contributions.


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