HENRY

Not a particularly good start to the International Year of Languages - the last traditional speaker of the Na-Dené Eyak language died yesterday, making the language extinct.

Goodbye Chief Marie Smith Jones, and goodbye Eyak.

I finally got sick of the ugliness that was the last henry theme, and since I don’t have time to make it prettier (countdown to the Ph.D hand-in in 2 months - eek!), I’ve picked an off-the-shelf theme to tart things up a tad.

The Guardian has an interesting, and rather damning article on the rise of personal DNA testing companies like 23andMe (tagline: “Genetics Just Got Personal”).

The service is likely to provoke controversy in the UK, where authorities have warned that genetic tests are often meaningless yet can provoke needless anxiety among those who take them. Last month the Human Genetics Commission condemned them as a dangerous waste of money and called for regulations to control their marketing

I’d be very interested in hearing what my fellow DNA-Network bloggers think of this (especially those affiliated with 23andMe!)

Interesting paper in the most recent PLoS Genetics on Discerning the Ancestry of European Americans using Genetic Association Studies (doi):

European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries.

Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure.

Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.

Pinker et al on “The Logic of Indirect Speech” (doi)

When people speak, they often insinuate their intent indirectly rather than stating it as a bald proposition. Examples include sexual come-ons, veiled threats, polite requests, and concealed bribes. We propose a three-part theory of indirect speech, based on the idea that human communication involves a mixture of cooperation and conflict.

First, indirect requests allow for plausible deniability, in which a cooperative listener can accept the request, but an uncooperative one cannot react adversarially to it. This intuition is supported by a game-theoretic model that predicts the costs and benefits to a speaker of direct and indirect requests.

Second, language has two functions: to convey information and to negotiate the type of relationship holding between speaker and hearer (in particular, dominance, communality, or reciprocity). The emotional costs of a mismatch in the assumed relationship type can create a need for plausible deniability and, thereby, select for indirectness even when there are no tangible costs.

Third, people perceive language as a digital medium, which allows a sentence to generate common knowledge, to propagate a message with high fidelity, and to serve as a reference point in coordination games. This feature makes an indirect request qualitatively different from a direct one even when the speaker and listener can infer each other’s intentions with high confidence.

..at this rate, there won’t be any left!

Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of 24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog.

However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFs—specifically, their properties in other primates.

We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to 20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes.

Paper: Distinguishing protein-coding and noncoding genes in the human genome (doi), and news coverage here.

Simply beautiful -

We present a visualization of all the nouns in the English language arranged by semantic meaning. Each of the tiles in the mosaic is an arithmetic average of images relating to one of 53,463 nouns. The images for each word were obtained using Google’s Image Search and other engines. A total of 7,527,697 images were used, each tile being the average of 140 images. (…) Thus the poster explores the relationship between visual and semantic similarity. For a large part of our language the two are closely correlated as shown by the extent of visual clustering within the poster.