A friend pointed out that the Iranian Genome Project site has been around for half a year. The research team is reputable. You can see the rationale at their blog. Though there are several Middle Eastern populations in the HGDP, and you can get other data sets as well, the total number of markers tends to be modest in comparison to the HapMap, let alone a full genome sequence. If you’re going to look for associations with particular traits (e.g., diseases) then it is best to have as many variants as possible (even if you have enough markers so that you can localize the region of the genome where there is an association, that is less useful than having the exact functional variant of interest pegged).
Norway is set to become the first country to incorporate genome sequencing into its national health-care system. The Scandinavian nation, which has a population of 4.8 million, will use ‘next-generation’ DNA sequencers to trawl for mutations in tumours that might reveal which cancer treatments would be most effective.
The consensus seems to be that ~2000 the main proponents of human genomics oversold the short-term biomedical yield on this line of inquiry. But one rule of thumb is that the consequences of novel technologies are often misunderstood; overestimated in straightforward ways in the short-term, but underestimated in unexpected ways over the long-term. To get a sense, you can reread some of the science fiction of the 1950s inspired by UNIVAC. These mass pushes for nation-wide human genomics projects have a comprehensible headline intent. But I wonder if the real results are going to be something we can’t anticipate.
By this point you have probably read about Jonathan Franzen’s comments about digital books. For example: “I think, for serious readers, a sense of permanence has always been part of the experience. Everything else in your life is fluid, but here is this text that doesn’t change.” This seems to be a recapitulation of the Lee Siegel’s attack on the internet from a few years back. I don’t think Franzen was copying Siegel, rather, he’s channeling a meme which seems to be prevalent in a certain cultural milieu. Carl Zimmer does a excellent job dispatching Franzen’s assertions on the merits. But I think we might benefit from a little historical perspective when evaluating these sorts of claims. After all, the book as we know it is the last in a long line of vessels for literacy.
Five to three thousand years ago cuneiform was state of the art. And if you want permanence, look no further. The tablet to the left dates to 2400 BC! With the decline in cuneiform there is something of a lacunae in our understanding and memory of the literary production of ancient societies. Scrolls of papyrus can certainly keep, but only under ideal conditions (e.g., very dry climates, such as Egypt). The codex, the technology which we know as the book, is more recent than the scroll. But it too relies on relatively perishable materials in comparison to cuneiform.
How is it that we have so much of ancient literature then? First, we don’t. There are constant mentions of great works of Greek and Roman antiquity which were obviously widely circulated judging by the references to them in the works we do have. These background elements of the ancient canon were never copied down to our present era. Why is the copying so important? Shouldn’t we have the originals? The Epic of Gilgamesh was retrieved from the remains of the library of the Assyrians (later literature mentions Gilgamesh, but for these earlier cuneiform copies we wouldn’t have the full work from what I know). This is where the perishable aspect comes in. There are classical-era works whose original production dates back to late antiquity, but from what I have read our modern distillation of the ancient canon is almost entirely filtered through three great bursts of copying at the nexus of late antiquity and the early medieval period:.
Over at Harappa DNA Zack ran ChromoPainter/fineStructure on his South Asian data set and posted the results. The new method immediately makes a few things clear:
1) The “South Asians” in the HGDP data set that’s been used for so long are rather on the inbred side, and relatively genetically distinct as far as South Asian populations go. It goes to illustrate the importance of finely calibrating geographic coverage, and the consequences of the “Permit Raj.”
2) Some of the Gujarati individuals in the HapMap also shake out as a moderately tight group (the square in the middle of the graphic above). Not too surprising, but rather striking. Another illustration of the importance of selecting representative and informative populations for any given region.
