Archive for DNA

Nature highlights

Posted in Books, Kids, pictures, Statistics with tags , , , , , , , on November 1, 2016 by xi'an

A mostly genetics issue of Nature this week (of October 13), as the journal contains an article on the genomes of 300 individuals from 142 diverse populations across the globe, and another one on the genetic history of Australia Aborigines, plus a third one of 483 individuals from 125 populations drawing genetic space barriers, leading to diverging opinions on the single versus multiple out-of-Africa scenario. As some of these papers are based on likelihood-based techniques, I wish I had more time to explore the statistics behind. Another paper builds a phylogeny of violence in mammals, rising as one nears the primates. I find the paper most interesting but I am not convinced by the genetic explanation of violence, in particular because it seems hard to believe that data about Palaeolithic, Mesolithic, and Neolithic periods can be that informative about the death rate due to intra-species violence. And to conclude on a “pessimistic” note, the paper that argues there is a maximum lifespan for humans, meaning that the 122 years enjoyed (?) by Jeanne Calment from France may remain a limit. However, the argument seems to be that the observed largest, second largest, &tc., ages at death reached a peak in 1997, the year Jeanne Calment died, and is declining since then. That does not sound super-convincing when considering extreme value theory, since 1997 is the extreme event and thus another extreme event of a similar magnitude is not going to happen immediately after.

Darwin’s radio [book review]

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , , , , , , , on September 10, 2016 by xi'an

When in Sacramento two weeks ago I came across the Beers Books Center bookstore, with a large collection of used and (nearly) new cheap books and among other books I bought Greg Bear’s Darwin Radio. I had (rather) enjoyed another book of his’, Hull Zero Three, not to mention one of his first books, Blood Music, I read in the mid 1980’s, and the premises of this novel sounded promising, not mentioning the Nebula award. The theme is of a major biological threat, apparently due to a new virus, and of the scientific unraveling of what the threat really means. (Spoilers alert!) In that respect it sounds rather similar to the (great) Crichton‘s The Andromeda Strain, which is actually mentioned by some characters in this book. As is Ebola, as a sort of contrapoint (since Ebola is a deadly virus, although the epidemic in Western Africa now seems to have vanished). The biological concept exploited here is dormant DNA in non-coding parts of the genome that periodically get awaken and induce massive steps in the evolution. So massive that carriers of those mutations are killed by locals. Until the day it happens in an all-connected World and the mutation can no longer be stopped. The concept is compelling if not completely convincing of course, while the outcome of a new human race, which is to Homo Sapiens what Homo Sapiens was to Neanderthal, is rather disappointing. (How could it be otherwise?!) But I did appreciate the postulate of a massive and immediate change in the genome, even though the details were disputable and the dismissal of Dawkins‘ perspective poorly defended. From a stylistic perspective, the style is at time heavy, while there are too many chance occurrences, like the main character happening to be in Georgia for a business deal (spoilers, spoilers!) at the times of the opening of collective graves, or the second main character coming upon a couple of Neanderthal mummies with a Sapiens baby, or yet this pair of main characters falling in love and delivering a live mutant baby-girl. But I enjoyed reading it between San Francisco and Melbourne, with a few hours of lost sleep and work. It is a page turner, no doubt! I also like the political undercurrents, from riots to emergency measures, to an effective dictatorship controlling pregnancies and detaining newborns and their mothers.

One important thread in the book deals with anthropology digs getting against Native claims to corpses and general opposition to such digs. This reminded me of a very recent article in Nature where a local Indian tribe had claimed rights to several thousand year old skeletons, whose DNA was then showed to be more related with far away groups than the claimants. But where the tribe was still granted the last word, in a rather worrying jurisprudence.

a bone of contention

Posted in pictures with tags , , , , , , on May 28, 2016 by xi'an

“In an age in which ancient genomes can reveal startling links between historical populations, we should ask not just whether remains should be reburied, but who decides and on what grounds.”

An article in Nature described the story of fairly old remains (of the Kennewick Man) in North America that were claimed for reburial by several Native American groups and that were found to be closer [in a genetic sense] to groups that were geographically farther (from South America and even Australian aboriginal Australians). What I find difficult to understand (while it stands at the centre of the legal dispute) is how any group of individuals can advance a claim on bones that are 8,000 year old. With such a time gap (and assuming the DNA analysis is trustworthy) the number of individuals who share the owner of the bones as one ancestor is presumably very large and it is hard to imagine all those descendants coming to an agreement about the management of the said bones. Or even that any descendant has any right on the said bones after so many generations which may have seen major changes in the way deceased members of the community are treated. I am thus surprised that a judiciary court or the US government could even consider such requests.

postdoc on Bayesian computation for statistical genomics

Posted in Kids, Statistics, Travel, University life with tags , , , , , on February 24, 2016 by xi'an

[An opportunity to work with Richard Everitt in Reading, UK, in a postdoc position starting this summer]

It is now possible to retrieve the complete DNA sequence of a bacterial strain relatively quickly and cheaply, and population genetics has been revolutionised in the past ten years through the availability of these data. To gain a deep understanding of sequence data, model-based statistical techniques are required. However, current approaches for performing inference in these models do not scale to whole genome sequence data. The BBSRC project “Understanding recombination through tractable statistical analysis of whole genome sequences” aims to address this issue. A position as Post-Doctoral Research Assistant is available on this project, supervised by Dr Richard Everitt in the Statistics group at the Department of Mathematics & Statistics at the University of Reading.

The deadline for applications is March 31, 2016 (details).

39% anglo-irish!

Posted in Kids, Statistics, Travel with tags , , , , , , , , on May 24, 2015 by xi'an

As I have always been curious about my ancestry, I made a DNA test on 23andMe. While the company no longer provides statistics about potential medical conditions because of a lawsuit, it does return an ancestry analysis of sorts. In my case, my major ancestry composition is Anglo-Irish!  (with 39% of my DNA) and northern European (with 32%), while only 19% is Franco-German… In retrospect, not so much of a surprise—not because of my well-known Anglophilia but—given that my (known, i.e., at least for the direct ancestral branches) family roots are in Normandy—whose duke invaded Britain in 1056—and Brittany—which was invaded by British Celts fleeing Anglo-Saxons in the 400’s.  What’s maybe more surprising to me is that the database contained 23 people identified as 4th degree cousins and a total of 652 relatives… While the potential number of my potential 4th degree cousins stands in the 10,000’s, and hence there may indeed be a few ending up as 23andMe—mostly American—customers, I am indeed surprised that a .37% coincidence in our genes qualifies for being 4th degree cousins! But given that I only share 3.1% with my great⁴-grandfather, it actually make sense that I share about .1% to .4% with such remote cousins. However I wonder at the precision of such an allocation: could those cousins be even more remotely related? Not related at all? [Warning: All the links to 23andMe in this post are part of their referral program.]